Correlation between copy number variations of arm-level result and selected clinical features
PANCANCER cohort with 12 disease types (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1DR2SPM
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1DR2SPM
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between subtypes identified by 80 different clustering approaches and 21 clinical features across 4563 patients, 329 significant findings detected with Q value < 0.25.

- 2 subtypes identified in current cancer cohort by '1p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '1q gain mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '2p gain mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by '2q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '3p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by '3q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '4p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '4q gain mutation analysis'. These subtypes do not correlate to any clinical features.

- 2 subtypes identified in current cancer cohort by '5p gain mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '5q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '6p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '6q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '7p gain mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '7q gain mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '8p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '8q gain mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '9p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '9q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '10p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by '10q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '11p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '11q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'STOPPEDSMOKINGYEAR'.

- 2 subtypes identified in current cancer cohort by '12p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '12q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '13q gain mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'COMPLETENESS.OF.RESECTION'.

- 2 subtypes identified in current cancer cohort by '14q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '15q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '16p gain mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '16q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '17p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '17q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '18p gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '18q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '19p gain mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '19q gain mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '20p gain mutation analysis'. These subtypes correlate to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'COMPLETENESS.OF.RESECTION'.

- 2 subtypes identified in current cancer cohort by '20q gain mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'COMPLETENESS.OF.RESECTION'.

- 2 subtypes identified in current cancer cohort by '21q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by '22q gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by 'Xq gain mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE'.

- 2 subtypes identified in current cancer cohort by '1p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by '1q loss mutation analysis'. These subtypes do not correlate to any clinical features.

- 2 subtypes identified in current cancer cohort by '2p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'GENDER'.

- 2 subtypes identified in current cancer cohort by '2q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by '3p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by '3q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '4p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '4q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '5p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '5q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '6p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '6q loss mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '7p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '7q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '8p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '8q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '9p loss mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by '9q loss mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '10p loss mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '10q loss mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '11p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by '11q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '12p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '12q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '13q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '14q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'PATHOLOGICSPREAD(M)'.

- 2 subtypes identified in current cancer cohort by '15q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '16p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '16q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'COMPLETENESS.OF.RESECTION', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by '17p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '17q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'COMPLETENESS.OF.RESECTION'.

- 2 subtypes identified in current cancer cohort by '18p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '18q loss mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '19p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by '19q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by '20p loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '20q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by '21q loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'STOPPEDSMOKINGYEAR'.

- 2 subtypes identified in current cancer cohort by '22q loss mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Xq loss mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between subtypes identified by 80 different clustering approaches and 21 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 329 significant findings detected.

Clinical Features | Time to Death | AGE | PRIMARY SITE OF DISEASE | GENDER | KARNOFSKY PERFORMANCE SCORE | HISTOLOGICAL TYPE | PATHOLOGY T | PATHOLOGY N | PATHOLOGICSPREAD(M) | TUMOR STAGE | RADIATIONS RADIATION REGIMENINDICATION | NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET | DISTANT METASTASIS | LYMPH NODE METASTASIS | COMPLETENESS OF RESECTION | NUMBER OF LYMPH NODES | TUMOR STAGECODE | NEOPLASM DISEASESTAGE
Statistical Tests | logrank test | t-test | Chi-square test | Fisher's exact test | t-test | Chi-square test | Chi-square test | Chi-square test | Chi-square test | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | t-test | Chi-square test | Chi-square test | Chi-square test | t-test | t-test | Chi-square test
1p gain | 0.212 (1.00) | 0.0112 (1.00) | 1.5e-28 (2.24e-25) | 8.6e-07 (0.00116) | 0.457 (1.00) | 1.45e-29 (2.17e-26) | 0.000161 (0.205) | 0.0519 (1.00) | 0.253 (1.00) | 0.312 (1.00) | 0.568 (1.00) | 0.674 (1.00) | 0.726 (1.00) | 0.389 (1.00) | 0.669 (1.00) | 0.935 (1.00) | 0.915 (1.00) | 0.0161 (1.00) | 0.545 (1.00) |  | 0.315 (1.00)
1q gain | 2.04e-10 (2.88e-07) | 0.841 (1.00) | 3.09e-135 (4.86e-132) | 1.89e-33 (2.85e-30) | 0.692 (1.00) | 2.19e-39 (3.33e-36) | 1.65e-05 (0.0217) | 0.329 (1.00) | 0.000871 (1.00) | 0.329 (1.00) | 0.965 (1.00) | 0.151 (1.00) | 0.304 (1.00) | 0.219 (1.00) | 0.71 (1.00) | 0.533 (1.00) | 0.37 (1.00) | 0.328 (1.00) | 0.229 (1.00) |  | 0.000266 (0.335)
2p gain | 0.868 (1.00) | 0.000113 (0.145) | 1.25e-30 (1.88e-27) | 0.663 (1.00) | 0.011 (1.00) | 1.8e-13 (2.57e-10) | 0.0316 (1.00) | 0.0328 (1.00) | 0.845 (1.00) | 0.000208 (0.264) | 6.7e-06 (0.0089) | 0.596 (1.00) | 0.0145 (1.00) | 0.00544 (1.00) | 0.285 (1.00) | 0.576 (1.00) | 0.385 (1.00) | 0.868 (1.00) | 0.622 (1.00) |  | 2.47e-05 (0.0322)
2q gain | 0.877 (1.00) | 0.000858 (1.00) | 1.17e-21 (1.73e-18) | 0.479 (1.00) | 0.785 (1.00) | 1e-08 (1.4e-05) | 0.186 (1.00) | 0.101 (1.00) | 0.627 (1.00) | 0.00618 (1.00) | 0.00163 (1.00) | 0.62 (1.00) | 0.119 (1.00) | 0.0754 (1.00) | 0.297 (1.00) | 0.501 (1.00) | 0.184 (1.00) | 0.82 (1.00) | 0.382 (1.00) |  | 0.0136 (1.00)
3p gain | 0.489 (1.00) | 0.0841 (1.00) | 2.71e-30 (4.06e-27) | 0.0798 (1.00) | 0.0182 (1.00) | 6.17e-19 (9e-16) | 0.071 (1.00) | 0.336 (1.00) | 0.104 (1.00) | 7.88e-05 (0.101) | 0.0472 (1.00) | 0.817 (1.00) | 0.0811 (1.00) | 0.00405 (1.00) | 0.153 (1.00) | 0.504 (1.00) | 0.064 (1.00) | 0.0182 (1.00) | 0.587 (1.00) |  | 4.65e-05 (0.0604)
3q gain | 0.152 (1.00) | 0.000438 (0.55) | 2.2e-87 (3.45e-84) | 0.837 (1.00) | 1.53e-05 (0.0201) | 1.25e-88 (1.97e-85) | 6.96e-07 (0.000944) | 9.15e-06 (0.0121) | 0.155 (1.00) | 1.34e-06 (0.00179) | 0.00013 (0.166) | 0.242 (1.00) | 0.0631 (1.00) | 0.818 (1.00) | 0.897 (1.00) | 0.407 (1.00) | 0.0233 (1.00) | 0.0631 (1.00) | 0.194 (1.00) |  | 0.000658 (0.82)
4p gain | 0.244 (1.00) | 0.282 (1.00) | 1.01e-06 (0.00136) | 0.493 (1.00) | 0.0377 (1.00) | 1.31e-06 (0.00176) | 0.204 (1.00) | 0.924 (1.00) | 0.647 (1.00) | 0.277 (1.00) | 0.391 (1.00) | 0.971 (1.00) | 0.792 (1.00) | 0.508 (1.00) | 0.447 (1.00) | 0.258 (1.00) | 0.844 (1.00) | 0.388 (1.00) | 0.0778 (1.00) |  | 0.00579 (1.00)
4q gain | 0.525 (1.00) | 0.364 (1.00) | 0.0341 (1.00) | 0.917 (1.00) | 0.476 (1.00) | 0.00527 (1.00) | 0.492 (1.00) | 0.962 (1.00) | 0.93 (1.00) | 0.275 (1.00) | 0.795 (1.00) | 0.748 (1.00) | 0.811 (1.00) | 0.266 (1.00) | 0.897 (1.00) | 0.378 (1.00) | 0.823 (1.00) | 0.296 (1.00) | 0.281 (1.00) |  | 0.0106 (1.00)
5p gain | 0.317 (1.00) | 3.72e-05 (0.0484) | 7.92e-83 (1.24e-79) | 0.000467 (0.585) | 0.00649 (1.00) | 1.28e-52 (1.97e-49) | 8.46e-10 (1.19e-06) | 0.577 (1.00) | 0.191 (1.00) | 0.0171 (1.00) | 1.41e-08 (1.95e-05) | 0.511 (1.00) | 0.0706 (1.00) | 0.0157 (1.00) | 0.714 (1.00) | 0.732 (1.00) | 0.0942 (1.00) | 0.284 (1.00) | 0.726 (1.00) |  | 0.534 (1.00)
5q gain | 0.00257 (1.00) | 0.00147 (1.00) | 9.05e-58 (1.4e-54) | 0.000301 (0.379) | 0.414 (1.00) | 4.57e-43 (6.96e-40) | 0.00575 (1.00) | 0.02 (1.00) | 0.0609 (1.00) | 0.00257 (1.00) | 0.00743 (1.00) | 0.863 (1.00) | 0.585 (1.00) | 0.764 (1.00) | 0.119 (1.00) | 0.214 (1.00) | 0.64 (1.00) | 0.368 (1.00) | 0.322 (1.00) |  | 0.938 (1.00)
6p gain | 0.00365 (1.00) | 0.249 (1.00) | 1.08e-35 (1.63e-32) | 3.41e-07 (0.000465) | 0.444 (1.00) | 4.48e-22 (6.6e-19) | 0.114 (1.00) | 0.0261 (1.00) | 0.00247 (1.00) | 6.63e-07 (0.000899) | 0.00161 (1.00) | 0.783 (1.00) | 0.321 (1.00) | 0.76 (1.00) | 0.356 (1.00) | 0.706 (1.00) | 0.917 (1.00) | 0.0914 (1.00) | 0.418 (1.00) |  | 0.661 (1.00)
6q gain | 0.0491 (1.00) | 0.0776 (1.00) | 1.31e-18 (1.9e-15) | 0.000741 (0.919) | 0.744 (1.00) | 2.41e-13 (3.44e-10) | 6.68e-05 (0.0861) | 0.129 (1.00) | 0.111 (1.00) | 1.85e-05 (0.0243) | 0.00972 (1.00) | 0.338 (1.00) | 0.793 (1.00) | 0.26 (1.00) | 0.249 (1.00) | 0.459 (1.00) | 0.601 (1.00) | 0.00978 (1.00) | 0.648 (1.00) |  | 0.697 (1.00)
7p gain | 0 (0) | 0.0159 (1.00) | 1.14e-166 (1.8e-163) | 6.39e-27 (9.51e-24) | 0.148 (1.00) | 1.01e-51 (1.55e-48) | 1.49e-09 (2.09e-06) | 0.00457 (1.00) | 7.41e-05 (0.0954) | 0.204 (1.00) | 6.56e-14 (9.4e-11) | 0.75 (1.00) | 0.567 (1.00) | 0.92 (1.00) | 0.334 (1.00) | 0.539 (1.00) | 0.262 (1.00) | 0.00611 (1.00) | 0.0724 (1.00) |  | 0.44 (1.00)
7q gain | 0 (0) | 0.106 (1.00) | 1.26e-182 (2e-179) | 8.98e-27 (1.33e-23) | 0.0433 (1.00) | 1.03e-38 (1.56e-35) | 1.08e-08 (1.5e-05) | 0.134 (1.00) | 9.32e-07 (0.00126) | 0.0824 (1.00) | 3.79e-17 (5.51e-14) | 0.372 (1.00) | 0.267 (1.00) | 0.618 (1.00) | 0.692 (1.00) | 0.0909 (1.00) | 0.164 (1.00) | 0.00826 (1.00) | 0.394 (1.00) |  | 0.265 (1.00)
8p gain | 0.00356 (1.00) | 0.593 (1.00) | 4.18e-25 (6.19e-22) | 0.00149 (1.00) | 0.061 (1.00) | 7.81e-08 (0.000108) | 2.28e-06 (0.00304) | 0.0413 (1.00) | 0.737 (1.00) | 0.00782 (1.00) | 0.151 (1.00) | 0.741 (1.00) | 0.00391 (1.00) | 0.00578 (1.00) | 0.0413 (1.00) | 0.485 (1.00) | 0.781 (1.00) | 0.073 (1.00) | 0.591 (1.00) |  | 0.417 (1.00)
8q gain | 0.000192 (0.244) | 0.576 (1.00) | 5.25e-86 (8.22e-83) | 9.07e-05 (0.116) | 0.00848 (1.00) | 8.16e-35 (1.23e-31) | 1.08e-14 (1.55e-11) | 1.34e-07 (0.000184) | 0.00811 (1.00) | 1.98e-09 (2.77e-06) | 7.22e-06 (0.00958) | 0.567 (1.00) | 0.0137 (1.00) | 0.0524 (1.00) | 0.167 (1.00) | 0.249 (1.00) | 0.124 (1.00) | 0.0946 (1.00) | 0.301 (1.00) |  | 0.138 (1.00)
9p gain | 0.0084 (1.00) | 0.737 (1.00) | 8.2e-26 (1.22e-22) | 0.127 (1.00) | 0.382 (1.00) | 8.4e-17 (1.22e-13) | 3.08e-05 (0.0402) | 0.618 (1.00) | 0.199 (1.00) | 0.00172 (1.00) | 0.00153 (1.00) | 0.584 (1.00) | 0.668 (1.00) | 0.491 (1.00) | 0.743 (1.00) | 0.89 (1.00) | 0.19 (1.00) | 0.479 (1.00) | 0.283 (1.00) |  | 0.108 (1.00)
9q gain | 0.69 (1.00) | 0.713 (1.00) | 1.21e-23 (1.79e-20) | 0.0157 (1.00) | 0.984 (1.00) | 1.32e-21 (1.94e-18) | 1.94e-07 (0.000267) | 0.603 (1.00) | 0.0581 (1.00) | 3.51e-07 (0.00048) | 0.811 (1.00) | 0.756 (1.00) | 0.304 (1.00) | 0.319 (1.00) | 0.742 (1.00) | 0.487 (1.00) | 0.212 (1.00) | 0.286 (1.00) | 0.576 (1.00) |  | 0.0674 (1.00)
10p gain | 0.0283 (1.00) | 0.922 (1.00) | 1.17e-58 (1.81e-55) | 2.19e-20 (3.2e-17) | 0.915 (1.00) | 1.7e-37 (2.58e-34) | 0.0657 (1.00) | 0.213 (1.00) | 0.00992 (1.00) | 3.16e-13 (4.51e-10) | 0.123 (1.00) | 0.461 (1.00) | 0.577 (1.00) | 7.13e-05 (0.0918) | 0.409 (1.00) | 0.404 (1.00) | 0.483 (1.00) | 0.00132 (1.00) | 0.12 (1.00) |  | 0.00751 (1.00)
10q gain | 0.0176 (1.00) | 0.847 (1.00) | 1.82e-46 (2.78e-43) | 3.74e-16 (5.41e-13) | 0.316 (1.00) | 3.63e-28 (5.42e-25) | 0.924 (1.00) | 0.0856 (1.00) | 0.394 (1.00) | 8.16e-07 (0.00111) | 0.8 (1.00) | 0.301 (1.00) | 0.838 (1.00) | 0.702 (1.00) | 0.838 (1.00) | 0.96 (1.00) | 0.957 (1.00) | 0.00735 (1.00) | 0.129 (1.00) |  | 0.0172 (1.00)
11p gain | 0.086 (1.00) | 0.225 (1.00) | 4.94e-15 (7.12e-12) | 0.733 (1.00) | 0.346 (1.00) | 5.54e-06 (0.00737) | 0.0258 (1.00) | 0.222 (1.00) | 0.165 (1.00) | 0.261 (1.00) | 0.0164 (1.00) | 0.253 (1.00) | 0.0325 (1.00) | 0.733 (1.00) | 0.757 (1.00) | 0.865 (1.00) | 0.72 (1.00) | 0.673 (1.00) | 0.304 (1.00) |  | 0.0164 (1.00)
11q gain | 0.732 (1.00) | 0.00297 (1.00) | 2.5e-16 (3.63e-13) | 0.793 (1.00) | 0.822 (1.00) | 5.8e-09 (8.1e-06) | 0.000622 (0.776) | 0.357 (1.00) | 0.228 (1.00) | 0.0331 (1.00) | 0.000705 (0.876) | 0.271 (1.00) | 8.26e-05 (0.106) | 0.144 (1.00) | 0.249 (1.00) | 0.731 (1.00) | 0.214 (1.00) | 0.422 (1.00) | 0.767 (1.00) |  | 0.0473 (1.00)
12p gain | 0.812 (1.00) | 0.00149 (1.00) | 1.45e-43 (2.21e-40) | 0.367 (1.00) | 0.0505 (1.00) | 4.59e-25 (6.8e-22) | 0.00034 (0.428) | 0.697 (1.00) | 0.918 (1.00) | 9.68e-09 (1.35e-05) | 4.22e-07 (0.000575) | 0.378 (1.00) | 0.112 (1.00) | 0.213 (1.00) | 0.565 (1.00) | 0.876 (1.00) | 0.778 (1.00) | 0.498 (1.00) | 0.93 (1.00) |  | 0.921 (1.00)
12q gain | 0.929 (1.00) | 0.00209 (1.00) | 7.1e-15 (1.02e-11) | 0.269 (1.00) | 0.258 (1.00) | 6.49e-05 (0.0837) | 0.0306 (1.00) | 0.688 (1.00) | 0.45 (1.00) | 0.000347 (0.436) | 0.000227 (0.288) | 0.38 (1.00) | 0.656 (1.00) | 0.929 (1.00) | 0.45 (1.00) | 0.0681 (1.00) | 0.948 (1.00) | 0.329 (1.00) | 0.0251 (1.00) |  | 0.983 (1.00)
13q gain | 0.00394 (1.00) | 6.48e-11 (9.17e-08) | 3.03e-280 (4.83e-277) | 3.06e-05 (0.0399) | 0.116 (1.00) | 2.32e-211 (3.69e-208) | 1.2e-34 (1.81e-31) | 1.68e-06 (0.00225) | 1.36e-05 (0.0179) | 7.91e-08 (0.000109) | 9.57e-15 (1.38e-11) | 0.945 (1.00) | 0.77 (1.00) | 5.18e-07 (0.000705) | 0.129 (1.00) | 0.43 (1.00) | 0.239 (1.00) | 2.95e-05 (0.0385) | 0.869 (1.00) |  | 0.0352 (1.00)
14q gain | 0.0299 (1.00) | 0.4 (1.00) | 7.71e-29 (1.15e-25) | 0.169 (1.00) | 0.0687 (1.00) | 4.79e-21 (7.03e-18) | 0.00301 (1.00) | 0.564 (1.00) | 0.00508 (1.00) | 0.552 (1.00) | 0.0185 (1.00) | 0.0554 (1.00) | 0.0673 (1.00) | 0.184 (1.00) | 0.283 (1.00) | 0.968 (1.00) | 0.614 (1.00) | 0.239 (1.00) | 0.0571 (1.00) |  | 0.14 (1.00)
15q gain | 0.116 (1.00) | 0.98 (1.00) | 4.82e-08 (6.65e-05) | 1 (1.00) | 0.213 (1.00) | 5.1e-07 (0.000695) | 0.00018 (0.229) | 0.503 (1.00) | 0.478 (1.00) | 0.321 (1.00) | 0.056 (1.00) | 0.239 (1.00) | 0.686 (1.00) | 0.696 (1.00) | 0.302 (1.00) | 0.349 (1.00) | 0.6 (1.00) | 0.459 (1.00) | 0.306 (1.00) |  | 0.883 (1.00)
16p gain | 2.01e-09 (2.82e-06) | 0.412 (1.00) | 1.31e-70 (2.04e-67) | 1.28e-06 (0.00172) | 0.0933 (1.00) | 4.74e-17 (6.88e-14) | 0.0296 (1.00) | 0.366 (1.00) | 0.669 (1.00) | 0.581 (1.00) | 0.0104 (1.00) | 0.497 (1.00) | 0.447 (1.00) | 0.36 (1.00) | 0.368 (1.00) | 0.0633 (1.00) | 0.182 (1.00) | 0.148 (1.00) | 0.104 (1.00) |  | 0.0039 (1.00)
16q gain | 0.0677 (1.00) | 0.848 (1.00) | 2.54e-28 (3.79e-25) | 0.00263 (1.00) | 0.685 (1.00) | 1.06e-21 (1.56e-18) | 0.00998 (1.00) | 0.0626 (1.00) | 0.693 (1.00) | 0.428 (1.00) | 4.1e-06 (0.00546) | 0.477 (1.00) | 0.818 (1.00) | 0.221 (1.00) | 0.329 (1.00) | 0.0841 (1.00) | 0.551 (1.00) | 0.458 (1.00) | 0.965 (1.00) |  | 0.000739 (0.917)
17p gain | 0.0936 (1.00) | 0.3 (1.00) | 1.5e-06 (0.00201) | 0.0403 (1.00) | 0.65 (1.00) | 9.33e-07 (0.00126) | 0.958 (1.00) | 0.36 (1.00) | 0.0267 (1.00) | 0.59 (1.00) | 0.837 (1.00) | 0.97 (1.00) | 0.262 (1.00) | 0.755 (1.00) | 0.0203 (1.00) | 0.851 (1.00) | 0.84 (1.00) | 0.24 (1.00) | 0.89 (1.00) |  | 0.628 (1.00)
17q gain | 0.0147 (1.00) | 0.129 (1.00) | 3.22e-30 (4.82e-27) | 0.075 (1.00) | 0.604 (1.00) | 1.46e-19 (2.14e-16) | 0.357 (1.00) | 0.075 (1.00) | 0.0503 (1.00) | 0.0252 (1.00) | 0.176 (1.00) | 0.599 (1.00) | 0.0909 (1.00) | 0.168 (1.00) | 0.183 (1.00) | 0.0255 (1.00) | 0.24 (1.00) | 0.155 (1.00) | 0.873 (1.00) |  | 0.524 (1.00)
18p gain | 0.19 (1.00) | 0.0722 (1.00) | 9.68e-18 (1.41e-14) | 0.559 (1.00) | 0.029 (1.00) | 2.74e-20 (4.01e-17) | 0.00168 (1.00) | 0.000984 (1.00) | 0.0368 (1.00) | 0.0237 (1.00) | 0.206 (1.00) | 0.00982 (1.00) | 0.258 (1.00) | 0.139 (1.00) | 0.795 (1.00) | 0.329 (1.00) | 0.682 (1.00) | 0.965 (1.00) | 0.166 (1.00) |  | 0.445 (1.00)
18q gain | 0.142 (1.00) | 0.485 (1.00) | 6.25e-08 (8.62e-05) | 0.313 (1.00) | 0.0821 (1.00) | 4.22e-08 (5.84e-05) | 0.00019 (0.242) | 0.416 (1.00) | 0.365 (1.00) | 0.225 (1.00) | 0.43 (1.00) | 0.0888 (1.00) | 0.0925 (1.00) | 0.132 (1.00) | 0.135 (1.00) | 0.25 (1.00) | 0.966 (1.00) | 0.864 (1.00) | 0.954 (1.00) |  | 0.504 (1.00)
19p gain | 1.12e-08 (1.56e-05) | 0.311 (1.00) | 5.15e-56 (7.95e-53) | 0.129 (1.00) | 0.464 (1.00) | 1.97e-20 (2.89e-17) | 0.136 (1.00) | 0.0519 (1.00) | 0.109 (1.00) | 0.00111 (1.00) | 3.56e-13 (5.08e-10) | 0.109 (1.00) | 0.135 (1.00) | 0.0228 (1.00) | 0.308 (1.00) | 0.437 (1.00) | 0.911 (1.00) | 0.641 (1.00) | 0.538 (1.00) |  | 0.814 (1.00)
19q gain | 4.08e-08 (5.64e-05) | 0.0978 (1.00) | 3.05e-30 (4.58e-27) | 0.0566 (1.00) | 0.478 (1.00) | 1.2e-15 (1.73e-12) | 0.0924 (1.00) | 0.176 (1.00) | 0.572 (1.00) | 0.0328 (1.00) | 1.22e-05 (0.0161) | 0.279 (1.00) | 0.0424 (1.00) | 0.0037 (1.00) | 0.231 (1.00) | 0.664 (1.00) | 0.141 (1.00) | 0.513 (1.00) | 0.167 (1.00) |  | 0.149 (1.00)
20p gain | 4.13e-05 (0.0537) | 7.61e-09 (1.06e-05) | 1.84e-64 (2.87e-61) | 0.0228 (1.00) | 0.965 (1.00) | 2.23e-68 (3.47e-65) | 6.36e-14 (9.12e-11) | 0.0267 (1.00) | 9.41e-06 (0.0124) | 2.76e-07 (0.000378) | 0.67 (1.00) | 0.304 (1.00) | 0.376 (1.00) | 0.00176 (1.00) | 0.0803 (1.00) | 0.0894 (1.00) | 0.222 (1.00) | 6.9e-06 (0.00916) | 0.055 (1.00) |  | 0.11 (1.00)
20q gain | 0.0121 (1.00) | 3.39e-07 (0.000464) | 1.97e-130 (3.1e-127) | 0.203 (1.00) | 0.344 (1.00) | 1.03e-135 (1.63e-132) | 5.56e-29 (8.32e-26) | 0.000927 (1.00) | 0.000206 (0.261) | 2.83e-15 (4.09e-12) | 0.0142 (1.00) | 0.18 (1.00) | 0.0627 (1.00) | 8.01e-06 (0.0106) | 0.576 (1.00) | 0.435 (1.00) | 0.332 (1.00) | 9.3e-07 (0.00126) | 0.313 (1.00) |  | 0.0652 (1.00)
21q gain | 0.454 (1.00) | 0.0303 (1.00) | 1.66e-15 (2.4e-12) | 0.00117 (1.00) | 0.307 (1.00) | 4.02e-10 (5.66e-07) | 0.0704 (1.00) | 0.229 (1.00) | 0.836 (1.00) | 0.0112 (1.00) | 0.772 (1.00) | 0.296 (1.00) | 0.471 (1.00) | 1.61e-05 (0.0212) | 0.742 (1.00) | 0.827 (1.00) | 0.0246 (1.00) | 0.135 (1.00) | 0.0824 (1.00) |  | 0.0112 (1.00)
22q gain | 0.543 (1.00) | 0.0113 (1.00) | 4.2e-36 (6.35e-33) | 2.26e-09 (3.17e-06) | 0.0767 (1.00) | 1.24e-43 (1.9e-40) | 5.6e-07 (0.000761) | 0.0156 (1.00) | 0.807 (1.00) | 0.0143 (1.00) | 0.0313 (1.00) | 0.0683 (1.00) | 0.00222 (1.00) | 0.0541 (1.00) | 0.0265 (1.00) | 0.643 (1.00) | 0.345 (1.00) | 0.315 (1.00) | 0.431 (1.00) |  | 0.155 (1.00)
Xq gain | 0.0223 (1.00) | 0.0802 (1.00) | 2.22e-08 (3.08e-05) | 0.931 (1.00) | 0.512 (1.00) | 0.00714 (1.00) | 0.0974 (1.00) | 0.0219 (1.00) | 0.0181 (1.00) | 0.123 (1.00) | 0.0169 (1.00) | 0.982 (1.00) | 0.567 (1.00) | 0.627 (1.00) | 0.864 (1.00) | 0.118 (1.00) | 0.0134 (1.00) | 0.405 (1.00) | 0.0954 (1.00) |  | 0.128 (1.00)
1p loss | 0.0632 (1.00) | 0.00323 (1.00) | 4.3e-20 (6.3e-17) | 0.527 (1.00) | 0.62 (1.00) | 4.74e-08 (6.56e-05) | 0.293 (1.00) | 0.0271 (1.00) | 0.205 (1.00) | 0.833 (1.00) | 0.0252 (1.00) | 0.00638 (1.00) | 0.331 (1.00) | 0.0311 (1.00) | 0.319 (1.00) | 0.14 (1.00) | 0.122 (1.00) | 0.165 (1.00) | 0.00378 (1.00) |  | 1.07e-05 (0.0142)
1q loss | 0.734 (1.00) | 0.205 (1.00) | 0.000556 (0.696) | 0.137 (1.00) | 0.228 (1.00) | 0.188 (1.00) | 0.0921 (1.00) | 0.306 (1.00) | 0.799 (1.00) | 0.76 (1.00) | 0.458 (1.00) | 0.117 (1.00) | 0.199 (1.00) | 0.852 (1.00) | 0.993 (1.00) | 0.418 (1.00) | 0.973 (1.00) | 0.0296 (1.00) | 0.366 (1.00) |  | 0.936 (1.00)
2p loss | 0.149 (1.00) | 0.319 (1.00) | 6.03e-17 (8.76e-14) | 6.09e-05 (0.0786) | 0.0276 (1.00) | 0.0848 (1.00) | 0.598 (1.00) | 0.889 (1.00) | 0.881 (1.00) | 0.439 (1.00) | 0.277 (1.00) | 0.539 (1.00) | 0.664 (1.00) | 0.0741 (1.00) | 0.626 (1.00) | 0.576 (1.00) | 0.665 (1.00) | 0.972 (1.00) | 0.463 (1.00) |  | 0.855 (1.00)
2q loss | 0.162 (1.00) | 0.875 (1.00) | 2.8e-22 (4.12e-19) | 0.00258 (1.00) | 0.0276 (1.00) | 0.205 (1.00) | 0.927 (1.00) | 0.628 (1.00) | 0.153 (1.00) | 0.421 (1.00) | 1 (1.00) | 0.0444 (1.00) | 0.999 (1.00) | 1.65e-05 (0.0216) | 0.768 (1.00) | 0.339 (1.00) | 0.335 (1.00) | 0.358 (1.00) | 0.281 (1.00) |  | 0.236 (1.00)
3p loss | 0.227 (1.00) | 0.637 (1.00) | 1.29e-218 (2.05e-215) | 7.17e-34 (1.08e-30) | 0.0732 (1.00) | 3.19e-144 (5.04e-141) | 5.56e-14 (7.98e-11) | 0.0222 (1.00) | 0.00016 (0.204) | 4.02e-13 (5.73e-10) | 2.88e-11 (4.08e-08) | 0.0372 (1.00) | 0.12 (1.00) | 5.35e-08 (7.38e-05) | 0.787 (1.00) | 0.771 (1.00) | 0.996 (1.00) | 0.399 (1.00) | 0.0729 (1.00) |  | 0.715 (1.00)
3q loss | 0.446 (1.00) | 0.56 (1.00) | 6.51e-39 (9.9e-36) | 2.54e-09 (3.55e-06) | 0.963 (1.00) | 3.54e-28 (5.28e-25) | 0.0222 (1.00) | 0.304 (1.00) | 0.0873 (1.00) | 0.000443 (0.555) | 0.345 (1.00) | 0.108 (1.00) | 0.498 (1.00) | 0.0918 (1.00) | 0.0383 (1.00) | 0.914 (1.00) | 0.48 (1.00) | 0.716 (1.00) | 0.609 (1.00) |  | 0.629 (1.00)
4p loss | 0.385 (1.00) | 0.664 (1.00) | 1.58e-69 (2.47e-66) | 0.0662 (1.00) | 0.00131 (1.00) | 5.22e-66 (8.13e-63) | 0.000198 (0.251) | 1.94e-05 (0.0254) | 0.78 (1.00) | 9.69e-14 (1.39e-10) | 3.67e-10 (5.17e-07) | 0.00449 (1.00) | 0.000486 (0.608) | 0.000563 (0.704) | 0.388 (1.00) | 0.743 (1.00) | 0.647 (1.00) | 0.552 (1.00) | 0.0064 (1.00) |  | 0.646 (1.00)
4q loss | 0.281 (1.00) | 0.332 (1.00) | 2.93e-108 (4.6e-105) | 1.63e-06 (0.00218) | 0.00244 (1.00) | 6.11e-88 (9.59e-85) | 5.52e-05 (0.0714) | 0.166 (1.00) | 0.909 (1.00) | 6.53e-24 (9.66e-21) | 3.28e-13 (4.68e-10) | 0.0401 (1.00) | 0.0218 (1.00) | 0.0254 (1.00) | 0.116 (1.00) | 0.581 (1.00) | 0.139 (1.00) | 0.467 (1.00) | 0.0279 (1.00) |  | 0.628 (1.00)
5p loss | 0.179 (1.00) | 0.944 (1.00) | 6.07e-16 (8.79e-13) | 0.000439 (0.551) | 0.827 (1.00) | 9.78e-19 (1.43e-15) | 0.164 (1.00) | 0.524 (1.00) | 0.663 (1.00) | 1.69e-06 (0.00226) | 0.464 (1.00) | 0.599 (1.00) | 0.969 (1.00) | 0.0939 (1.00) | 0.63 (1.00) | 0.835 (1.00) | 0.236 (1.00) | 0.668 (1.00) | 0.179 (1.00) |  | 0.641 (1.00)
5q loss | 0.434 (1.00) | 0.212 (1.00) | 5.52e-60 (8.57e-57) | 0.86 (1.00) | 0.00434 (1.00) | 2.65e-59 (4.11e-56) | 5.38e-05 (0.0698) | 0.855 (1.00) | 0.152 (1.00) | 1.53e-05 (0.0201) | 0.000245 (0.31) | 0.0874 (1.00) | 0.505 (1.00) | 0.0051 (1.00) | 0.661 (1.00) | 0.46 (1.00) | 0.18 (1.00) | 0.563 (1.00) | 0.339 (1.00) |  | 0.0064 (1.00)
6p loss | 0.0535 (1.00) | 0.001 (1.00) | 3.98e-28 (5.94e-25) | 1 (1.00) | 0.452 (1.00) | 4.31e-26 (6.4e-23) | 0.501 (1.00) | 0.79 (1.00) | 0.457 (1.00) | 0.000212 (0.269) | 0.797 (1.00) | 0.95 (1.00) | 0.683 (1.00) | 0.561 (1.00) | 0.246 (1.00) | 0.0332 (1.00) | 0.848 (1.00) | 0.000685 (0.852) | 0.351 (1.00) |  | 0.0844 (1.00)
6q loss | 0.0275 (1.00) | 6.15e-07 (0.000835) | 1.12e-54 (1.73e-51) | 0.00173 (1.00) | 0.173 (1.00) | 7.11e-54 (1.1e-50) | 0.126 (1.00) | 0.853 (1.00) | 0.749 (1.00) | 2.29e-06 (0.00306) | 0.427 (1.00) | 0.00819 (1.00) | 0.94 (1.00) | 0.0348 (1.00) | 0.106 (1.00) | 0.0937 (1.00) | 0.951 (1.00) | 0.0249 (1.00) | 0.588 (1.00) |  | 0.055 (1.00)
7p loss | 0.45 (1.00) | 0.253 (1.00) | 3.37e-48 (5.16e-45) | 1e-13 (1.43e-10) | 0.319 (1.00) | 1.84e-37 (2.79e-34) | 9e-05 (0.115) | 0.377 (1.00) | 0.735 (1.00) | 1.66e-14 (2.38e-11) | 0.0908 (1.00) | 0.135 (1.00) | 0.00903 (1.00) | 0.515 (1.00) | 0.0224 (1.00) | 0.649 (1.00) | 0.888 (1.00) | 0.42 (1.00) | 0.391 (1.00) |  | 0.0434 (1.00)
7q loss | 0.745 (1.00) | 0.493 (1.00) | 4.47e-20 (6.54e-17) | 3.65e-11 (5.16e-08) | 0.029 (1.00) | 1.83e-23 (2.7e-20) | 3.89e-05 (0.0506) | 0.517 (1.00) | 0.55 (1.00) | 0.0189 (1.00) | 1 (1.00) | 0.769 (1.00) | 0.738 (1.00) | 0.69 (1.00) | 0.734 (1.00) | 0.0422 (1.00) | 0.99 (1.00) | 0.766 (1.00) | 0.221 (1.00) |  | 0.0454 (1.00)
8p loss | 0.929 (1.00) | 0.041 (1.00) | 7.91e-53 (1.22e-49) | 0.00238 (1.00) | 0.0785 (1.00) | 8.98e-35 (1.35e-31) | 0.037 (1.00) | 0.141 (1.00) | 0.783 (1.00) | 1.33e-07 (0.000182) | 6.06e-10 (8.53e-07) | 0.068 (1.00) | 0.696 (1.00) | 0.134 (1.00) | 0.529 (1.00) | 0.586 (1.00) | 0.0967 (1.00) | 0.296 (1.00) | 0.00172 (1.00) |  | 0.865 (1.00)
8q loss | 0.185 (1.00) | 0.203 (1.00) | 1.78e-12 (2.53e-09) | 1 (1.00) | 0.0058 (1.00) | 8.37e-10 (1.18e-06) | 0.0646 (1.00) | 0.404 (1.00) | 0.8 (1.00) | 0.000142 (0.182) | 0.719 (1.00) | 0.335 (1.00) | 0.902 (1.00) | 0.286 (1.00) | 0.818 (1.00) | 0.412 (1.00) | 0.525 (1.00) | 0.106 (1.00) | 0.656 (1.00) |  | 0.642 (1.00)
9p loss | 2.53e-13 (3.61e-10) | 0.0669 (1.00) | 3.23e-49 (4.96e-46) | 0.00234 (1.00) | 0.22 (1.00) | 2.07e-49 (3.18e-46) | 9.7e-09 (1.35e-05) | 0.349 (1.00) | 0.742 (1.00) | 0.014 (1.00) | 0.127 (1.00) | 0.00247 (1.00) | 0.392 (1.00) | 0.187 (1.00) | 0.0454 (1.00) | 0.342 (1.00) | 0.0351 (1.00) | 0.0671 (1.00) | 0.274 (1.00) |  | 0.0254 (1.00)
9q loss | 0.00016 (0.204) | 0.000739 (0.917) | 8.8e-58 (1.36e-54) | 0.00104 (1.00) | 0.787 (1.00) | 1.1e-56 (1.7e-53) | 0.00031 (0.39) | 0.00849 (1.00) | 0.434 (1.00) | 7.3e-09 (1.02e-05) | 0.00372 (1.00) | 0.151 (1.00) | 0.708 (1.00) | 0.0259 (1.00) | 0.0626 (1.00) | 0.305 (1.00) | 0.0552 (1.00) | 0.0286 (1.00) | 0.368 (1.00) |  | 0.0174 (1.00)
10p loss | 0 (0) | 0.379 (1.00) | 0 (0) | 2.5e-22 (3.68e-19) | 0.00339 (1.00) | 9.96e-37 (1.51e-33) | 0.00377 (1.00) | 0.285 (1.00) | 0.85 (1.00) | 0.446 (1.00) | 9.03e-59 (1.4e-55) | 0.974 (1.00) | 0.0223 (1.00) | 0.593 (1.00) | 0.474 (1.00) | 0.884 (1.00) | 0.824 (1.00) | 0.66 (1.00) | 0.794 (1.00) |  | 0.514 (1.00)
10q loss | 0 (0) | 0.0541 (1.00) | 0 (0) | 2.6e-17 (3.78e-14) | 0.000962 (1.00) | 5.71e-41 (8.7e-38) | 0.0807 (1.00) | 0.75 (1.00) | 0.633 (1.00) | 0.902 (1.00) | 2.56e-56 (3.96e-53) | 0.886 (1.00) | 0.104 (1.00) | 0.108 (1.00) | 0.503 (1.00) | 0.871 (1.00) | 0.277 (1.00) | 0.644 (1.00) | 0.972 (1.00) |  | 0.419 (1.00)
11p loss | 0.00257 (1.00) | 0.469 (1.00) | 7.63e-41 (1.16e-37) | 1.95e-05 (0.0255) | 0.758 (1.00) | 1.17e-36 (1.76e-33) | 0.105 (1.00) | 4.77e-05 (0.0619) | 0.685 (1.00) | 2.7e-12 (3.84e-09) | 0.251 (1.00) | 0.344 (1.00) | 0.16 (1.00) | 2.25e-06 (0.00301) | 0.0494 (1.00) | 0.678 (1.00) | 0.0685 (1.00) | 0.815 (1.00) | 0.00279 (1.00) |  | 0.000208 (0.264)
11q loss | 0.632 (1.00) | 0.974 (1.00) | 2.05e-44 (3.13e-41) | 5.76e-05 (0.0745) | 0.88 (1.00) | 4.7e-22 (6.92e-19) | 0.0392 (1.00) | 0.00121 (1.00) | 0.741 (1.00) | 1.04e-05 (0.0138) | 0.777 (1.00) | 0.899 (1.00) | 0.75 (1.00) | 0.069 (1.00) | 0.0573 (1.00) | 0.836 (1.00) | 0.129 (1.00) | 0.459 (1.00) | 0.0695 (1.00) |  | 0.0386 (1.00)
12p loss | 0.0587 (1.00) | 0.206 (1.00) | 2.2e-07 (0.000301) | 0.00625 (1.00) | 0.961 (1.00) | 1.32e-10 (1.86e-07) | 0.00588 (1.00) | 0.0277 (1.00) | 0.152 (1.00) | 0.137 (1.00) | 0.155 (1.00) | 0.0079 (1.00) | 0.647 (1.00) | 0.764 (1.00) | 0.000571 (0.713) | 0.554 (1.00) | 0.555 (1.00) | 0.578 (1.00) | 0.883 (1.00) |  | 0.414 (1.00)
12q loss | 0.163 (1.00) | 0.325 (1.00) | 3.31e-16 (4.79e-13) | 0.00183 (1.00) | 0.95 (1.00) | 7.04e-16 (1.02e-12) | 0.132 (1.00) | 0.075 (1.00) | 0.286 (1.00) | 0.00992 (1.00) | 0.862 (1.00) | 0.593 (1.00) | 0.626 (1.00) | 0.347 (1.00) | 0.0973 (1.00) | 0.703 (1.00) | 0.584 (1.00) | 0.615 (1.00) | 0.488 (1.00) |  | 0.129 (1.00)
13q loss | 0.00165 (1.00) | 0.194 (1.00) | 7.7e-88 (1.21e-84) | 1.22e-06 (0.00165) | 0.173 (1.00) | 1.53e-83 (2.4e-80) | 9.98e-12 (1.42e-08) | 0.0228 (1.00) | 0.42 (1.00) | 1.38e-08 (1.92e-05) | 0.211 (1.00) | 0.27 (1.00) | 0.0886 (1.00) | 0.0203 (1.00) | 0.563 (1.00) | 0.913 (1.00) | 0.0971 (1.00) | 0.604 (1.00) | 0.139 (1.00) |  | 0.22 (1.00)
14q loss | 0.00277 (1.00) | 0.205 (1.00) | 1.77e-38 (2.68e-35) | 0.0381 (1.00) | 0.823 (1.00) | 1.06e-38 (1.61e-35) | 2.02e-07 (0.000277) | 0.000151 (0.193) | 5.75e-05 (0.0744) | 0.000671 (0.836) | 0.0861 (1.00) | 0.339 (1.00) | 0.111 (1.00) | 0.283 (1.00) | 0.741 (1.00) | 0.942 (1.00) | 0.189 (1.00) | 0.109 (1.00) | 0.345 (1.00) |  | 0.248 (1.00)
15q loss | 0.283 (1.00) | 0.00988 (1.00) | 3.19e-60 (4.96e-57) | 1.96e-12 (2.78e-09) | 0.936 (1.00) | 3.38e-63 (5.25e-60) | 1.85e-06 (0.00248) | 0.0822 (1.00) | 0.136 (1.00) | 3.04e-14 (4.37e-11) | 0.00398 (1.00) | 0.704 (1.00) | 0.362 (1.00) | 0.608 (1.00) | 0.454 (1.00) | 0.12 (1.00) | 0.539 (1.00) | 0.191 (1.00) | 0.0579 (1.00) |  | 0.704 (1.00)
16p loss | 0.00995 (1.00) | 0.758 (1.00) | 3.63e-173 (5.75e-170) | 8.69e-20 (1.27e-16) | 0.304 (1.00) | 1.47e-134 (2.31e-131) | 0.00102 (1.00) | 0.813 (1.00) | 0.774 (1.00) | 9.54e-28 (1.42e-24) | 3.42e-06 (0.00456) | 0.283 (1.00) | 0.941 (1.00) | 0.0613 (1.00) | 0.44 (1.00) | 0.939 (1.00) | 0.83 (1.00) | 0.0073 (1.00) | 0.966 (1.00) |  | 0.601 (1.00)
16q loss | 0.00145 (1.00) | 0.668 (1.00) | 1.19e-229 (1.89e-226) | 7.3e-72 (1.14e-68) | 0.0846 (1.00) | 1.95e-195 (3.1e-192) | 1.01e-06 (0.00136) | 0.392 (1.00) | 0.643 (1.00) | 3.38e-42 (5.15e-39) | 0.000689 (0.857) | 0.229 (1.00) | 0.387 (1.00) | 0.032 (1.00) | 0.797 (1.00) | 0.146 (1.00) | 0.0779 (1.00) | 1.07e-05 (0.0141) | 0.221 (1.00) |  | 9.99e-06 (0.0132)
17p loss | 0.0253 (1.00) | 0.362 (1.00) | 2.2e-195 (3.49e-192) | 1.96e-32 (2.94e-29) | 0.00321 (1.00) | 5.37e-162 (8.48e-159) | 2.22e-07 (0.000304) | 0.00366 (1.00) | 0.0556 (1.00) | 2.74e-31 (4.12e-28) | 3.23e-23 (4.76e-20) | 0.292 (1.00) | 0.483 (1.00) | 0.259 (1.00) | 0.714 (1.00) | 0.61 (1.00) | 0.77 (1.00) | 0.00132 (1.00) | 0.0512 (1.00) |  | 0.0524 (1.00)
17q loss | 0.869 (1.00) | 0.00759 (1.00) | 9.79e-204 (1.56e-200) | 8.72e-49 (1.34e-45) | 0.945 (1.00) | 1.38e-170 (2.19e-167) | 0.544 (1.00) | 0.0672 (1.00) | 0.277 (1.00) | 2.14e-45 (3.27e-42) | 2.1e-08 (2.91e-05) | 0.5 (1.00) | 0.831 (1.00) | 0.164 (1.00) | 0.39 (1.00) | 0.502 (1.00) | 0.367 (1.00) | 8.95e-05 (0.115) | 0.467 (1.00) |  | 0.13 (1.00)
18p loss | 0.805 (1.00) | 0.000808 (0.999) | 1.86e-147 (2.94e-144) | 0.057 (1.00) | 0.916 (1.00) | 1.74e-130 (2.74e-127) | 1.75e-26 (2.6e-23) | 0.000217 (0.275) | 4.8e-09 (6.72e-06) | 5e-12 (7.09e-09) | 4.81e-12 (6.83e-09) | 0.00564 (1.00) | 0.449 (1.00) | 0.701 (1.00) | 0.00913 (1.00) | 0.328 (1.00) | 0.36 (1.00) | 0.000346 (0.435) | 0.0572 (1.00) |  | 0.41 (1.00)
18q loss | 0.842 (1.00) | 3.22e-05 (0.042) | 6.45e-148 (1.02e-144) | 0.887 (1.00) | 0.373 (1.00) | 1.9e-112 (2.98e-109) | 3.09e-24 (4.58e-21) | 8.37e-07 (0.00113) | 2.29e-05 (0.0299) | 5.26e-14 (7.55e-11) | 2.46e-19 (3.59e-16) | 0.299 (1.00) | 0.733 (1.00) | 0.0675 (1.00) | 0.0135 (1.00) | 0.395 (1.00) | 0.387 (1.00) | 0.00296 (1.00) | 0.0708 (1.00) |  | 0.096 (1.00)
19p loss | 0.00671 (1.00) | 0.832 (1.00) | 6.43e-67 (1e-63) | 0.00229 (1.00) | 0.669 (1.00) | 3.63e-51 (5.59e-48) | 2.22e-07 (0.000304) | 0.307 (1.00) | 0.0399 (1.00) | 3.85e-06 (0.00513) | 2.75e-06 (0.00367) | 0.72 (1.00) | 0.648 (1.00) | 0.00738 (1.00) | 0.0133 (1.00) | 0.128 (1.00) | 0.0726 (1.00) | 0.3 (1.00) | 0.318 (1.00) |  | 0.153 (1.00)
19q loss | 0.0664 (1.00) | 0.273 (1.00) | 5.1e-64 (7.94e-61) | 5.16e-07 (0.000703) | 0.873 (1.00) | 1.28e-50 (1.97e-47) | 0.00706 (1.00) | 0.971 (1.00) | 0.167 (1.00) | 8.01e-10 (1.13e-06) | 0.00171 (1.00) | 0.188 (1.00) | 0.572 (1.00) | 0.145 (1.00) | 0.0111 (1.00) | 0.695 (1.00) | 0.109 (1.00) | 0.00413 (1.00) | 0.864 (1.00) |  | 0.116 (1.00)
20p loss | 0.724 (1.00) | 0.779 (1.00) | 1.02e-10 (1.45e-07) | 0.422 (1.00) | 0.963 (1.00) | 5.75e-09 (8.03e-06) | 0.00253 (1.00) | 0.044 (1.00) | 0.401 (1.00) | 0.179 (1.00) | 0.0187 (1.00) | 0.994 (1.00) | 0.457 (1.00) | 0.629 (1.00) | 0.0616 (1.00) | 0.527 (1.00) | 0.561 (1.00) | 0.906 (1.00) | 0.261 (1.00) |  | 0.215 (1.00)
20q loss | 0.631 (1.00) | 0.534 (1.00) | 9.63e-09 (1.34e-05) | 0.92 (1.00) | 0.335 (1.00) | 8.42e-07 (0.00114) | 0.0205 (1.00) | 0.472 (1.00) | 0.617 (1.00) | 0.165 (1.00) | 0.0577 (1.00) | 0.644 (1.00) | 0.722 (1.00) | 0.623 (1.00) | 0.159 (1.00) | 0.546 (1.00) | 0.928 (1.00) | 0.336 (1.00) | 0.459 (1.00) |  | 0.666 (1.00)
21q loss | 0.817 (1.00) | 0.342 (1.00) | 2.1e-46 (3.21e-43) | 0.147 (1.00) | 0.0337 (1.00) | 1.61e-27 (2.4e-24) | 0.0199 (1.00) | 0.00555 (1.00) | 0.726 (1.00) | 5.65e-06 (0.00751) | 1.08e-07 (0.000149) | 0.11 (1.00) | 5.24e-05 (0.068) | 0.0646 (1.00) | 0.996 (1.00) | 0.0811 (1.00) | 0.677 (1.00) | 0.83 (1.00) | 0.0647 (1.00) |  | 0.0334 (1.00)
22q loss | 5.47e-05 (0.0708) | 0.266 (1.00) | 2.28e-167 (3.61e-164) | 5.59e-34 (8.42e-31) | 0.017 (1.00) | 8.78e-170 (1.39e-166) | 0.000676 (0.842) | 0.000747 (0.925) | 0.53 (1.00) | 3.92e-53 (6.04e-50) | 0.659 (1.00) | 0.401 (1.00) | 0.863 (1.00) | 0.102 (1.00) | 0.0119 (1.00) | 0.658 (1.00) | 0.116 (1.00) | 0.000853 (1.00) | 0.182 (1.00) |  | 0.188 (1.00)
Xq loss | 0.394 (1.00) | 0.0846 (1.00) | 5.04e-48 (7.72e-45) | 4.06e-07 (0.000553) | 0.838 (1.00) | 5.42e-35 (8.18e-32) | 0.82 (1.00) | 0.556 (1.00) | 0.975 (1.00) | 2.78e-10 (3.92e-07) | 0.00345 (1.00) | 0.136 (1.00) | 0.246 (1.00) | 0.585 (1.00) | 0.925 (1.00) | 0.684 (1.00) | 1 (1.00) | 0.102 (1.00) | 0.444 (1.00) |  | 0.000281 (0.354)

Clustering Approach #1: '1p gain mutation analysis'

Table S1. Get Full Table Description of clustering approach #1: '1p gain mutation analysis'

Cluster Labels | 1P GAIN MUTATED | 1P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 359 | 4204

'1p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.5e-28 (Chi-square test), Q value = 2.2e-25

Table S2. Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
1P GAIN MUTATED | 15 | 38 | 97 | 9 | 17 | 11 | 5 | 76 | 1 | 85 | 1 | 4
1P GAIN WILD-TYPE | 110 | 506 | 749 | 403 | 430 | 308 | 488 | 586 | 1 | 463 | 1 | 155

Figure S1. Get High-res Image Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'1p gain mutation analysis' versus 'GENDER'

P value = 8.6e-07 (Fisher's exact test), Q value = 0.0012

Table S3. Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
1P GAIN MUTATED | 269 | 90
1P GAIN WILD-TYPE | 2612 | 1592

Figure S2. Get High-res Image Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'1p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.45e-29 (Chi-square test), Q value = 2.2e-26

Table S4. Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
1P GAIN MUTATED | 8 | 1 | 10 | 11 | 5 | 1 | 10 | 30 | 4 | 0 | 3 | 0 | 1 | 0 | 2 | 0 | 0 | 1 | 0 | 23 | 0 | 1 | 3 | 1 | 87 | 7 | 0 | 1
1P GAIN WILD-TYPE | 348 | 53 | 340 | 308 | 488 | 9 | 65 | 175 | 3 | 3 | 12 | 2 | 2 | 2 | 11 | 1 | 1 | 0 | 2 | 292 | 18 | 6 | 140 | 12 | 465 | 72 | 1 | 19

Figure S3. Get High-res Image Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'1p gain mutation analysis' versus 'PATHOLOGY.T'

P value = 0.000161 (Chi-square test), Q value = 0.21

Table S5. Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
1P GAIN MUTATED | 19 | 53 | 24 | 7
1P GAIN WILD-TYPE | 447 | 579 | 670 | 202

Figure S4. Get High-res Image Clustering Approach #1: '1p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #2: '1q gain mutation analysis'

Table S6. Get Full Table Description of clustering approach #2: '1q gain mutation analysis'

Cluster Labels | 1Q GAIN MUTATED | 1Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 1174 | 3389

'1q gain mutation analysis' versus 'Time to Death'

P value = 2.04e-10 (logrank test), Q value = 2.9e-07

Table S7. Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
1Q GAIN MUTATED | 1116 | 275 | 0.0 - 223.4 (15.2)
1Q GAIN WILD-TYPE | 3180 | 1126 | 0.0 - 224.0 (14.5)

Figure S5. Get High-res Image Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'1q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.09e-135 (Chi-square test), Q value = 4.9e-132

Table S8. Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
1Q GAIN MUTATED | 29 | 42 | 464 | 51 | 133 | 39 | 31 | 206 | 1 | 150 | 2 | 25
1Q GAIN WILD-TYPE | 96 | 502 | 382 | 361 | 314 | 280 | 462 | 456 | 1 | 398 | 0 | 134

Figure S6. Get High-res Image Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'1q gain mutation analysis' versus 'GENDER'

P value = 1.89e-33 (Fisher's exact test), Q value = 2.8e-30

Table S9. Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
1Q GAIN MUTATED | 909 | 265
1Q GAIN WILD-TYPE | 1972 | 1417

Figure S7. Get High-res Image Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'1q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.19e-39 (Chi-square test), Q value = 3.3e-36

Table S10. Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
1Q GAIN MUTATED | 48 | 3 | 116 | 39 | 31 | 4 | 34 | 75 | 6 | 0 | 7 | 1 | 2 | 0 | 7 | 0 | 0 | 1 | 1 | 66 | 3 | 2 | 21 | 4 | 153 | 14 | 0 | 1
1Q GAIN WILD-TYPE | 308 | 51 | 234 | 280 | 462 | 6 | 41 | 130 | 1 | 3 | 8 | 1 | 1 | 2 | 6 | 1 | 1 | 0 | 1 | 249 | 15 | 5 | 122 | 9 | 399 | 65 | 1 | 19

Figure S8. Get High-res Image Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'1q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 1.65e-05 (Chi-square test), Q value = 0.022

Table S11. Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
1Q GAIN MUTATED | 71 | 140 | 88 | 45
1Q GAIN WILD-TYPE | 395 | 492 | 606 | 164

Figure S9. Get High-res Image Clustering Approach #2: '1q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #3: '2p gain mutation analysis'

Table S12. Get Full Table Description of clustering approach #3: '2p gain mutation analysis'

Cluster Labels | 2P GAIN MUTATED | 2P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 518 | 4045

'2p gain mutation analysis' versus 'AGE'

P value = 0.000113 (t-test), Q value = 0.15

Table S13. Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
2P GAIN MUTATED | 507 | 63.8 (12.1)
2P GAIN WILD-TYPE | 4000 | 61.6 (12.7)

Figure S10. Get High-res Image Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #2: 'AGE'

'2p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.25e-30 (Chi-square test), Q value = 1.9e-27

Table S14. Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
2P GAIN MUTATED | 26 | 18 | 50 | 39 | 47 | 31 | 46 | 119 | 0 | 122 | 0 | 20
2P GAIN WILD-TYPE | 99 | 526 | 796 | 373 | 400 | 288 | 447 | 543 | 2 | 426 | 2 | 139

Figure S11. Get High-res Image Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'2p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.8e-13 (Chi-square test), Q value = 2.6e-10

Table S15. Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
2P GAIN MUTATED | 38 | 1 | 31 | 31 | 46 | 1 | 11 | 26 | 5 | 0 | 1 | 1 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 70 | 3 | 0 | 20 | 0 | 122 | 13 | 0 | 0
2P GAIN WILD-TYPE | 318 | 53 | 319 | 288 | 447 | 9 | 64 | 179 | 2 | 3 | 14 | 1 | 3 | 2 | 10 | 0 | 1 | 1 | 2 | 245 | 15 | 7 | 123 | 13 | 430 | 66 | 1 | 20

Figure S12. Get High-res Image Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'2p gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.7e-06 (Fisher's exact test), Q value = 0.0089

Table S16. Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
2P GAIN MUTATED | 58 | 460
2P GAIN WILD-TYPE | 768 | 3277

Figure S13. Get High-res Image Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'2p gain mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.47e-05 (Chi-square test), Q value = 0.032

Table S17. Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
2P GAIN MUTATED | 1 | 3 | 0 | 8 | 21 | 10 | 7 | 6 | 0 | 2 | 13 | 0 | 3
2P GAIN WILD-TYPE | 71 | 59 | 7 | 35 | 266 | 176 | 35 | 118 | 25 | 39 | 46 | 1 | 13

Figure S14. Get High-res Image Clustering Approach #3: '2p gain mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #4: '2q gain mutation analysis'

Table S18. Get Full Table Description of clustering approach #4: '2q gain mutation analysis'

Cluster Labels | 2Q GAIN MUTATED | 2Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 396 | 4167

'2q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.17e-21 (Chi-square test), Q value = 1.7e-18

Table S19. Clustering Approach #4: '2q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
2Q GAIN MUTATED | 14 | 15 | 27 | 38 | 37 | 22 | 48 | 78 | 0 | 96 | 0 | 21
2Q GAIN WILD-TYPE | 111 | 529 | 819 | 374 | 410 | 297 | 445 | 584 | 2 | 452 | 2 | 138

Figure S15. Get High-res Image Clustering Approach #4: '2q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'2q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1e-08 (Chi-square test), Q value = 1.4e-05

Table S20. Clustering Approach #4: '2q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
2Q GAIN MUTATED | 37 | 1 | 25 | 22 | 48 | 1 | 8 | 25 | 5 | 0 | 0 | 0 | 0 | 0 | 4 | 1 | 0 | 0 | 0 | 34 | 1 | 0 | 21 | 0 | 96 | 11 | 0 | 0
2Q GAIN WILD-TYPE | 319 | 53 | 325 | 297 | 445 | 9 | 67 | 180 | 2 | 3 | 15 | 2 | 3 | 2 | 9 | 0 | 1 | 1 | 2 | 281 | 17 | 7 | 122 | 13 | 456 | 68 | 1 | 20

Figure S16. Get High-res Image Clustering Approach #4: '2q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #5: '3p gain mutation analysis'

Table S21. Get Full Table Description of clustering approach #5: '3p gain mutation analysis'

Cluster Labels | 3P GAIN MUTATED | 3P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 365 | 4198

'3p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.71e-30 (Chi-square test), Q value = 4.1e-27

Table S22. Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
3P GAIN MUTATED | 28 | 28 | 58 | 19 | 24 | 29 | 5 | 58 | 0 | 99 | 1 | 15
3P GAIN WILD-TYPE | 97 | 516 | 788 | 393 | 423 | 290 | 488 | 604 | 2 | 449 | 1 | 144

Figure S17. Get High-res Image Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'3p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.17e-19 (Chi-square test), Q value = 9e-16

Table S23. Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
3P GAIN MUTATED | 18 | 1 | 18 | 29 | 5 | 1 | 2 | 8 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 45 | 0 | 0 | 15 | 0 | 100 | 6 | 0 | 1
3P GAIN WILD-TYPE | 338 | 53 | 332 | 290 | 488 | 9 | 73 | 197 | 6 | 3 | 15 | 2 | 3 | 2 | 12 | 1 | 1 | 1 | 2 | 270 | 18 | 7 | 128 | 13 | 452 | 73 | 1 | 19

Figure S18. Get High-res Image Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'3p gain mutation analysis' versus 'TUMOR.STAGE'

P value = 7.88e-05 (Chi-square test), Q value = 0.1

Table S24. Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
3P GAIN MUTATED | 37 | 39 | 103 | 37
3P GAIN WILD-TYPE | 675 | 459 | 778 | 386

Figure S19. Get High-res Image Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'3p gain mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.65e-05 (Chi-square test), Q value = 0.06

Table S25. Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
3P GAIN MUTATED | 4 | 1 | 0 | 9 | 25 | 7 | 5 | 13 | 4 | 2 | 14 | 0 | 0
3P GAIN WILD-TYPE | 68 | 61 | 7 | 34 | 262 | 179 | 37 | 111 | 21 | 39 | 45 | 1 | 16

Figure S20. Get High-res Image Clustering Approach #5: '3p gain mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #6: '3q gain mutation analysis'

Table S26. Get Full Table Description of clustering approach #6: '3q gain mutation analysis'

Cluster Labels | 3Q GAIN MUTATED | 3Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 758 | 3805

'3q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.2e-87 (Chi-square test), Q value = 3.5e-84

Table S27. Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
3Q GAIN MUTATED | 36 | 28 | 99 | 28 | 44 | 104 | 20 | 180 | 0 | 193 | 2 | 23
3Q GAIN WILD-TYPE | 89 | 516 | 747 | 384 | 403 | 215 | 473 | 482 | 2 | 355 | 0 | 136

Figure S21. Get High-res Image Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'3q gain mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 1.53e-05 (t-test), Q value = 0.02

Table S28. Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
3Q GAIN MUTATED | 90 | 58.8 (34.9)
3Q GAIN WILD-TYPE | 550 | 76.0 (20.7)

Figure S22. Get High-res Image Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'3q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.25e-88 (Chi-square test), Q value = 2e-85

Table S29. Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
3Q GAIN MUTATED | 26 | 2 | 24 | 104 | 20 | 1 | 4 | 16 | 5 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 152 | 2 | 0 | 23 | 0 | 195 | 18 | 0 | 1
3Q GAIN WILD-TYPE | 330 | 52 | 326 | 215 | 473 | 9 | 71 | 189 | 2 | 3 | 15 | 2 | 3 | 2 | 11 | 1 | 1 | 1 | 2 | 163 | 16 | 7 | 120 | 13 | 357 | 61 | 1 | 19

Figure S23. Get High-res Image Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'3q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 6.96e-07 (Chi-square test), Q value = 0.00094

Table S30. Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
3Q GAIN MUTATED | 72 | 138 | 80 | 48
3Q GAIN WILD-TYPE | 394 | 494 | 614 | 161

Figure S24. Get High-res Image Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'3q gain mutation analysis' versus 'PATHOLOGY.N'

P value = 9.15e-06 (Chi-square test), Q value = 0.012

Table S31. Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
3Q GAIN MUTATED | 166 | 86 | 63 | 6
3Q GAIN WILD-TYPE | 901 | 267 | 219 | 5

Figure S25. Get High-res Image Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'3q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 1.34e-06 (Chi-square test), Q value = 0.0018

Table S32. Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
3Q GAIN MUTATED | 112 | 86 | 228 | 98
3Q GAIN WILD-TYPE | 600 | 412 | 653 | 325

Figure S26. Get High-res Image Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'3q gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.00013 (Fisher's exact test), Q value = 0.17

Table S33. Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
3Q GAIN MUTATED | 101 | 657
3Q GAIN WILD-TYPE | 725 | 3080

Figure S27. Get High-res Image Clustering Approach #6: '3q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #7: '4p gain mutation analysis'

Table S34. Get Full Table Description of clustering approach #7: '4p gain mutation analysis'

Cluster Labels | 4P GAIN MUTATED | 4P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 151 | 4412

'4p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.01e-06 (Chi-square test), Q value = 0.0014

Table S35. Clustering Approach #7: '4p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
4P GAIN MUTATED | 8 | 11 | 32 | 2 | 5 | 14 | 8 | 37 | 0 | 30 | 0 | 4
4P GAIN WILD-TYPE | 117 | 533 | 814 | 410 | 442 | 305 | 485 | 625 | 2 | 518 | 2 | 155

Figure S28. Get High-res Image Clustering Approach #7: '4p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'4p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.31e-06 (Chi-square test), Q value = 0.0018

Table S36. Clustering Approach #7: '4p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
4P GAIN MUTATED | 2 | 0 | 1 | 14 | 8 | 1 | 3 | 18 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 13 | 0 | 0 | 4 | 0 | 30 | 4 | 0 | 0
4P GAIN WILD-TYPE | 354 | 54 | 349 | 305 | 485 | 9 | 72 | 187 | 6 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 1 | 302 | 18 | 7 | 139 | 13 | 522 | 75 | 1 | 20

Figure S29. Get High-res Image Clustering Approach #7: '4p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #8: '4q gain mutation analysis'

Table S37. Get Full Table Description of clustering approach #8: '4q gain mutation analysis'

Cluster Labels | 4Q GAIN MUTATED | 4Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 101 | 4462

Clustering Approach #9: '5p gain mutation analysis'

Table S38. Get Full Table Description of clustering approach #9: '5p gain mutation analysis'

Cluster Labels | 5P GAIN MUTATED | 5P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 963 | 3600

'5p gain mutation analysis' versus 'AGE'

P value = 3.72e-05 (t-test), Q value = 0.048

Table S39. Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
5P GAIN MUTATED | 949 | 63.3 (11.7)
5P GAIN WILD-TYPE | 3558 | 61.5 (12.8)

Figure S30. Get High-res Image Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #2: 'AGE'

'5p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.92e-83 (Chi-square test), Q value = 1.2e-79

Table S40. Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
5P GAIN MUTATED | 38 | 27 | 166 | 37 | 29 | 81 | 133 | 287 | 0 | 142 | 2 | 21
5P GAIN WILD-TYPE | 87 | 517 | 680 | 375 | 418 | 238 | 360 | 375 | 2 | 406 | 0 | 138

Figure S31. Get High-res Image Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'5p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.28e-52 (Chi-square test), Q value = 2e-49

Table S41. Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
5P GAIN MUTATED | 34 | 3 | 11 | 81 | 133 | 2 | 31 | 82 | 4 | 1 | 6 | 2 | 2 | 0 | 4 | 0 | 0 | 1 | 1 | 151 | 1 | 0 | 21 | 0 | 144 | 17 | 1 | 1
5P GAIN WILD-TYPE | 322 | 51 | 339 | 238 | 360 | 8 | 44 | 123 | 3 | 2 | 9 | 0 | 1 | 2 | 9 | 1 | 1 | 0 | 1 | 164 | 17 | 7 | 122 | 13 | 408 | 62 | 0 | 19

Figure S32. Get High-res Image Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'5p gain mutation analysis' versus 'PATHOLOGY.T'

P value = 8.46e-10 (Chi-square test), Q value = 1.2e-06

Table S42. Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
5P GAIN MUTATED | 133 | 225 | 135 | 50
5P GAIN WILD-TYPE | 333 | 407 | 559 | 159

Figure S33. Get High-res Image Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'5p gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.41e-08 (Fisher's exact test), Q value = 2e-05

Table S43. Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
5P GAIN MUTATED | 116 | 847
5P GAIN WILD-TYPE | 710 | 2890

Figure S34. Get High-res Image Clustering Approach #9: '5p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #10: '5q gain mutation analysis'

Table S44. Get Full Table Description of clustering approach #10: '5q gain mutation analysis'

Cluster Labels | 5Q GAIN MUTATED | 5Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 463 | 4100

'5q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.05e-58 (Chi-square test), Q value = 1.4e-54

Table S45. Clustering Approach #10: '5q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
5Q GAIN MUTATED | 16 | 20 | 100 | 20 | 8 | 30 | 145 | 83 | 0 | 29 | 1 | 11
5Q GAIN WILD-TYPE | 109 | 524 | 746 | 392 | 439 | 289 | 348 | 579 | 2 | 519 | 1 | 148

Figure S35. Get High-res Image Clustering Approach #10: '5q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'5q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.57e-43 (Chi-square test), Q value = 7e-40

Table S46. Clustering Approach #10: '5q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
5Q GAIN MUTATED | 19 | 1 | 3 | 30 | 145 | 1 | 11 | 28 | 1 | 1 | 1 | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 37 | 0 | 0 | 11 | 0 | 30 | 5 | 1 | 0
5Q GAIN WILD-TYPE | 337 | 53 | 347 | 289 | 348 | 9 | 64 | 177 | 6 | 2 | 14 | 1 | 3 | 2 | 11 | 1 | 1 | 1 | 2 | 278 | 18 | 7 | 132 | 13 | 522 | 74 | 0 | 20

Figure S36. Get High-res Image Clustering Approach #10: '5q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #11: '6p gain mutation analysis'

Table S47. Get Full Table Description of clustering approach #11: '6p gain mutation analysis'

Cluster Labels | 6P GAIN MUTATED | 6P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 453 | 4110

'6p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.08e-35 (Chi-square test), Q value = 1.6e-32

Table S48. Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
6P GAIN MUTATED | 10 | 5 | 100 | 47 | 34 | 26 | 5 | 83 | 0 | 115 | 1 | 27
6P GAIN WILD-TYPE | 115 | 539 | 746 | 365 | 413 | 293 | 488 | 579 | 2 | 433 | 1 | 132

Figure S37. Get High-res Image Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'6p gain mutation analysis' versus 'GENDER'

P value = 3.41e-07 (Fisher's exact test), Q value = 0.00047

Table S49. Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
6P GAIN MUTATED | 335 | 118
6P GAIN WILD-TYPE | 2546 | 1564

Figure S38. Get High-res Image Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'6p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.48e-22 (Chi-square test), Q value = 6.6e-19

Table S50. Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
6P GAIN MUTATED | 40 | 7 | 20 | 26 | 5 | 3 | 13 | 28 | 0 | 0 | 4 | 1 | 1 | 0 | 2 | 0 | 0 | 1 | 0 | 30 | 0 | 0 | 27 | 0 | 116 | 14 | 0 | 0
6P GAIN WILD-TYPE | 316 | 47 | 330 | 293 | 488 | 7 | 62 | 177 | 7 | 3 | 11 | 1 | 2 | 2 | 11 | 1 | 1 | 0 | 2 | 285 | 18 | 7 | 116 | 13 | 436 | 65 | 1 | 20

Figure S39. Get High-res Image Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'6p gain mutation analysis' versus 'TUMOR.STAGE'

P value = 6.63e-07 (Chi-square test), Q value = 9e-04

Table S51. Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
6P GAIN MUTATED | 53 | 54 | 144 | 45
6P GAIN WILD-TYPE | 659 | 444 | 737 | 378

Figure S40. Get High-res Image Clustering Approach #11: '6p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #12: '6q gain mutation analysis'

Table S52. Get Full Table Description of clustering approach #12: '6q gain mutation analysis'

Cluster Labels | 6Q GAIN MUTATED | 6Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 295 | 4268

'6q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.31e-18 (Chi-square test), Q value = 1.9e-15

Table S53. Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
6Q GAIN MUTATED | 6 | 7 | 65 | 43 | 31 | 19 | 4 | 33 | 0 | 60 | 0 | 26
6Q GAIN WILD-TYPE | 119 | 537 | 781 | 369 | 416 | 300 | 489 | 629 | 2 | 488 | 2 | 133

Figure S41. Get High-res Image Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'6q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.41e-13 (Chi-square test), Q value = 3.4e-10

Table S54. Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
6Q GAIN MUTATED | 38 | 5 | 17 | 19 | 4 | 0 | 2 | 11 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 18 | 0 | 0 | 26 | 0 | 60 | 14 | 0 | 0
6Q GAIN WILD-TYPE | 318 | 49 | 333 | 300 | 489 | 10 | 73 | 194 | 7 | 3 | 15 | 2 | 3 | 2 | 12 | 1 | 1 | 0 | 2 | 297 | 18 | 7 | 117 | 13 | 492 | 65 | 1 | 20

Figure S42. Get High-res Image Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'6q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 6.68e-05 (Chi-square test), Q value = 0.086

Table S55. Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
6Q GAIN MUTATED | 13 | 31 | 63 | 16
6Q GAIN WILD-TYPE | 453 | 601 | 631 | 193

Figure S43. Get High-res Image Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'6q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 1.85e-05 (Chi-square test), Q value = 0.024

Table S56. Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
6Q GAIN MUTATED | 24 | 38 | 86 | 32
6Q GAIN WILD-TYPE | 688 | 460 | 795 | 391

Figure S44. Get High-res Image Clustering Approach #12: '6q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #13: '7p gain mutation analysis'

Table S57. Get Full Table Description of clustering approach #13: '7p gain mutation analysis'

Cluster Labels | 7P GAIN MUTATED | 7P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 1455 | 3108

'7p gain mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S58. Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
7P GAIN MUTATED | 1360 | 572 | 0.0 - 224.0 (11.0)
7P GAIN WILD-TYPE | 2936 | 829 | 0.0 - 223.4 (17.5)

Figure S45. Get High-res Image Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'7p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.14e-166 (Chi-square test), Q value = 1.8e-163

Table S59. Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
7P GAIN MUTATED | 35 | 412 | 156 | 199 | 40 | 73 | 127 | 210 | 0 | 112 | 0 | 89
7P GAIN WILD-TYPE | 90 | 132 | 690 | 213 | 407 | 246 | 366 | 452 | 2 | 436 | 2 | 70

Figure S46. Get High-res Image Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'7p gain mutation analysis' versus 'GENDER'

P value = 6.39e-27 (Fisher's exact test), Q value = 9.5e-24

Table S60. Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
7P GAIN MUTATED | 754 | 701
7P GAIN WILD-TYPE | 2127 | 981

Figure S47. Get High-res Image Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'7p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.01e-51 (Chi-square test), Q value = 1.6e-48

Table S61. Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
7P GAIN MUTATED | 184 | 15 | 27 | 73 | 127 | 5 | 20 | 78 | 3 | 2 | 4 | 0 | 1 | 0 | 5 | 1 | 0 | 0 | 1 | 89 | 1 | 1 | 87 | 2 | 112 | 12 | 0 | 14
7P GAIN WILD-TYPE | 172 | 39 | 323 | 246 | 366 | 5 | 55 | 127 | 4 | 1 | 11 | 2 | 2 | 2 | 8 | 0 | 1 | 1 | 1 | 226 | 17 | 6 | 56 | 11 | 440 | 67 | 1 | 6

Figure S48. Get High-res Image Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'7p gain mutation analysis' versus 'PATHOLOGY.T'

P value = 1.49e-09 (Chi-square test), Q value = 2.1e-06

Table S62. Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
7P GAIN MUTATED | 110 | 221 | 294 | 67
7P GAIN WILD-TYPE | 356 | 411 | 400 | 142

Figure S49. Get High-res Image Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'7p gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 7.41e-05 (Chi-square test), Q value = 0.095

Table S63. Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
7P GAIN MUTATED | 479 | 80 | 8 | 1 | 59
7P GAIN WILD-TYPE | 945 | 88 | 1 | 2 | 106

Figure S50. Get High-res Image Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'7p gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.56e-14 (Fisher's exact test), Q value = 9.4e-11

Table S64. Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
7P GAIN MUTATED | 356 | 1099
7P GAIN WILD-TYPE | 470 | 2638

Figure S51. Get High-res Image Clustering Approach #13: '7p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #14: '7q gain mutation analysis'

Table S65. Get Full Table Description of clustering approach #14: '7q gain mutation analysis'

Cluster Labels | 7Q GAIN MUTATED | 7Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 1359 | 3204

'7q gain mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S66. Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
7Q GAIN MUTATED | 1274 | 559 | 0.0 - 224.0 (11.1)
7Q GAIN WILD-TYPE | 3022 | 842 | 0.0 - 223.4 (17.2)

Figure S52. Get High-res Image Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'7q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.26e-182 (Chi-square test), Q value = 2e-179

Table S67. Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
7Q GAIN MUTATED | 35 | 419 | 115 | 175 | 39 | 50 | 130 | 177 | 0 | 138 | 1 | 78
7Q GAIN WILD-TYPE | 90 | 125 | 731 | 237 | 408 | 269 | 363 | 485 | 2 | 410 | 1 | 81

Figure S53. Get High-res Image Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'7q gain mutation analysis' versus 'GENDER'

P value = 8.98e-27 (Fisher's exact test), Q value = 1.3e-23

Table S68. Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
7Q GAIN MUTATED | 697 | 662
7Q GAIN WILD-TYPE | 2184 | 1020

Figure S54. Get High-res Image Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'7q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-38 (Chi-square test), Q value = 1.6e-35

Table S69. Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
7Q GAIN MUTATED | 161 | 14 | 29 | 50 | 130 | 3 | 19 | 56 | 2 | 2 | 3 | 0 | 1 | 0 | 4 | 1 | 0 | 0 | 0 | 86 | 1 | 0 | 77 | 1 | 139 | 9 | 1 | 15
7Q GAIN WILD-TYPE | 195 | 40 | 321 | 269 | 363 | 7 | 56 | 149 | 5 | 1 | 12 | 2 | 2 | 2 | 9 | 0 | 1 | 1 | 2 | 229 | 17 | 7 | 66 | 12 | 413 | 70 | 0 | 5

Figure S55. Get High-res Image Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'7q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 1.08e-08 (Chi-square test), Q value = 1.5e-05

Table S70. Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
7Q GAIN MUTATED | 99 | 186 | 265 | 56
7Q GAIN WILD-TYPE | 367 | 446 | 429 | 153

Figure S56. Get High-res Image Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'7q gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 9.32e-07 (Chi-square test), Q value = 0.0013

Table S71. Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
7Q GAIN MUTATED | 421 | 78 | 8 | 1 | 51
7Q GAIN WILD-TYPE | 1003 | 90 | 1 | 2 | 114

Figure S57. Get High-res Image Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'7q gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.79e-17 (Fisher's exact test), Q value = 5.5e-14

Table S72. Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
7Q GAIN MUTATED | 349 | 1010
7Q GAIN WILD-TYPE | 477 | 2727

Figure S58. Get High-res Image Clustering Approach #14: '7q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #15: '8p gain mutation analysis'

Table S73. Get Full Table Description of clustering approach #15: '8p gain mutation analysis'

Cluster Labels | 8P GAIN MUTATED | 8P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 643 | 3920

'8p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.18e-25 (Chi-square test), Q value = 6.2e-22

Table S74. Clustering Approach #15: '8p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
8P GAIN MUTATED | 17 | 24 | 178 | 74 | 80 | 54 | 14 | 96 | 0 | 80 | 1 | 25
8P GAIN WILD-TYPE | 108 | 520 | 668 | 338 | 367 | 265 | 479 | 566 | 2 | 468 | 1 | 134

Figure S59. Get High-res Image Clustering Approach #15: '8p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'8p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.81e-08 (Chi-square test), Q value = 0.00011

Table S75. Clustering Approach #15: '8p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
8P GAIN MUTATED | 64 | 10 | 61 | 54 | 14 | 3 | 11 | 28 | 2 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 49 | 4 | 0 | 23 | 2 | 81 | 15 | 0 | 0
8P GAIN WILD-TYPE | 292 | 44 | 289 | 265 | 479 | 7 | 64 | 177 | 5 | 3 | 14 | 2 | 3 | 2 | 12 | 1 | 1 | 0 | 2 | 266 | 14 | 7 | 120 | 11 | 471 | 64 | 1 | 20

Figure S60. Get High-res Image Clustering Approach #15: '8p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'8p gain mutation analysis' versus 'PATHOLOGY.T'

P value = 2.28e-06 (Chi-square test), Q value = 0.003

Table S76. Clustering Approach #15: '8p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
8P GAIN MUTATED | 26 | 96 | 97 | 35
8P GAIN WILD-TYPE | 440 | 536 | 597 | 174

Figure S61. Get High-res Image Clustering Approach #15: '8p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #16: '8q gain mutation analysis'

Table S77. Get Full Table Description of clustering approach #16: '8q gain mutation analysis'

Cluster Labels | 8Q GAIN MUTATED | 8Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 1335 | 3228

'8q gain mutation analysis' versus 'Time to Death'

P value = 0.000192 (logrank test), Q value = 0.24

Table S78. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
8Q GAIN MUTATED | 1223 | 345 | 0.0 - 220.9 (15.1)
8Q GAIN WILD-TYPE | 3073 | 1056 | 0.0 - 224.0 (14.7)

Figure S62. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'8q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.25e-86 (Chi-square test), Q value = 8.2e-83

Table S79. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
8Q GAIN MUTATED | 35 | 28 | 368 | 163 | 103 | 132 | 36 | 208 | 1 | 189 | 2 | 70
8Q GAIN WILD-TYPE | 90 | 516 | 478 | 249 | 344 | 187 | 457 | 454 | 1 | 359 | 0 | 89

Figure S63. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'8q gain mutation analysis' versus 'GENDER'

P value = 9.07e-05 (Fisher's exact test), Q value = 0.12

Table S80. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
8Q GAIN MUTATED | 901 | 434
8Q GAIN WILD-TYPE | 1980 | 1248

Figure S64. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'8q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.16e-35 (Chi-square test), Q value = 1.2e-31

Table S81. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
8Q GAIN MUTATED | 149 | 13 | 70 | 132 | 36 | 5 | 25 | 65 | 3 | 0 | 4 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 2 | 100 | 5 | 0 | 65 | 3 | 192 | 28 | 0 | 0
8Q GAIN WILD-TYPE | 207 | 41 | 280 | 187 | 457 | 5 | 50 | 140 | 4 | 3 | 11 | 2 | 3 | 2 | 9 | 1 | 1 | 1 | 0 | 215 | 13 | 7 | 78 | 10 | 360 | 51 | 1 | 20

Figure S65. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'8q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 1.08e-14 (Chi-square test), Q value = 1.6e-11

Table S82. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
8Q GAIN MUTATED | 70 | 207 | 226 | 87
8Q GAIN WILD-TYPE | 396 | 425 | 468 | 122

Figure S66. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'8q gain mutation analysis' versus 'PATHOLOGY.N'

P value = 1.34e-07 (Chi-square test), Q value = 0.00018

Table S83. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
8Q GAIN MUTATED | 300 | 123 | 130 | 5
8Q GAIN WILD-TYPE | 767 | 230 | 152 | 6

Figure S67. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'8q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 1.98e-09 (Chi-square test), Q value = 2.8e-06

Table S84. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
8Q GAIN MUTATED | 152 | 163 | 297 | 159
8Q GAIN WILD-TYPE | 560 | 335 | 584 | 264

Figure S68. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'8q gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.22e-06 (Fisher's exact test), Q value = 0.0096

Table S85. Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
8Q GAIN MUTATED | 189 | 1146
8Q GAIN WILD-TYPE | 637 | 2591

Figure S69. Get High-res Image Clustering Approach #16: '8q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #17: '9p gain mutation analysis'

Table S86. Get Full Table Description of clustering approach #17: '9p gain mutation analysis'

Cluster Labels | 9P GAIN MUTATED | 9P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 337 | 4226

'9p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.2e-26 (Chi-square test), Q value = 1.2e-22

Table S87. Clustering Approach #17: '9p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
9P GAIN MUTATED | 14 | 15 | 71 | 48 | 13 | 38 | 8 | 33 | 0 | 62 | 0 | 35
9P GAIN WILD-TYPE | 111 | 529 | 775 | 364 | 434 | 281 | 485 | 629 | 2 | 486 | 2 | 124

Figure S70. Get High-res Image Clustering Approach #17: '9p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'9p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.4e-17 (Chi-square test), Q value = 1.2e-13

Table S88. Clustering Approach #17: '9p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
9P GAIN MUTATED | 40 | 8 | 7 | 38 | 8 | 1 | 4 | 6 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 19 | 1 | 0 | 31 | 3 | 62 | 5 | 0 | 1
9P GAIN WILD-TYPE | 316 | 46 | 343 | 281 | 485 | 9 | 71 | 199 | 4 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 296 | 17 | 7 | 112 | 10 | 490 | 74 | 1 | 19

Figure S71. Get High-res Image Clustering Approach #17: '9p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'9p gain mutation analysis' versus 'PATHOLOGY.T'

P value = 3.08e-05 (Chi-square test), Q value = 0.04

Table S89. Clustering Approach #17: '9p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
9P GAIN MUTATED | 16 | 46 | 72 | 25
9P GAIN WILD-TYPE | 450 | 586 | 622 | 184

Figure S72. Get High-res Image Clustering Approach #17: '9p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #18: '9q gain mutation analysis'

Table S90. Get Full Table Description of clustering approach #18: '9q gain mutation analysis'

Cluster Labels | 9Q GAIN MUTATED | 9Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 284 | 4279

'9q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.21e-23 (Chi-square test), Q value = 1.8e-20

Table S91. Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
9Q GAIN MUTATED | 13 | 26 | 57 | 40 | 4 | 50 | 7 | 34 | 0 | 27 | 0 | 26
9Q GAIN WILD-TYPE | 112 | 518 | 789 | 372 | 443 | 269 | 486 | 628 | 2 | 521 | 2 | 133

Figure S73. Get High-res Image Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'9q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.32e-21 (Chi-square test), Q value = 1.9e-18

Table S92. Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
9Q GAIN MUTATED | 34 | 6 | 1 | 50 | 7 | 0 | 2 | 4 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 26 | 1 | 0 | 23 | 2 | 27 | 2 | 1 | 1
9Q GAIN WILD-TYPE | 322 | 48 | 349 | 269 | 486 | 10 | 73 | 201 | 5 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 289 | 17 | 7 | 120 | 11 | 525 | 77 | 0 | 19

Figure S74. Get High-res Image Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'9q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 1.94e-07 (Chi-square test), Q value = 0.00027

Table S93. Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
9Q GAIN MUTATED | 14 | 44 | 63 | 32
9Q GAIN WILD-TYPE | 452 | 588 | 631 | 177

Figure S75. Get High-res Image Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'9q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 3.51e-07 (Chi-square test), Q value = 0.00048

Table S94. Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
9Q GAIN MUTATED | 30 | 55 | 45 | 43
9Q GAIN WILD-TYPE | 682 | 443 | 836 | 380

Figure S76. Get High-res Image Clustering Approach #18: '9q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #19: '10p gain mutation analysis'

Table S95. Get Full Table Description of clustering approach #19: '10p gain mutation analysis'

Cluster Labels | 10P GAIN MUTATED | 10P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 454 | 4109

'10p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.17e-58 (Chi-square test), Q value = 1.8e-55

Table S96. Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
10P GAIN MUTATED | 25 | 10 | 108 | 19 | 82 | 13 | 5 | 53 | 0 | 129 | 2 | 8
10P GAIN WILD-TYPE | 100 | 534 | 738 | 393 | 365 | 306 | 488 | 609 | 2 | 419 | 0 | 151

Figure S77. Get High-res Image Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'10p gain mutation analysis' versus 'GENDER'

P value = 2.19e-20 (Fisher's exact test), Q value = 3.2e-17

Table S97. Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
10P GAIN MUTATED | 373 | 81
10P GAIN WILD-TYPE | 2508 | 1601

Figure S78. Get High-res Image Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'10p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.7e-37 (Chi-square test), Q value = 2.6e-34

Table S98. Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
10P GAIN MUTATED | 17 | 1 | 69 | 13 | 5 | 1 | 10 | 22 | 0 | 0 | 0 | 0 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 16 | 2 | 0 | 8 | 0 | 131 | 11 | 0 | 0
10P GAIN WILD-TYPE | 339 | 53 | 281 | 306 | 488 | 9 | 65 | 183 | 7 | 3 | 15 | 2 | 2 | 2 | 10 | 1 | 1 | 1 | 2 | 299 | 16 | 7 | 135 | 13 | 421 | 68 | 1 | 20

Figure S79. Get High-res Image Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'10p gain mutation analysis' versus 'TUMOR.STAGE'

P value = 3.16e-13 (Chi-square test), Q value = 4.5e-10

Table S99. Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
10P GAIN MUTATED | 35 | 25 | 130 | 33
10P GAIN WILD-TYPE | 677 | 473 | 751 | 390

Figure S80. Get High-res Image Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'10p gain mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 7.13e-05 (Chi-square test), Q value = 0.092

Table S100. Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
10P GAIN MUTATED | 5 | 4 | 10 | 4 | 0 | 28 | 17 | 18 | 2
10P GAIN WILD-TYPE | 23 | 19 | 27 | 25 | 2 | 327 | 200 | 232 | 126

Figure S81. Get High-res Image Clustering Approach #19: '10p gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #20: '10q gain mutation analysis'

Table S101. Get Full Table Description of clustering approach #20: '10q gain mutation analysis'

Cluster Labels | 10Q GAIN MUTATED | 10Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 249 | 4314

'10q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.82e-46 (Chi-square test), Q value = 2.8e-43

Table S102. Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
10Q GAIN MUTATED | 7 | 0 | 48 | 8 | 78 | 6 | 3 | 31 | 0 | 63 | 1 | 4
10Q GAIN WILD-TYPE | 118 | 544 | 798 | 404 | 369 | 313 | 490 | 631 | 2 | 485 | 1 | 155

Figure S82. Get High-res Image Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'10q gain mutation analysis' versus 'GENDER'

P value = 3.74e-16 (Fisher's exact test), Q value = 5.4e-13

Table S103. Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
10Q GAIN MUTATED | 214 | 35
10Q GAIN WILD-TYPE | 2667 | 1647

Figure S83. Get High-res Image Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'10q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.63e-28 (Chi-square test), Q value = 5.4e-25

Table S104. Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
10Q GAIN MUTATED | 6 | 2 | 66 | 6 | 3 | 1 | 7 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 8 | 2 | 0 | 4 | 0 | 64 | 10 | 0 | 0
10Q GAIN WILD-TYPE | 350 | 52 | 284 | 313 | 490 | 9 | 68 | 193 | 7 | 3 | 15 | 2 | 3 | 2 | 10 | 1 | 1 | 1 | 2 | 307 | 16 | 7 | 139 | 13 | 488 | 69 | 1 | 20

Figure S84. Get High-res Image Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'10q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 8.16e-07 (Chi-square test), Q value = 0.0011

Table S105. Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
10Q GAIN MUTATED | 23 | 12 | 67 | 11
10Q GAIN WILD-TYPE | 689 | 486 | 814 | 412

Figure S85. Get High-res Image Clustering Approach #20: '10q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #21: '11p gain mutation analysis'

Table S106. Get Full Table Description of clustering approach #21: '11p gain mutation analysis'

Cluster Labels | 11P GAIN MUTATED | 11P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 244 | 4319

'11p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.94e-15 (Chi-square test), Q value = 7.1e-12

Table S107. Clustering Approach #21: '11p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
11P GAIN MUTATED | 6 | 3 | 66 | 19 | 6 | 16 | 17 | 50 | 0 | 38 | 1 | 22
11P GAIN WILD-TYPE | 119 | 541 | 780 | 393 | 441 | 303 | 476 | 612 | 2 | 510 | 1 | 137

Figure S86. Get High-res Image Clustering Approach #21: '11p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'11p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.54e-06 (Chi-square test), Q value = 0.0074

Table S108. Clustering Approach #21: '11p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
11P GAIN MUTATED | 19 | 0 | 2 | 16 | 17 | 1 | 7 | 17 | 0 | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 22 | 0 | 0 | 22 | 0 | 39 | 4 | 0 | 0
11P GAIN WILD-TYPE | 337 | 54 | 348 | 303 | 476 | 9 | 68 | 188 | 7 | 2 | 15 | 2 | 3 | 2 | 11 | 1 | 1 | 1 | 2 | 293 | 18 | 7 | 121 | 13 | 513 | 75 | 1 | 20

Figure S87. Get High-res Image Clustering Approach #21: '11p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #22: '11q gain mutation analysis'

Table S109. Get Full Table Description of clustering approach #22: '11q gain mutation analysis'

Cluster Labels | 11Q GAIN MUTATED | 11Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 264 | 4299

'11q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.5e-16 (Chi-square test), Q value = 3.6e-13

Table S110. Clustering Approach #22: '11q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
11Q GAIN MUTATED | 6 | 6 | 49 | 22 | 7 | 16 | 15 | 66 | 0 | 60 | 0 | 17
11Q GAIN WILD-TYPE | 119 | 538 | 797 | 390 | 440 | 303 | 478 | 596 | 2 | 488 | 2 | 142

Figure S88. Get High-res Image Clustering Approach #22: '11q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'11q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.8e-09 (Chi-square test), Q value = 8.1e-06

Table S111. Clustering Approach #22: '11q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
11Q GAIN MUTATED | 22 | 0 | 4 | 16 | 15 | 1 | 7 | 31 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 24 | 0 | 0 | 17 | 0 | 60 | 3 | 0 | 0
11Q GAIN WILD-TYPE | 334 | 54 | 346 | 303 | 478 | 9 | 68 | 174 | 6 | 2 | 15 | 2 | 3 | 2 | 12 | 1 | 1 | 1 | 2 | 291 | 18 | 7 | 126 | 13 | 492 | 76 | 1 | 20

Figure S89. Get High-res Image Clustering Approach #22: '11q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'11q gain mutation analysis' versus 'STOPPEDSMOKINGYEAR'

P value = 8.26e-05 (t-test), Q value = 0.11

Table S112. Clustering Approach #22: '11q gain mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 568 | 1995.2 (13.5)
11Q GAIN MUTATED | 51 | 2001.3 (10.6)
11Q GAIN WILD-TYPE | 517 | 1994.6 (13.6)

Figure S90. Get High-res Image Clustering Approach #22: '11q gain mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

Clustering Approach #23: '12p gain mutation analysis'

Table S113. Get Full Table Description of clustering approach #23: '12p gain mutation analysis'

Cluster Labels | 12P GAIN MUTATED | 12P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 765 | 3798

'12p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.45e-43 (Chi-square test), Q value = 2.2e-40

Table S114. Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
12P GAIN MUTATED | 22 | 35 | 113 | 67 | 33 | 61 | 78 | 131 | 0 | 195 | 2 | 28
12P GAIN WILD-TYPE | 103 | 509 | 733 | 345 | 414 | 258 | 415 | 531 | 2 | 353 | 0 | 131

Figure S91. Get High-res Image Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'12p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.59e-25 (Chi-square test), Q value = 6.8e-22

Table S115. Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
12P GAIN MUTATED | 58 | 8 | 19 | 61 | 78 | 0 | 9 | 29 | 2 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 88 | 1 | 1 | 26 | 2 | 197 | 13 | 0 | 1
12P GAIN WILD-TYPE | 298 | 46 | 331 | 258 | 415 | 10 | 66 | 176 | 5 | 3 | 15 | 1 | 3 | 2 | 12 | 1 | 1 | 1 | 2 | 227 | 17 | 6 | 117 | 11 | 355 | 66 | 1 | 19

Figure S92. Get High-res Image Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'12p gain mutation analysis' versus 'TUMOR.STAGE'

P value = 9.68e-09 (Chi-square test), Q value = 1.3e-05

Table S116. Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
12P GAIN MUTATED | 109 | 111 | 248 | 81
12P GAIN WILD-TYPE | 603 | 387 | 633 | 342

Figure S93. Get High-res Image Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'12p gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.22e-07 (Fisher's exact test), Q value = 0.00057

Table S117. Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
12P GAIN MUTATED | 91 | 674
12P GAIN WILD-TYPE | 735 | 3063

Figure S94. Get High-res Image Clustering Approach #23: '12p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #24: '12q gain mutation analysis'

Table S118. Get Full Table Description of clustering approach #24: '12q gain mutation analysis'

Cluster Labels | 12Q GAIN MUTATED | 12Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 525 | 4038

'12q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.1e-15 (Chi-square test), Q value = 1e-11

Table S119. Clustering Approach #24: '12q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
12Q GAIN MUTATED | 17 | 26 | 88 | 60 | 26 | 26 | 79 | 79 | 0 | 105 | 1 | 18
12Q GAIN WILD-TYPE | 108 | 518 | 758 | 352 | 421 | 293 | 414 | 583 | 2 | 443 | 1 | 141

Figure S95. Get High-res Image Clustering Approach #24: '12q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'12q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.49e-05 (Chi-square test), Q value = 0.084

Table S120. Clustering Approach #24: '12q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
12Q GAIN MUTATED | 50 | 9 | 18 | 26 | 79 | 1 | 7 | 23 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 43 | 1 | 1 | 17 | 1 | 106 | 7 | 0 | 1
12Q GAIN WILD-TYPE | 306 | 45 | 332 | 293 | 414 | 9 | 68 | 182 | 6 | 3 | 15 | 1 | 3 | 2 | 12 | 1 | 1 | 1 | 1 | 272 | 17 | 6 | 126 | 12 | 446 | 72 | 1 | 19

Figure S96. Get High-res Image Clustering Approach #24: '12q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #25: '13q gain mutation analysis'

Table S121. Get Full Table Description of clustering approach #25: '13q gain mutation analysis'

Cluster Labels | 13Q GAIN MUTATED | 13Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 491 | 4072

'13q gain mutation analysis' versus 'AGE'

P value = 6.48e-11 (t-test), Q value = 9.2e-08

Table S122. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
13Q GAIN MUTATED | 489 | 65.2 (11.9)
13Q GAIN WILD-TYPE | 4018 | 61.4 (12.7)

Figure S97. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #2: 'AGE'

'13q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.03e-280 (Chi-square test), Q value = 4.8e-277

Table S123. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
13Q GAIN MUTATED | 21 | 1 | 46 | 211 | 19 | 18 | 12 | 24 | 0 | 38 | 0 | 98
13Q GAIN WILD-TYPE | 104 | 543 | 800 | 201 | 428 | 301 | 481 | 638 | 2 | 510 | 2 | 61

Figure S98. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'13q gain mutation analysis' versus 'GENDER'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.04

Table S124. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
13Q GAIN MUTATED | 267 | 224
13Q GAIN WILD-TYPE | 2614 | 1458

Figure S99. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'13q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.32e-211 (Chi-square test), Q value = 3.7e-208

Table S125. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
13Q GAIN MUTATED | 199 | 12 | 6 | 18 | 12 | 0 | 4 | 8 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 9 | 1 | 0 | 95 | 2 | 38 | 12 | 0 | 0
13Q GAIN WILD-TYPE | 157 | 42 | 344 | 301 | 481 | 10 | 71 | 197 | 7 | 3 | 15 | 1 | 3 | 2 | 12 | 1 | 1 | 0 | 2 | 306 | 17 | 7 | 48 | 11 | 514 | 67 | 1 | 20

Figure S100. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'13q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 1.2e-34 (Chi-square test), Q value = 1.8e-31

Table S126. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
13Q GAIN MUTATED | 20 | 79 | 220 | 44
13Q GAIN WILD-TYPE | 446 | 553 | 474 | 165

Figure S101. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'13q gain mutation analysis' versus 'PATHOLOGY.N'

P value = 1.68e-06 (Chi-square test), Q value = 0.0023

Table S127. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
13Q GAIN MUTATED | 177 | 101 | 68 | 0
13Q GAIN WILD-TYPE | 890 | 252 | 214 | 11

Figure S102. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'13q gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 1.36e-05 (Chi-square test), Q value = 0.018

Table S128. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
13Q GAIN MUTATED | 258 | 51 | 6 | 0 | 31
13Q GAIN WILD-TYPE | 1166 | 117 | 3 | 3 | 134

Figure S103. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'13q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 7.91e-08 (Chi-square test), Q value = 0.00011

Table S129. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
13Q GAIN MUTATED | 66 | 107 | 147 | 67
13Q GAIN WILD-TYPE | 646 | 391 | 734 | 356

Figure S104. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'13q gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.57e-15 (Fisher's exact test), Q value = 1.4e-11

Table S130. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
13Q GAIN MUTATED | 32 | 459
13Q GAIN WILD-TYPE | 794 | 3278

Figure S105. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'13q gain mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 5.18e-07 (Chi-square test), Q value = 7e-04

Table S131. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
13Q GAIN MUTATED | 4 | 6 | 6 | 4 | 1 | 13 | 13 | 10 | 5
13Q GAIN WILD-TYPE | 24 | 17 | 31 | 25 | 1 | 342 | 204 | 240 | 123

Figure S106. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

'13q gain mutation analysis' versus 'COMPLETENESS.OF.RESECTION'

P value = 2.95e-05 (Chi-square test), Q value = 0.038

Table S132. Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

nPatients | R0 | R1 | R2 | RX
--- | --- | --- | --- | ---
ALL | 1171 | 69 | 59 | 77
13Q GAIN MUTATED | 254 | 5 | 24 | 11
13Q GAIN WILD-TYPE | 917 | 64 | 35 | 66

Figure S107. Get High-res Image Clustering Approach #25: '13q gain mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

Clustering Approach #26: '14q gain mutation analysis'

Table S133. Get Full Table Description of clustering approach #26: '14q gain mutation analysis'

Cluster Labels | 14Q GAIN MUTATED | 14Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 294 | 4269

'14q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.71e-29 (Chi-square test), Q value = 1.2e-25

Table S134. Clustering Approach #26: '14q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
14Q GAIN MUTATED | 10 | 4 | 77 | 15 | 16 | 53 | 5 | 76 | 0 | 33 | 0 | 5
14Q GAIN WILD-TYPE | 115 | 540 | 769 | 397 | 431 | 266 | 488 | 586 | 2 | 515 | 2 | 154

Figure S108. Get High-res Image Clustering Approach #26: '14q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'14q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.79e-21 (Chi-square test), Q value = 7e-18

Table S135. Clustering Approach #26: '14q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
14Q GAIN MUTATED | 12 | 3 | 9 | 53 | 5 | 2 | 5 | 30 | 1 | 1 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 0 | 1 | 33 | 0 | 0 | 5 | 0 | 33 | 7 | 1 | 0
14Q GAIN WILD-TYPE | 344 | 51 | 341 | 266 | 488 | 8 | 70 | 175 | 6 | 2 | 15 | 2 | 2 | 2 | 11 | 1 | 1 | 1 | 1 | 282 | 18 | 7 | 138 | 13 | 519 | 72 | 0 | 20

Figure S109. Get High-res Image Clustering Approach #26: '14q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #27: '15q gain mutation analysis'

Table S136. Get Full Table Description of clustering approach #27: '15q gain mutation analysis'

Cluster Labels | 15Q GAIN MUTATED | 15Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 155 | 4408

'15q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.82e-08 (Chi-square test), Q value = 6.7e-05

Table S137. Clustering Approach #27: '15q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
15Q GAIN MUTATED | 4 | 3 | 43 | 5 | 5 | 14 | 14 | 43 | 0 | 21 | 0 | 3
15Q GAIN WILD-TYPE | 121 | 541 | 803 | 407 | 442 | 305 | 479 | 619 | 2 | 527 | 2 | 156

Figure S110. Get High-res Image Clustering Approach #27: '15q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'15q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.1e-07 (Chi-square test), Q value = 7e-04

Table S138. Clustering Approach #27: '15q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
15Q GAIN MUTATED | 5 | 0 | 4 | 14 | 14 | 1 | 3 | 5 | 2 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 30 | 0 | 0 | 2 | 1 | 21 | 1 | 0 | 0
15Q GAIN WILD-TYPE | 351 | 54 | 346 | 305 | 479 | 9 | 72 | 200 | 5 | 2 | 15 | 2 | 3 | 2 | 12 | 1 | 1 | 1 | 2 | 285 | 18 | 7 | 141 | 12 | 531 | 78 | 1 | 20

Figure S111. Get High-res Image Clustering Approach #27: '15q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'15q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 0.00018 (Chi-square test), Q value = 0.23

Table S139. Clustering Approach #27: '15q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
15Q GAIN MUTATED | 15 | 40 | 12 | 8
15Q GAIN WILD-TYPE | 451 | 592 | 682 | 201

Figure S112. Get High-res Image Clustering Approach #27: '15q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #28: '16p gain mutation analysis'

Table S140. Get Full Table Description of clustering approach #28: '16p gain mutation analysis'

Cluster Labels | 16P GAIN MUTATED | 16P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 569 | 3994

'16p gain mutation analysis' versus 'Time to Death'

P value = 2.01e-09 (logrank test), Q value = 2.8e-06

Table S141. Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
16P GAIN MUTATED | 529 | 109 | 0.0 - 224.0 (15.0)
16P GAIN WILD-TYPE | 3767 | 1292 | 0.0 - 220.9 (14.9)

Figure S113. Get High-res Image Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'16p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.31e-70 (Chi-square test), Q value = 2e-67

Table S142. Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
16P GAIN MUTATED | 11 | 14 | 249 | 68 | 11 | 24 | 65 | 66 | 0 | 31 | 0 | 29
16P GAIN WILD-TYPE | 114 | 530 | 597 | 344 | 436 | 295 | 428 | 596 | 2 | 517 | 2 | 130

Figure S114. Get High-res Image Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'16p gain mutation analysis' versus 'GENDER'

P value = 1.28e-06 (Fisher's exact test), Q value = 0.0017

Table S143. Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
16P GAIN MUTATED | 411 | 158
16P GAIN WILD-TYPE | 2470 | 1524

Figure S115. Get High-res Image Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'16p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.74e-17 (Chi-square test), Q value = 6.9e-14

Table S144. Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
16P GAIN MUTATED | 65 | 3 | 5 | 24 | 65 | 3 | 7 | 34 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 16 | 0 | 1 | 29 | 0 | 31 | 6 | 0 | 0
16P GAIN WILD-TYPE | 291 | 51 | 345 | 295 | 428 | 7 | 68 | 171 | 6 | 3 | 14 | 2 | 2 | 2 | 12 | 1 | 1 | 0 | 2 | 299 | 18 | 6 | 114 | 13 | 521 | 73 | 1 | 20

Figure S116. Get High-res Image Clustering Approach #28: '16p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #29: '16q gain mutation analysis'

Table S145. Get Full Table Description of clustering approach #29: '16q gain mutation analysis'

Cluster Labels | 16Q GAIN MUTATED | 16Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 334 | 4229

'16q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.54e-28 (Chi-square test), Q value = 3.8e-25

Table S146. Clustering Approach #29: '16q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
16Q GAIN MUTATED | 13 | 14 | 53 | 66 | 4 | 27 | 58 | 53 | 0 | 15 | 0 | 30
16Q GAIN WILD-TYPE | 112 | 530 | 793 | 346 | 443 | 292 | 435 | 609 | 2 | 533 | 2 | 129

Figure S117. Get High-res Image Clustering Approach #29: '16q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'16q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.06e-21 (Chi-square test), Q value = 1.6e-18

Table S147. Clustering Approach #29: '16q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
16Q GAIN MUTATED | 63 | 3 | 3 | 27 | 58 | 2 | 1 | 24 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 21 | 0 | 1 | 30 | 0 | 15 | 1 | 0 | 0
16Q GAIN WILD-TYPE | 293 | 51 | 347 | 292 | 435 | 8 | 74 | 181 | 7 | 3 | 14 | 2 | 2 | 2 | 12 | 1 | 1 | 0 | 2 | 294 | 18 | 6 | 113 | 13 | 537 | 78 | 1 | 20

Figure S118. Get High-res Image Clustering Approach #29: '16q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'16q gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.1e-06 (Fisher's exact test), Q value = 0.0055

Table S148. Clustering Approach #29: '16q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
16Q GAIN MUTATED | 31 | 303
16Q GAIN WILD-TYPE | 795 | 3434

Figure S119. Get High-res Image Clustering Approach #29: '16q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #30: '17p gain mutation analysis'

Table S149. Get Full Table Description of clustering approach #30: '17p gain mutation analysis'

Cluster Labels | 17P GAIN MUTATED | 17P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 166 | 4397

'17p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.5e-06 (Chi-square test), Q value = 0.002

Table S150. Clustering Approach #30: '17p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
17P GAIN MUTATED | 10 | 9 | 50 | 11 | 6 | 19 | 16 | 32 | 0 | 9 | 0 | 4
17P GAIN WILD-TYPE | 115 | 535 | 796 | 401 | 441 | 300 | 477 | 630 | 2 | 539 | 2 | 155

Figure S120. Get High-res Image Clustering Approach #30: '17p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'17p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.33e-07 (Chi-square test), Q value = 0.0013

Table S151. Clustering Approach #30: '17p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
17P GAIN MUTATED | 11 | 0 | 4 | 19 | 16 | 1 | 5 | 13 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 11 | 0 | 0 | 4 | 0 | 9 | 2 | 0 | 1
17P GAIN WILD-TYPE | 345 | 54 | 346 | 300 | 477 | 9 | 70 | 192 | 7 | 3 | 15 | 2 | 3 | 1 | 13 | 0 | 1 | 1 | 2 | 304 | 18 | 7 | 139 | 13 | 543 | 77 | 1 | 19

Figure S121. Get High-res Image Clustering Approach #30: '17p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #31: '17q gain mutation analysis'

Table S152. Get Full Table Description of clustering approach #31: '17q gain mutation analysis'

Cluster Labels | 17Q GAIN MUTATED | 17Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 405 | 4158

'17q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.22e-30 (Chi-square test), Q value = 4.8e-27

Table S153. Clustering Approach #31: '17q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
17Q GAIN MUTATED | 23 | 17 | 126 | 48 | 10 | 23 | 22 | 100 | 0 | 19 | 0 | 17
17Q GAIN WILD-TYPE | 102 | 527 | 720 | 364 | 437 | 296 | 471 | 562 | 2 | 529 | 2 | 142

Figure S122. Get High-res Image Clustering Approach #31: '17q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'17q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.46e-19 (Chi-square test), Q value = 2.1e-16

Table S154. Clustering Approach #31: '17q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
17Q GAIN MUTATED | 45 | 2 | 7 | 23 | 22 | 2 | 14 | 40 | 2 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 38 | 0 | 0 | 17 | 0 | 19 | 3 | 1 | 2
17Q GAIN WILD-TYPE | 311 | 52 | 343 | 296 | 471 | 8 | 61 | 165 | 5 | 3 | 15 | 1 | 3 | 1 | 12 | 1 | 1 | 1 | 1 | 277 | 18 | 7 | 126 | 13 | 533 | 76 | 0 | 18

Figure S123. Get High-res Image Clustering Approach #31: '17q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #32: '18p gain mutation analysis'

Table S155. Get Full Table Description of clustering approach #32: '18p gain mutation analysis'

Cluster Labels | 18P GAIN MUTATED | 18P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 419 | 4144

'18p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.68e-18 (Chi-square test), Q value = 1.4e-14

Table S156. Clustering Approach #32: '18p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
18P GAIN MUTATED | 19 | 26 | 85 | 15 | 33 | 53 | 18 | 88 | 0 | 75 | 0 | 7
18P GAIN WILD-TYPE | 106 | 518 | 761 | 397 | 414 | 266 | 475 | 574 | 2 | 473 | 2 | 152

Figure S124. Get High-res Image Clustering Approach #32: '18p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.74e-20 (Chi-square test), Q value = 4e-17

Table S157. Clustering Approach #32: '18p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
18P GAIN MUTATED | 10 | 5 | 11 | 53 | 18 | 4 | 8 | 18 | 3 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 53 | 2 | 0 | 6 | 1 | 75 | 20 | 0 | 1
18P GAIN WILD-TYPE | 346 | 49 | 339 | 266 | 475 | 6 | 67 | 187 | 4 | 3 | 15 | 2 | 3 | 2 | 11 | 1 | 1 | 1 | 2 | 262 | 16 | 7 | 137 | 12 | 477 | 59 | 1 | 19

Figure S125. Get High-res Image Clustering Approach #32: '18p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #33: '18q gain mutation analysis'

Table S158. Get Full Table Description of clustering approach #33: '18q gain mutation analysis'

Cluster Labels | 18Q GAIN MUTATED | 18Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 288 | 4275

'18q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.25e-08 (Chi-square test), Q value = 8.6e-05

Table S159. Clustering Approach #33: '18q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
18Q GAIN MUTATED | 7 | 27 | 78 | 9 | 16 | 23 | 18 | 63 | 0 | 43 | 0 | 4
18Q GAIN WILD-TYPE | 118 | 517 | 768 | 403 | 431 | 296 | 475 | 599 | 2 | 505 | 2 | 155

Figure S126. Get High-res Image Clustering Approach #33: '18q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.22e-08 (Chi-square test), Q value = 5.8e-05

Table S160. Clustering Approach #33: '18q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
18Q GAIN MUTATED | 6 | 3 | 7 | 23 | 18 | 2 | 5 | 12 | 3 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 39 | 2 | 0 | 4 | 0 | 43 | 7 | 0 | 1
18Q GAIN WILD-TYPE | 350 | 51 | 343 | 296 | 475 | 8 | 70 | 193 | 4 | 3 | 15 | 2 | 3 | 2 | 11 | 1 | 1 | 1 | 2 | 276 | 16 | 7 | 139 | 13 | 509 | 72 | 1 | 19

Figure S127. Get High-res Image Clustering Approach #33: '18q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'18q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 0.00019 (Chi-square test), Q value = 0.24

Table S161. Clustering Approach #33: '18q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
18Q GAIN MUTATED | 23 | 54 | 21 | 12
18Q GAIN WILD-TYPE | 443 | 578 | 673 | 197

Figure S128. Get High-res Image Clustering Approach #33: '18q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #34: '19p gain mutation analysis'

Table S162. Get Full Table Description of clustering approach #34: '19p gain mutation analysis'

Cluster Labels | 19P GAIN MUTATED | 19P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 503 | 4060

'19p gain mutation analysis' versus 'Time to Death'

P value = 1.12e-08 (logrank test), Q value = 1.6e-05

Table S163. Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
19P GAIN MUTATED | 485 | 210 | 0.0 - 180.2 (13.3)
19P GAIN WILD-TYPE | 3811 | 1191 | 0.0 - 224.0 (15.0)

Figure S129. Get High-res Image Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'19p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.15e-56 (Chi-square test), Q value = 8e-53

Table S164. Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
19P GAIN MUTATED | 13 | 167 | 69 | 34 | 27 | 15 | 24 | 48 | 0 | 87 | 0 | 19
19P GAIN WILD-TYPE | 112 | 377 | 777 | 378 | 420 | 304 | 469 | 614 | 2 | 461 | 2 | 140

Figure S130. Get High-res Image Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'19p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.97e-20 (Chi-square test), Q value = 2.9e-17

Table S165. Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
19P GAIN MUTATED | 33 | 1 | 12 | 15 | 24 | 0 | 1 | 10 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 32 | 0 | 0 | 19 | 0 | 87 | 15 | 1 | 6
19P GAIN WILD-TYPE | 323 | 53 | 338 | 304 | 469 | 10 | 74 | 195 | 2 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 283 | 18 | 7 | 124 | 13 | 465 | 64 | 0 | 14

Figure S131. Get High-res Image Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'19p gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.56e-13 (Fisher's exact test), Q value = 5.1e-10

Table S166. Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
19P GAIN MUTATED | 154 | 349
19P GAIN WILD-TYPE | 672 | 3388

Figure S132. Get High-res Image Clustering Approach #34: '19p gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #35: '19q gain mutation analysis'

Table S167. Get Full Table Description of clustering approach #35: '19q gain mutation analysis'

Cluster Labels | 19Q GAIN MUTATED | 19Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 536 | 4027

'19q gain mutation analysis' versus 'Time to Death'

P value = 4.08e-08 (logrank test), Q value = 5.6e-05

Table S168. Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
19Q GAIN MUTATED | 513 | 210 | 0.0 - 180.2 (12.6)
19Q GAIN WILD-TYPE | 3783 | 1191 | 0.0 - 224.0 (15.1)

Figure S133. Get High-res Image Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'19q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.05e-30 (Chi-square test), Q value = 4.6e-27

Table S169. Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
19Q GAIN MUTATED | 25 | 142 | 84 | 41 | 24 | 21 | 28 | 72 | 0 | 76 | 0 | 23
19Q GAIN WILD-TYPE | 100 | 402 | 762 | 371 | 423 | 298 | 465 | 590 | 2 | 472 | 2 | 136

Figure S134. Get High-res Image Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'19q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.2e-15 (Chi-square test), Q value = 1.7e-12

Table S170. Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
19Q GAIN MUTATED | 37 | 4 | 7 | 21 | 28 | 0 | 3 | 18 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 46 | 0 | 0 | 23 | 0 | 76 | 17 | 1 | 3
19Q GAIN WILD-TYPE | 319 | 50 | 343 | 298 | 465 | 10 | 72 | 187 | 2 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 269 | 18 | 7 | 120 | 13 | 476 | 62 | 0 | 17

Figure S135. Get High-res Image Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'19q gain mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.016

Table S171. Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
19Q GAIN MUTATED | 135 | 401
19Q GAIN WILD-TYPE | 691 | 3336

Figure S136. Get High-res Image Clustering Approach #35: '19q gain mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #36: '20p gain mutation analysis'

Table S172. Get Full Table Description of clustering approach #36: '20p gain mutation analysis'

Cluster Labels | 20P GAIN MUTATED | 20P GAIN WILD-TYPE
--- | --- | ---
Number of samples | 1300 | 3263

'20p gain mutation analysis' versus 'Time to Death'

P value = 4.13e-05 (logrank test), Q value = 0.054

Table S173. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
20P GAIN MUTATED | 1200 | 433 | 0.0 - 224.0 (13.1)
20P GAIN WILD-TYPE | 3096 | 968 | 0.0 - 223.4 (15.1)

Figure S137. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'20p gain mutation analysis' versus 'AGE'

P value = 7.61e-09 (t-test), Q value = 1.1e-05

Table S174. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
20P GAIN MUTATED | 1289 | 63.5 (12.3)
20P GAIN WILD-TYPE | 3218 | 61.2 (12.7)

Figure S138. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #2: 'AGE'

'20p gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.84e-64 (Chi-square test), Q value = 2.9e-61

Table S175. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
20P GAIN MUTATED | 48 | 174 | 233 | 197 | 52 | 64 | 66 | 148 | 1 | 223 | 1 | 91
20P GAIN WILD-TYPE | 77 | 370 | 613 | 215 | 395 | 255 | 427 | 514 | 1 | 325 | 1 | 68

Figure S139. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.23e-68 (Chi-square test), Q value = 3.5e-65

Table S176. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
20P GAIN MUTATED | 182 | 13 | 26 | 64 | 66 | 2 | 11 | 34 | 5 | 1 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 1 | 0 | 91 | 3 | 0 | 87 | 2 | 225 | 23 | 1 | 7
20P GAIN WILD-TYPE | 174 | 41 | 324 | 255 | 427 | 8 | 64 | 171 | 2 | 2 | 15 | 2 | 2 | 2 | 11 | 1 | 1 | 0 | 2 | 224 | 15 | 7 | 56 | 11 | 327 | 56 | 0 | 13

Figure S140. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'20p gain mutation analysis' versus 'PATHOLOGY.T'

P value = 6.36e-14 (Chi-square test), Q value = 9.1e-11

Table S177. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
20P GAIN MUTATED | 71 | 171 | 255 | 59
20P GAIN WILD-TYPE | 395 | 461 | 439 | 150

Figure S141. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'20p gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 9.41e-06 (Chi-square test), Q value = 0.012

Table S178. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
20P GAIN MUTATED | 387 | 66 | 8 | 0 | 43
20P GAIN WILD-TYPE | 1037 | 102 | 1 | 3 | 122

Figure S142. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'20p gain mutation analysis' versus 'TUMOR.STAGE'

P value = 2.76e-07 (Chi-square test), Q value = 0.00038

Table S179. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
20P GAIN MUTATED | 160 | 153 | 315 | 132
20P GAIN WILD-TYPE | 552 | 345 | 566 | 291

Figure S143. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'20p gain mutation analysis' versus 'COMPLETENESS.OF.RESECTION'

P value = 6.9e-06 (Chi-square test), Q value = 0.0092

Table S180. Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

nPatients | R0 | R1 | R2 | RX
--- | --- | --- | --- | ---
ALL | 1171 | 69 | 59 | 77
20P GAIN MUTATED | 342 | 15 | 33 | 14
20P GAIN WILD-TYPE | 829 | 54 | 26 | 63

Figure S144. Get High-res Image Clustering Approach #36: '20p gain mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

Clustering Approach #37: '20q gain mutation analysis'

Table S181. Get Full Table Description of clustering approach #37: '20q gain mutation analysis'

Cluster Labels | 20Q GAIN MUTATED | 20Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 1509 | 3054

'20q gain mutation analysis' versus 'AGE'

P value = 3.39e-07 (t-test), Q value = 0.00046

Table S182. Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
20Q GAIN MUTATED | 1498 | 63.2 (12.4)
20Q GAIN WILD-TYPE | 3009 | 61.2 (12.7)

Figure S145. Get High-res Image Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #2: 'AGE'

'20q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.97e-130 (Chi-square test), Q value = 3.1e-127

Table S183. Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
20Q GAIN MUTATED | 52 | 171 | 271 | 267 | 60 | 68 | 68 | 151 | 1 | 264 | 1 | 132
20Q GAIN WILD-TYPE | 73 | 373 | 575 | 145 | 387 | 251 | 425 | 511 | 1 | 284 | 1 | 27

Figure S146. Get High-res Image Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-135 (Chi-square test), Q value = 1.6e-132

Table S184. Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
20Q GAIN MUTATED | 249 | 16 | 27 | 68 | 68 | 3 | 14 | 44 | 5 | 1 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 1 | 1 | 79 | 3 | 0 | 125 | 5 | 266 | 30 | 1 | 6
20Q GAIN WILD-TYPE | 107 | 38 | 323 | 251 | 425 | 7 | 61 | 161 | 2 | 2 | 15 | 2 | 2 | 2 | 11 | 1 | 1 | 0 | 1 | 236 | 15 | 7 | 18 | 8 | 286 | 49 | 0 | 14

Figure S147. Get High-res Image Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'20q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 5.56e-29 (Chi-square test), Q value = 8.3e-26

Table S185. Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
20Q GAIN MUTATED | 74 | 198 | 336 | 71
20Q GAIN WILD-TYPE | 392 | 434 | 358 | 138

Figure S148. Get High-res Image Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'20q gain mutation analysis' versus 'TUMOR.STAGE'

P value = 2.83e-15 (Chi-square test), Q value = 4.1e-12

Table S186. Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
20Q GAIN MUTATED | 176 | 199 | 394 | 152
20Q GAIN WILD-TYPE | 536 | 299 | 487 | 271

Figure S149. Get High-res Image Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'20q gain mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 8.01e-06 (Chi-square test), Q value = 0.011

Table S187. Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
20Q GAIN MUTATED | 7 | 12 | 15 | 17 | 0 | 91 | 43 | 54 | 27
20Q GAIN WILD-TYPE | 21 | 11 | 22 | 12 | 2 | 264 | 174 | 196 | 101

Figure S150. Get High-res Image Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

'20q gain mutation analysis' versus 'COMPLETENESS.OF.RESECTION'

P value = 9.3e-07 (Chi-square test), Q value = 0.0013

Table S188. Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

nPatients | R0 | R1 | R2 | RX
--- | --- | --- | --- | ---
ALL | 1171 | 69 | 59 | 77
20Q GAIN MUTATED | 428 | 19 | 40 | 20
20Q GAIN WILD-TYPE | 743 | 50 | 19 | 57

Figure S151. Get High-res Image Clustering Approach #37: '20q gain mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

Clustering Approach #38: '21q gain mutation analysis'

Table S189. Get Full Table Description of clustering approach #38: '21q gain mutation analysis'

Cluster Labels | 21Q GAIN MUTATED | 21Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 347 | 4216

'21q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.66e-15 (Chi-square test), Q value = 2.4e-12

Table S190. Clustering Approach #38: '21q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
21Q GAIN MUTATED | 23 | 31 | 98 | 11 | 20 | 8 | 33 | 51 | 0 | 63 | 1 | 7
21Q GAIN WILD-TYPE | 102 | 513 | 748 | 401 | 427 | 311 | 460 | 611 | 2 | 485 | 1 | 152

Figure S152. Get High-res Image Clustering Approach #38: '21q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'21q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.02e-10 (Chi-square test), Q value = 5.7e-07

Table S191. Clustering Approach #38: '21q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
21Q GAIN MUTATED | 10 | 1 | 9 | 8 | 33 | 1 | 5 | 24 | 2 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 16 | 0 | 0 | 7 | 0 | 64 | 11 | 0 | 1
21Q GAIN WILD-TYPE | 346 | 53 | 341 | 311 | 460 | 9 | 70 | 181 | 5 | 3 | 15 | 2 | 2 | 2 | 12 | 1 | 1 | 0 | 2 | 299 | 18 | 7 | 136 | 13 | 488 | 68 | 1 | 19

Figure S153. Get High-res Image Clustering Approach #38: '21q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'21q gain mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 1.61e-05 (Chi-square test), Q value = 0.021

Table S192. Clustering Approach #38: '21q gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
21Q GAIN MUTATED | 6 | 2 | 8 | 7 | 0 | 23 | 13 | 10 | 12
21Q GAIN WILD-TYPE | 22 | 21 | 29 | 22 | 2 | 332 | 204 | 240 | 116

Figure S154. Get High-res Image Clustering Approach #38: '21q gain mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #39: '22q gain mutation analysis'

Table S193. Get Full Table Description of clustering approach #39: '22q gain mutation analysis'

Cluster Labels | 22Q GAIN MUTATED | 22Q GAIN WILD-TYPE
--- | --- | ---
Number of samples | 240 | 4323

'22q gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.2e-36 (Chi-square test), Q value = 6.3e-33

Table S194. Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
22Q GAIN MUTATED | 11 | 11 | 38 | 2 | 6 | 39 | 25 | 93 | 0 | 10 | 0 | 5
22Q GAIN WILD-TYPE | 114 | 533 | 808 | 410 | 441 | 280 | 468 | 569 | 2 | 538 | 2 | 154

Figure S155. Get High-res Image Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'22q gain mutation analysis' versus 'GENDER'

P value = 2.26e-09 (Fisher's exact test), Q value = 3.2e-06

Table S195. Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
22Q GAIN MUTATED | 107 | 133
22Q GAIN WILD-TYPE | 2774 | 1549

Figure S156. Get High-res Image Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #4: 'GENDER'

'22q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.24e-43 (Chi-square test), Q value = 1.9e-40

Table S196. Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
22Q GAIN MUTATED | 2 | 0 | 2 | 39 | 25 | 0 | 1 | 15 | 2 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 74 | 0 | 0 | 5 | 0 | 10 | 4 | 0 | 0
22Q GAIN WILD-TYPE | 354 | 54 | 348 | 280 | 468 | 10 | 74 | 190 | 5 | 3 | 15 | 2 | 2 | 2 | 13 | 1 | 1 | 1 | 2 | 241 | 18 | 7 | 138 | 13 | 542 | 75 | 1 | 20

Figure S157. Get High-res Image Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'22q gain mutation analysis' versus 'PATHOLOGY.T'

P value = 5.6e-07 (Chi-square test), Q value = 0.00076

Table S197. Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
22Q GAIN MUTATED | 26 | 79 | 33 | 19
22Q GAIN WILD-TYPE | 440 | 553 | 661 | 190

Figure S158. Get High-res Image Clustering Approach #39: '22q gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #40: 'Xq gain mutation analysis'

Table S198. Get Full Table Description of clustering approach #40: 'Xq gain mutation analysis'

Cluster Labels | XQ GAIN MUTATED | XQ GAIN WILD-TYPE
--- | --- | ---
Number of samples | 149 | 4414

'Xq gain mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.22e-08 (Chi-square test), Q value = 3.1e-05

Table S199. Clustering Approach #40: 'Xq gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
XQ GAIN MUTATED | 8 | 3 | 21 | 11 | 8 | 20 | 7 | 29 | 0 | 36 | 0 | 6
XQ GAIN WILD-TYPE | 117 | 541 | 825 | 401 | 439 | 299 | 486 | 633 | 2 | 512 | 2 | 153

Figure S159. Get High-res Image Clustering Approach #40: 'Xq gain mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

Clustering Approach #41: '1p loss mutation analysis'

Table S200. Get Full Table Description of clustering approach #41: '1p loss mutation analysis'

Cluster Labels | 1P LOSS MUTATED | 1P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 351 | 4212

'1p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.3e-20 (Chi-square test), Q value = 6.3e-17

Table S201. Clustering Approach #41: '1p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
1P LOSS MUTATED | 2 | 9 | 113 | 49 | 11 | 15 | 31 | 62 | 0 | 36 | 0 | 22
1P LOSS WILD-TYPE | 123 | 535 | 733 | 363 | 436 | 304 | 462 | 600 | 2 | 512 | 2 | 137

Figure S160. Get High-res Image Clustering Approach #41: '1p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'1p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.74e-08 (Chi-square test), Q value = 6.6e-05

Table S202. Clustering Approach #41: '1p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
1P LOSS MUTATED | 46 | 3 | 5 | 15 | 31 | 1 | 6 | 11 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 40 | 2 | 1 | 21 | 0 | 36 | 4 | 0 | 0
1P LOSS WILD-TYPE | 310 | 51 | 345 | 304 | 462 | 9 | 69 | 194 | 7 | 3 | 15 | 2 | 3 | 2 | 11 | 0 | 1 | 1 | 2 | 275 | 16 | 6 | 122 | 13 | 516 | 75 | 1 | 20

Figure S161. Get High-res Image Clustering Approach #41: '1p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'1p loss mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.07e-05 (Chi-square test), Q value = 0.014

Table S203. Clustering Approach #41: '1p loss mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
1P LOSS MUTATED | 4 | 5 | 0 | 1 | 36 | 19 | 1 | 21 | 11 | 7 | 5 | 0 | 4
1P LOSS WILD-TYPE | 68 | 57 | 7 | 42 | 251 | 167 | 41 | 103 | 14 | 34 | 54 | 1 | 12

Figure S162. Get High-res Image Clustering Approach #41: '1p loss mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #42: '1q loss mutation analysis'

Table S204. Get Full Table Description of clustering approach #42: '1q loss mutation analysis'

Cluster Labels | 1Q LOSS MUTATED | 1Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 112 | 4451

Clustering Approach #43: '2p loss mutation analysis'

Table S205. Get Full Table Description of clustering approach #43: '2p loss mutation analysis'

Cluster Labels | 2P LOSS MUTATED | 2P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 148 | 4415

'2p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.03e-17 (Chi-square test), Q value = 8.8e-14

Table S206. Clustering Approach #43: '2p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
2P LOSS MUTATED | 6 | 13 | 69 | 4 | 5 | 6 | 10 | 4 | 0 | 24 | 0 | 7
2P LOSS WILD-TYPE | 119 | 531 | 777 | 408 | 442 | 313 | 483 | 658 | 2 | 524 | 2 | 152

Figure S163. Get High-res Image Clustering Approach #43: '2p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'2p loss mutation analysis' versus 'GENDER'

P value = 6.09e-05 (Fisher's exact test), Q value = 0.079

Table S207. Clustering Approach #43: '2p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
2P LOSS MUTATED | 116 | 32
2P LOSS WILD-TYPE | 2765 | 1650

Figure S164. Get High-res Image Clustering Approach #43: '2p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

Clustering Approach #44: '2q loss mutation analysis'

Table S208. Get Full Table Description of clustering approach #44: '2q loss mutation analysis'

Cluster Labels | 2Q LOSS MUTATED | 2Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 188 | 4375

'2q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.8e-22 (Chi-square test), Q value = 4.1e-19

Table S209. Clustering Approach #44: '2q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
2Q LOSS MUTATED | 13 | 12 | 83 | 6 | 7 | 11 | 11 | 11 | 0 | 28 | 1 | 5
2Q LOSS WILD-TYPE | 112 | 532 | 763 | 406 | 440 | 308 | 482 | 651 | 2 | 520 | 1 | 154

Figure S165. Get High-res Image Clustering Approach #44: '2q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'2q loss mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 1.65e-05 (Chi-square test), Q value = 0.022

Table S210. Clustering Approach #44: '2q loss mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
2Q LOSS MUTATED | 3 | 1 | 4 | 4 | 0 | 4 | 1 | 11 | 4
2Q LOSS WILD-TYPE | 25 | 22 | 33 | 25 | 2 | 351 | 216 | 239 | 124

Figure S166. Get High-res Image Clustering Approach #44: '2q loss mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #45: '3p loss mutation analysis'

Table S211. Get Full Table Description of clustering approach #45: '3p loss mutation analysis'

Cluster Labels | 3P LOSS MUTATED | 3P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 868 | 3695

'3p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.29e-218 (Chi-square test), Q value = 2.1e-215

Table S212. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
3P LOSS MUTATED | 7 | 25 | 85 | 28 | 26 | 121 | 318 | 193 | 1 | 56 | 0 | 8
3P LOSS WILD-TYPE | 118 | 519 | 761 | 384 | 421 | 198 | 175 | 469 | 1 | 492 | 2 | 151

Figure S167. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'3p loss mutation analysis' versus 'GENDER'

P value = 7.17e-34 (Fisher's exact test), Q value = 1.1e-30

Table S213. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
3P LOSS MUTATED | 390 | 478
3P LOSS WILD-TYPE | 2491 | 1204

Figure S168. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'3p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.19e-144 (Chi-square test), Q value = 5e-141

Table S214. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
3P LOSS MUTATED | 27 | 1 | 11 | 121 | 318 | 3 | 17 | 44 | 1 | 0 | 1 | 0 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 122 | 4 | 1 | 5 | 2 | 57 | 11 | 0 | 1
3P LOSS WILD-TYPE | 329 | 53 | 339 | 198 | 175 | 7 | 58 | 161 | 6 | 3 | 14 | 2 | 3 | 2 | 11 | 0 | 1 | 0 | 2 | 193 | 14 | 6 | 138 | 11 | 495 | 68 | 1 | 19

Figure S169. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'3p loss mutation analysis' versus 'PATHOLOGY.T'

P value = 5.56e-14 (Chi-square test), Q value = 8e-11

Table S215. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
3P LOSS MUTATED | 222 | 183 | 189 | 55
3P LOSS WILD-TYPE | 244 | 449 | 505 | 154

Figure S170. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'3p loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.00016 (Chi-square test), Q value = 0.2

Table S216. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
3P LOSS MUTATED | 469 | 57 | 1 | 0 | 27
3P LOSS WILD-TYPE | 955 | 111 | 8 | 3 | 138

Figure S171. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'3p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 4.02e-13 (Chi-square test), Q value = 5.7e-10

Table S217. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
3P LOSS MUTATED | 268 | 116 | 186 | 130
3P LOSS WILD-TYPE | 444 | 382 | 695 | 293

Figure S172. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'3p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.88e-11 (Fisher's exact test), Q value = 4.1e-08

Table S218. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
3P LOSS MUTATED | 92 | 776
3P LOSS WILD-TYPE | 734 | 2961

Figure S173. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'3p loss mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 5.35e-08 (Chi-square test), Q value = 7.4e-05

Table S219. Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
3P LOSS MUTATED | 0 | 1 | 4 | 1 | 0 | 121 | 61 | 93 | 29
3P LOSS WILD-TYPE | 28 | 22 | 33 | 28 | 2 | 234 | 156 | 157 | 99

Figure S174. Get High-res Image Clustering Approach #45: '3p loss mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #46: '3q loss mutation analysis'

Table S220. Get Full Table Description of clustering approach #46: '3q loss mutation analysis'

Cluster Labels | 3Q LOSS MUTATED | 3Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 291 | 4272

'3q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.51e-39 (Chi-square test), Q value = 9.9e-36

Table S221. Clustering Approach #46: '3q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
3Q LOSS MUTATED | 1 | 20 | 41 | 13 | 12 | 21 | 97 | 63 | 1 | 18 | 0 | 4
3Q LOSS WILD-TYPE | 124 | 524 | 805 | 399 | 435 | 298 | 396 | 599 | 1 | 530 | 2 | 155

Figure S175. Get High-res Image Clustering Approach #46: '3q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'3q loss mutation analysis' versus 'GENDER'

P value = 2.54e-09 (Fisher's exact test), Q value = 3.6e-06

Table S222. Clustering Approach #46: '3q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
3Q LOSS MUTATED | 135 | 156
3Q LOSS WILD-TYPE | 2746 | 1526

Figure S176. Get High-res Image Clustering Approach #46: '3q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'3q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.54e-28 (Chi-square test), Q value = 5.3e-25

Table S223. Clustering Approach #46: '3q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
3Q LOSS MUTATED | 13 | 0 | 6 | 21 | 97 | 3 | 10 | 26 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 21 | 0 | 0 | 1 | 3 | 19 | 6 | 0 | 0
3Q LOSS WILD-TYPE | 343 | 54 | 344 | 298 | 396 | 7 | 65 | 179 | 7 | 3 | 14 | 2 | 3 | 2 | 12 | 0 | 1 | 1 | 2 | 294 | 18 | 7 | 142 | 10 | 533 | 73 | 1 | 20

Figure S177. Get High-res Image Clustering Approach #46: '3q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #47: '4p loss mutation analysis'

Table S224. Get Full Table Description of clustering approach #47: '4p loss mutation analysis'

Cluster Labels | 4P LOSS MUTATED | 4P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 917 | 3646

'4p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.58e-69 (Chi-square test), Q value = 2.5e-66

Table S225. Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
4P LOSS MUTATED | 22 | 29 | 174 | 85 | 47 | 77 | 35 | 169 | 2 | 235 | 0 | 39
4P LOSS WILD-TYPE | 103 | 515 | 672 | 327 | 400 | 242 | 458 | 493 | 0 | 313 | 2 | 120

Figure S178. Get High-res Image Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'4p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.22e-66 (Chi-square test), Q value = 8.1e-63

Table S226. Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
4P LOSS MUTATED | 81 | 4 | 18 | 77 | 35 | 2 | 7 | 19 | 2 | 0 | 1 | 0 | 0 | 1 | 1 | 1 | 0 | 1 | 0 | 133 | 3 | 1 | 37 | 1 | 237 | 26 | 0 | 2
4P LOSS WILD-TYPE | 275 | 50 | 332 | 242 | 458 | 8 | 68 | 186 | 5 | 3 | 14 | 2 | 3 | 1 | 12 | 0 | 1 | 0 | 2 | 182 | 15 | 6 | 106 | 12 | 315 | 53 | 1 | 18

Figure S179. Get High-res Image Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'4p loss mutation analysis' versus 'PATHOLOGY.N'

P value = 1.94e-05 (Chi-square test), Q value = 0.025

Table S227. Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
4P LOSS MUTATED | 199 | 84 | 84 | 6
4P LOSS WILD-TYPE | 868 | 269 | 198 | 5

Figure S180. Get High-res Image Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'4p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 9.69e-14 (Chi-square test), Q value = 1.4e-10

Table S228. Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
4P LOSS MUTATED | 125 | 92 | 290 | 117
4P LOSS WILD-TYPE | 587 | 406 | 591 | 306

Figure S181. Get High-res Image Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'4p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.67e-10 (Fisher's exact test), Q value = 5.2e-07

Table S229. Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
4P LOSS MUTATED | 103 | 814
4P LOSS WILD-TYPE | 723 | 2923

Figure S182. Get High-res Image Clustering Approach #47: '4p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #48: '4q loss mutation analysis'

Table S230. Get Full Table Description of clustering approach #48: '4q loss mutation analysis'

Cluster Labels | 4Q LOSS MUTATED | 4Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 859 | 3704

'4q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.93e-108 (Chi-square test), Q value = 4.6e-105

Table S231. Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
4Q LOSS MUTATED | 18 | 28 | 139 | 70 | 45 | 50 | 29 | 154 | 2 | 277 | 1 | 42
4Q LOSS WILD-TYPE | 107 | 516 | 707 | 342 | 402 | 269 | 464 | 508 | 0 | 271 | 1 | 117

Figure S183. Get High-res Image Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'4q loss mutation analysis' versus 'GENDER'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.0022

Table S232. Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
4Q LOSS MUTATED | 603 | 256
4Q LOSS WILD-TYPE | 2278 | 1426

Figure S184. Get High-res Image Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'4q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.11e-88 (Chi-square test), Q value = 9.6e-85

Table S233. Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
4Q LOSS MUTATED | 67 | 3 | 19 | 50 | 29 | 2 | 8 | 22 | 1 | 0 | 2 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 1 | 114 | 4 | 1 | 40 | 1 | 280 | 22 | 0 | 1
4Q LOSS WILD-TYPE | 289 | 51 | 331 | 269 | 464 | 8 | 67 | 183 | 6 | 3 | 13 | 2 | 3 | 2 | 12 | 0 | 1 | 0 | 1 | 201 | 14 | 6 | 103 | 12 | 272 | 57 | 1 | 19

Figure S185. Get High-res Image Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'4q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 5.52e-05 (Chi-square test), Q value = 0.071

Table S234. Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
4Q LOSS MUTATED | 47 | 126 | 123 | 44
4Q LOSS WILD-TYPE | 419 | 506 | 571 | 165

Figure S186. Get High-res Image Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'4q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 6.53e-24 (Chi-square test), Q value = 9.7e-21

Table S235. Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
4Q LOSS MUTATED | 120 | 79 | 320 | 93
4Q LOSS WILD-TYPE | 592 | 419 | 561 | 330

Figure S187. Get High-res Image Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'4q loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.28e-13 (Fisher's exact test), Q value = 4.7e-10

Table S236. Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
4Q LOSS MUTATED | 85 | 774
4Q LOSS WILD-TYPE | 741 | 2963

Figure S188. Get High-res Image Clustering Approach #48: '4q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #49: '5p loss mutation analysis'

Table S237. Get Full Table Description of clustering approach #49: '5p loss mutation analysis'

Cluster Labels | 5P LOSS MUTATED | 5P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 271 | 4292

'5p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.07e-16 (Chi-square test), Q value = 8.8e-13

Table S238. Clustering Approach #49: '5p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
5P LOSS MUTATED | 12 | 24 | 59 | 27 | 21 | 9 | 2 | 34 | 1 | 71 | 0 | 11
5P LOSS WILD-TYPE | 113 | 520 | 787 | 385 | 426 | 310 | 491 | 628 | 1 | 477 | 2 | 148

Figure S189. Get High-res Image Clustering Approach #49: '5p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'5p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.78e-19 (Chi-square test), Q value = 1.4e-15

Table S239. Clustering Approach #49: '5p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
5P LOSS MUTATED | 26 | 1 | 8 | 9 | 2 | 2 | 4 | 3 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 21 | 0 | 0 | 11 | 0 | 72 | 13 | 0 | 0
5P LOSS WILD-TYPE | 330 | 53 | 342 | 310 | 491 | 8 | 71 | 202 | 7 | 3 | 14 | 2 | 3 | 2 | 11 | 0 | 1 | 1 | 2 | 294 | 18 | 7 | 132 | 13 | 480 | 66 | 1 | 20

Figure S190. Get High-res Image Clustering Approach #49: '5p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'5p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 1.69e-06 (Chi-square test), Q value = 0.0023

Table S240. Clustering Approach #49: '5p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
5P LOSS MUTATED | 22 | 25 | 82 | 21
5P LOSS WILD-TYPE | 690 | 473 | 799 | 402

Figure S191. Get High-res Image Clustering Approach #49: '5p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #50: '5q loss mutation analysis'

Table S241. Get Full Table Description of clustering approach #50: '5q loss mutation analysis'

Cluster Labels | 5Q LOSS MUTATED | 5Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 638 | 3925

'5q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.52e-60 (Chi-square test), Q value = 8.6e-57

Table S242. Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
5Q LOSS MUTATED | 30 | 24 | 110 | 39 | 35 | 59 | 2 | 158 | 1 | 157 | 1 | 22
5Q LOSS WILD-TYPE | 95 | 520 | 736 | 373 | 412 | 260 | 491 | 504 | 1 | 391 | 1 | 137

Figure S192. Get High-res Image Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'5q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.65e-59 (Chi-square test), Q value = 4.1e-56

Table S243. Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
5Q LOSS MUTATED | 38 | 1 | 12 | 59 | 2 | 2 | 13 | 19 | 1 | 0 | 3 | 0 | 2 | 1 | 3 | 1 | 0 | 1 | 0 | 112 | 1 | 0 | 20 | 1 | 159 | 22 | 0 | 0
5Q LOSS WILD-TYPE | 318 | 53 | 338 | 260 | 491 | 8 | 62 | 186 | 6 | 3 | 12 | 2 | 1 | 1 | 10 | 0 | 1 | 0 | 2 | 203 | 17 | 7 | 123 | 12 | 393 | 57 | 1 | 20

Figure S193. Get High-res Image Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'5q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 5.38e-05 (Chi-square test), Q value = 0.07

Table S244. Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
5Q LOSS MUTATED | 46 | 110 | 77 | 40
5Q LOSS WILD-TYPE | 420 | 522 | 617 | 169

Figure S194. Get High-res Image Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'5q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 1.53e-05 (Chi-square test), Q value = 0.02

Table S245. Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
5Q LOSS MUTATED | 97 | 70 | 193 | 64
5Q LOSS WILD-TYPE | 615 | 428 | 688 | 359

Figure S195. Get High-res Image Clustering Approach #50: '5q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #51: '6p loss mutation analysis'

Table S246. Get Full Table Description of clustering approach #51: '6p loss mutation analysis'

Cluster Labels | 6P LOSS MUTATED | 6P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 450 | 4113

'6p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.98e-28 (Chi-square test), Q value = 5.9e-25

Table S247. Clustering Approach #51: '6p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
6P LOSS MUTATED | 12 | 60 | 90 | 13 | 8 | 21 | 61 | 59 | 1 | 118 | 0 | 6
6P LOSS WILD-TYPE | 113 | 484 | 756 | 399 | 439 | 298 | 432 | 603 | 1 | 430 | 2 | 153

Figure S196. Get High-res Image Clustering Approach #51: '6p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'6p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.31e-26 (Chi-square test), Q value = 6.4e-23

Table S248. Clustering Approach #51: '6p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
6P LOSS MUTATED | 12 | 1 | 3 | 21 | 61 | 2 | 9 | 10 | 2 | 0 | 1 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 30 | 0 | 1 | 4 | 2 | 119 | 5 | 0 | 4
6P LOSS WILD-TYPE | 344 | 53 | 347 | 298 | 432 | 8 | 66 | 195 | 5 | 3 | 14 | 2 | 3 | 2 | 10 | 0 | 1 | 1 | 2 | 285 | 18 | 6 | 139 | 11 | 433 | 74 | 1 | 16

Figure S197. Get High-res Image Clustering Approach #51: '6p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #52: '6q loss mutation analysis'

Table S249. Get Full Table Description of clustering approach #52: '6q loss mutation analysis'

Cluster Labels | 6Q LOSS MUTATED | 6Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 711 | 3852

'6q loss mutation analysis' versus 'AGE'

P value = 6.15e-07 (t-test), Q value = 0.00083

Table S250. Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
6Q LOSS MUTATED | 698 | 59.7 (12.4)
6Q LOSS WILD-TYPE | 3809 | 62.2 (12.6)

Figure S198. Get High-res Image Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'6q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.12e-54 (Chi-square test), Q value = 1.7e-51

Table S251. Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
6Q LOSS MUTATED | 24 | 90 | 151 | 21 | 9 | 22 | 84 | 108 | 2 | 187 | 0 | 11
6Q LOSS WILD-TYPE | 101 | 454 | 695 | 391 | 438 | 297 | 409 | 554 | 0 | 361 | 2 | 148

Figure S199. Get High-res Image Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'6q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.11e-54 (Chi-square test), Q value = 1.1e-50

Table S252. Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
6Q LOSS MUTATED | 18 | 3 | 4 | 22 | 84 | 4 | 19 | 39 | 2 | 2 | 3 | 0 | 0 | 0 | 5 | 1 | 0 | 0 | 0 | 32 | 0 | 1 | 8 | 3 | 189 | 5 | 0 | 6
6Q LOSS WILD-TYPE | 338 | 51 | 346 | 297 | 409 | 6 | 56 | 166 | 5 | 1 | 12 | 2 | 3 | 2 | 8 | 0 | 1 | 1 | 2 | 283 | 18 | 6 | 135 | 10 | 363 | 74 | 1 | 14

Figure S200. Get High-res Image Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'6q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 2.29e-06 (Chi-square test), Q value = 0.0031

Table S253. Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
6Q LOSS MUTATED | 104 | 60 | 195 | 65
6Q LOSS WILD-TYPE | 608 | 438 | 686 | 358

Figure S201. Get High-res Image Clustering Approach #52: '6q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #53: '7p loss mutation analysis'

Table S254. Get Full Table Description of clustering approach #53: '7p loss mutation analysis'

Cluster Labels | 7P LOSS MUTATED | 7P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 200 | 4363

'7p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.37e-48 (Chi-square test), Q value = 5.2e-45

Table S255. Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
7P LOSS MUTATED | 0 | 4 | 44 | 0 | 28 | 5 | 1 | 29 | 0 | 86 | 1 | 2
7P LOSS WILD-TYPE | 125 | 540 | 802 | 412 | 419 | 314 | 492 | 633 | 2 | 462 | 1 | 157

Figure S202. Get High-res Image Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'7p loss mutation analysis' versus 'GENDER'

P value = 1e-13 (Fisher's exact test), Q value = 1.4e-10

Table S256. Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
7P LOSS MUTATED | 173 | 27
7P LOSS WILD-TYPE | 2708 | 1655

Figure S203. Get High-res Image Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'7p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.84e-37 (Chi-square test), Q value = 2.8e-34

Table S257. Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
7P LOSS MUTATED | 0 | 0 | 11 | 5 | 1 | 0 | 1 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 19 | 1 | 0 | 1 | 1 | 87 | 16 | 0 | 0
7P LOSS WILD-TYPE | 356 | 54 | 339 | 314 | 492 | 10 | 74 | 198 | 7 | 3 | 15 | 2 | 3 | 2 | 11 | 1 | 1 | 1 | 2 | 296 | 17 | 7 | 142 | 12 | 465 | 63 | 1 | 20

Figure S204. Get High-res Image Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'7p loss mutation analysis' versus 'PATHOLOGY.T'

P value = 9e-05 (Chi-square test), Q value = 0.12

Table S258. Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
7P LOSS MUTATED | 7 | 23 | 2 | 4
7P LOSS WILD-TYPE | 459 | 609 | 692 | 205

Figure S205. Get High-res Image Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'7p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 1.66e-14 (Chi-square test), Q value = 2.4e-11

Table S259. Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
7P LOSS MUTATED | 20 | 7 | 85 | 11
7P LOSS WILD-TYPE | 692 | 491 | 796 | 412

Figure S206. Get High-res Image Clustering Approach #53: '7p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #54: '7q loss mutation analysis'

Table S260. Get Full Table Description of clustering approach #54: '7q loss mutation analysis'

Cluster Labels | 7Q LOSS MUTATED | 7Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 162 | 4401

'7q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.47e-20 (Chi-square test), Q value = 6.5e-17

Table S261. Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
7Q LOSS MUTATED | 2 | 3 | 61 | 1 | 23 | 8 | 1 | 21 | 0 | 39 | 1 | 2
7Q LOSS WILD-TYPE | 123 | 541 | 785 | 411 | 424 | 311 | 492 | 641 | 2 | 509 | 1 | 157

Figure S207. Get High-res Image Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'7q loss mutation analysis' versus 'GENDER'

P value = 3.65e-11 (Fisher's exact test), Q value = 5.2e-08

Table S262. Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
7Q LOSS MUTATED | 140 | 22
7Q LOSS WILD-TYPE | 2741 | 1660

Figure S208. Get High-res Image Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'7q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.83e-23 (Chi-square test), Q value = 2.7e-20

Table S263. Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
7Q LOSS MUTATED | 1 | 0 | 6 | 8 | 1 | 0 | 0 | 8 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 9 | 1 | 2 | 1 | 1 | 40 | 16 | 0 | 0
7Q LOSS WILD-TYPE | 355 | 54 | 344 | 311 | 492 | 10 | 75 | 197 | 7 | 3 | 15 | 1 | 3 | 2 | 12 | 1 | 1 | 1 | 2 | 306 | 17 | 5 | 142 | 12 | 512 | 63 | 1 | 20

Figure S209. Get High-res Image Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'7q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 3.89e-05 (Chi-square test), Q value = 0.051

Table S264. Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
7Q LOSS MUTATED | 4 | 22 | 3 | 2
7Q LOSS WILD-TYPE | 462 | 610 | 691 | 207

Figure S210. Get High-res Image Clustering Approach #54: '7q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #55: '8p loss mutation analysis'

Table S265. Get Full Table Description of clustering approach #55: '8p loss mutation analysis'

Cluster Labels | 8P LOSS MUTATED | 8P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 1074 | 3489

'8p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.91e-53 (Chi-square test), Q value = 1.2e-49

Table S266. Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
8P LOSS MUTATED | 40 | 39 | 249 | 93 | 43 | 57 | 94 | 175 | 2 | 225 | 0 | 55
8P LOSS WILD-TYPE | 85 | 505 | 597 | 319 | 404 | 262 | 399 | 487 | 0 | 323 | 2 | 104

Figure S211. Get High-res Image Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'8p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.98e-35 (Chi-square test), Q value = 1.4e-31

Table S267. Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
8P LOSS MUTATED | 86 | 6 | 11 | 57 | 94 | 2 | 16 | 56 | 2 | 0 | 5 | 1 | 3 | 0 | 2 | 1 | 0 | 0 | 0 | 87 | 2 | 0 | 51 | 4 | 227 | 30 | 0 | 3
8P LOSS WILD-TYPE | 270 | 48 | 339 | 262 | 399 | 8 | 59 | 149 | 5 | 3 | 10 | 1 | 0 | 2 | 11 | 0 | 1 | 1 | 2 | 228 | 16 | 7 | 92 | 9 | 325 | 49 | 1 | 17

Figure S212. Get High-res Image Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'8p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 1.33e-07 (Chi-square test), Q value = 0.00018

Table S268. Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
8P LOSS MUTATED | 162 | 116 | 303 | 106
8P LOSS WILD-TYPE | 550 | 382 | 578 | 317

Figure S213. Get High-res Image Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'8p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.06e-10 (Fisher's exact test), Q value = 8.5e-07

Table S269. Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
8P LOSS MUTATED | 128 | 946
8P LOSS WILD-TYPE | 698 | 2791

Figure S214. Get High-res Image Clustering Approach #55: '8p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #56: '8q loss mutation analysis'

Table S270. Get Full Table Description of clustering approach #56: '8q loss mutation analysis'

Cluster Labels | 8Q LOSS MUTATED | 8Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 219 | 4344

'8q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.78e-12 (Chi-square test), Q value = 2.5e-09

Table S271. Clustering Approach #56: '8q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
8Q LOSS MUTATED | 5 | 28 | 39 | 9 | 8 | 6 | 40 | 19 | 0 | 58 | 0 | 6
8Q LOSS WILD-TYPE | 120 | 516 | 807 | 403 | 439 | 313 | 453 | 643 | 2 | 490 | 2 | 153

Figure S215. Get High-res Image Clustering Approach #56: '8q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'8q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.37e-10 (Chi-square test), Q value = 1.2e-06

Table S272. Clustering Approach #56: '8q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
8Q LOSS MUTATED | 8 | 1 | 1 | 6 | 40 | 0 | 1 | 8 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 0 | 0 | 6 | 0 | 58 | 7 | 0 | 1
8Q LOSS WILD-TYPE | 348 | 53 | 349 | 313 | 453 | 10 | 74 | 197 | 7 | 3 | 15 | 2 | 2 | 2 | 13 | 1 | 1 | 1 | 2 | 306 | 18 | 7 | 137 | 13 | 494 | 72 | 1 | 19

Figure S216. Get High-res Image Clustering Approach #56: '8q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'8q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000142 (Chi-square test), Q value = 0.18

Table S273. Clustering Approach #56: '8q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
8Q LOSS MUTATED | 32 | 19 | 71 | 13
8Q LOSS WILD-TYPE | 680 | 479 | 810 | 410

Figure S217. Get High-res Image Clustering Approach #56: '8q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #57: '9p loss mutation analysis'

Table S274. Get Full Table Description of clustering approach #57: '9p loss mutation analysis'

Cluster Labels | 9P LOSS MUTATED | 9P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 1105 | 3458

'9p loss mutation analysis' versus 'Time to Death'

P value = 2.53e-13 (logrank test), Q value = 3.6e-10

Table S275. Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
9P LOSS MUTATED | 1051 | 438 | 0.0 - 162.0 (14.3)
9P LOSS WILD-TYPE | 3245 | 963 | 0.0 - 224.0 (14.9)

Figure S218. Get High-res Image Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'9p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.23e-49 (Chi-square test), Q value = 5e-46

Table S276. Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
9P LOSS MUTATED | 38 | 180 | 178 | 27 | 61 | 86 | 88 | 234 | 0 | 199 | 2 | 12
9P LOSS WILD-TYPE | 87 | 364 | 668 | 385 | 386 | 233 | 405 | 428 | 2 | 349 | 0 | 147

Figure S219. Get High-res Image Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'9p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.07e-49 (Chi-square test), Q value = 3.2e-46

Table S277. Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
9P LOSS MUTATED | 25 | 2 | 23 | 86 | 88 | 5 | 24 | 57 | 2 | 1 | 3 | 0 | 1 | 1 | 4 | 1 | 0 | 1 | 2 | 130 | 4 | 2 | 11 | 1 | 201 | 34 | 0 | 9
9P LOSS WILD-TYPE | 331 | 52 | 327 | 233 | 405 | 5 | 51 | 148 | 5 | 2 | 12 | 2 | 2 | 1 | 9 | 0 | 1 | 0 | 0 | 185 | 14 | 5 | 132 | 12 | 351 | 45 | 1 | 11

Figure S220. Get High-res Image Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'9p loss mutation analysis' versus 'PATHOLOGY.T'

P value = 9.7e-09 (Chi-square test), Q value = 1.4e-05

Table S278. Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
9P LOSS MUTATED | 101 | 186 | 105 | 42
9P LOSS WILD-TYPE | 365 | 446 | 589 | 167

Figure S221. Get High-res Image Clustering Approach #57: '9p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #58: '9q loss mutation analysis'

Table S279. Get Full Table Description of clustering approach #58: '9q loss mutation analysis'

Cluster Labels | 9Q LOSS MUTATED | 9Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 900 | 3663

'9q loss mutation analysis' versus 'Time to Death'

P value = 0.00016 (logrank test), Q value = 0.2

Table S280. Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
9Q LOSS MUTATED | 853 | 343 | 0.1 - 162.0 (17.9)
9Q LOSS WILD-TYPE | 3443 | 1058 | 0.0 - 224.0 (14.2)

Figure S222. Get High-res Image Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'9q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.8e-58 (Chi-square test), Q value = 1.4e-54

Table S281. Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
9Q LOSS MUTATED | 36 | 92 | 134 | 24 | 80 | 29 | 92 | 171 | 0 | 228 | 2 | 10
9Q LOSS WILD-TYPE | 89 | 452 | 712 | 388 | 367 | 290 | 401 | 491 | 2 | 320 | 0 | 149

Figure S223. Get High-res Image Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'9q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.1e-56 (Chi-square test), Q value = 1.7e-53

Table S282. Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
9Q LOSS MUTATED | 23 | 1 | 36 | 29 | 92 | 5 | 17 | 52 | 1 | 0 | 3 | 0 | 1 | 0 | 4 | 1 | 0 | 1 | 2 | 83 | 5 | 1 | 9 | 1 | 230 | 39 | 0 | 5
9Q LOSS WILD-TYPE | 333 | 53 | 314 | 290 | 401 | 5 | 58 | 153 | 6 | 3 | 12 | 2 | 2 | 2 | 9 | 0 | 1 | 0 | 0 | 232 | 13 | 6 | 134 | 12 | 322 | 40 | 1 | 15

Figure S224. Get High-res Image Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'9q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 7.3e-09 (Chi-square test), Q value = 1e-05

Table S283. Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
9Q LOSS MUTATED | 132 | 82 | 254 | 79
9Q LOSS WILD-TYPE | 580 | 416 | 627 | 344

Figure S225. Get High-res Image Clustering Approach #58: '9q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #59: '10p loss mutation analysis'

Table S284. Get Full Table Description of clustering approach #59: '10p loss mutation analysis'

Cluster Labels | 10P LOSS MUTATED | 10P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 808 | 3755

'10p loss mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S285. Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
10P LOSS MUTATED | 787 | 439 | 0.0 - 131.2 (10.6)
10P LOSS WILD-TYPE | 3509 | 962 | 0.0 - 224.0 (16.6)

Figure S226. Get High-res Image Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'10p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0 (Chi-square test), Q value = 0

Table S286. Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
10P LOSS MUTATED | 16 | 432 | 65 | 23 | 18 | 48 | 32 | 97 | 0 | 59 | 0 | 17
10P LOSS WILD-TYPE | 109 | 112 | 781 | 389 | 429 | 271 | 461 | 565 | 2 | 489 | 2 | 142

Figure S227. Get High-res Image Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'10p loss mutation analysis' versus 'GENDER'

P value = 2.5e-22 (Fisher's exact test), Q value = 3.7e-19

Table S287. Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
10P LOSS MUTATED | 387 | 421
10P LOSS WILD-TYPE | 2494 | 1261

Figure S228. Get High-res Image Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'10p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.96e-37 (Chi-square test), Q value = 1.5e-33

Table S288. Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
10P LOSS MUTATED | 20 | 3 | 7 | 48 | 32 | 2 | 2 | 19 | 2 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 68 | 1 | 1 | 13 | 4 | 59 | 10 | 1 | 16
10P LOSS WILD-TYPE | 336 | 51 | 343 | 271 | 461 | 8 | 73 | 186 | 5 | 2 | 15 | 2 | 2 | 2 | 13 | 0 | 1 | 1 | 2 | 247 | 17 | 6 | 130 | 9 | 493 | 69 | 0 | 4

Figure S229. Get High-res Image Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'10p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.03e-59 (Fisher's exact test), Q value = 1.4e-55

Table S289. Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
10P LOSS MUTATED | 320 | 488
10P LOSS WILD-TYPE | 506 | 3249

Figure S230. Get High-res Image Clustering Approach #59: '10p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #60: '10q loss mutation analysis'

Table S290. Get Full Table Description of clustering approach #60: '10q loss mutation analysis'

Cluster Labels | 10Q LOSS MUTATED | 10Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 895 | 3668

'10q loss mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S291. Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
10Q LOSS MUTATED | 865 | 463 | 0.0 - 131.2 (11.2)
10Q LOSS WILD-TYPE | 3431 | 938 | 0.0 - 224.0 (16.7)

Figure S231. Get High-res Image Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'10q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0 (Chi-square test), Q value = 0

Table S292. Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
10Q LOSS MUTATED | 24 | 448 | 102 | 24 | 17 | 29 | 48 | 99 | 0 | 81 | 0 | 22
10Q LOSS WILD-TYPE | 101 | 96 | 744 | 388 | 430 | 290 | 445 | 563 | 2 | 467 | 2 | 137

Figure S232. Get High-res Image Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'10q loss mutation analysis' versus 'GENDER'

P value = 2.6e-17 (Fisher's exact test), Q value = 3.8e-14

Table S293. Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
10Q LOSS MUTATED | 454 | 441
10Q LOSS WILD-TYPE | 2427 | 1241

Figure S233. Get High-res Image Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'10q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.71e-41 (Chi-square test), Q value = 8.7e-38

Table S294. Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
10Q LOSS MUTATED | 21 | 3 | 9 | 29 | 48 | 1 | 5 | 17 | 1 | 1 | 0 | 0 | 2 | 0 | 0 | 1 | 0 | 0 | 2 | 68 | 1 | 1 | 18 | 4 | 81 | 7 | 1 | 18
10Q LOSS WILD-TYPE | 335 | 51 | 341 | 290 | 445 | 9 | 70 | 188 | 6 | 2 | 15 | 2 | 1 | 2 | 13 | 0 | 1 | 1 | 0 | 247 | 17 | 6 | 125 | 9 | 471 | 72 | 0 | 2

Figure S234. Get High-res Image Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'10q loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.56e-56 (Fisher's exact test), Q value = 4e-53

Table S295. Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
10Q LOSS MUTATED | 337 | 558
10Q LOSS WILD-TYPE | 489 | 3179

Figure S235. Get High-res Image Clustering Approach #60: '10q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #61: '11p loss mutation analysis'

Table S296. Get Full Table Description of clustering approach #61: '11p loss mutation analysis'

Cluster Labels | 11P LOSS MUTATED | 11P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 587 | 3976

'11p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.63e-41 (Chi-square test), Q value = 1.2e-37

Table S297. Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
11P LOSS MUTATED | 39 | 66 | 133 | 21 | 45 | 43 | 5 | 73 | 0 | 143 | 0 | 19
11P LOSS WILD-TYPE | 86 | 478 | 713 | 391 | 402 | 276 | 488 | 589 | 2 | 405 | 2 | 140

Figure S236. Get High-res Image Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'11p loss mutation analysis' versus 'GENDER'

P value = 1.95e-05 (Fisher's exact test), Q value = 0.026

Table S298. Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
11P LOSS MUTATED | 417 | 170
11P LOSS WILD-TYPE | 2464 | 1512

Figure S237. Get High-res Image Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'11p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.17e-36 (Chi-square test), Q value = 1.8e-33

Table S299. Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
11P LOSS MUTATED | 21 | 0 | 21 | 43 | 5 | 0 | 4 | 16 | 1 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 48 | 4 | 0 | 14 | 4 | 143 | 20 | 0 | 3
11P LOSS WILD-TYPE | 335 | 54 | 329 | 276 | 488 | 10 | 71 | 189 | 6 | 3 | 14 | 1 | 3 | 2 | 12 | 1 | 1 | 0 | 2 | 267 | 14 | 7 | 129 | 9 | 409 | 59 | 1 | 17

Figure S238. Get High-res Image Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'11p loss mutation analysis' versus 'PATHOLOGY.N'

P value = 4.77e-05 (Chi-square test), Q value = 0.062

Table S300. Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
11P LOSS MUTATED | 68 | 47 | 29 | 3
11P LOSS WILD-TYPE | 999 | 306 | 253 | 8

Figure S239. Get High-res Image Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'11p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 2.7e-12 (Chi-square test), Q value = 3.8e-09

Table S301. Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
11P LOSS MUTATED | 48 | 40 | 158 | 47
11P LOSS WILD-TYPE | 664 | 458 | 723 | 376

Figure S240. Get High-res Image Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'11p loss mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 2.25e-06 (Chi-square test), Q value = 0.003

Table S302. Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
11P LOSS MUTATED | 10 | 6 | 10 | 9 | 1 | 49 | 18 | 38 | 8
11P LOSS WILD-TYPE | 18 | 17 | 27 | 20 | 1 | 306 | 199 | 212 | 120

Figure S241. Get High-res Image Clustering Approach #61: '11p loss mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #62: '11q loss mutation analysis'

Table S303. Get Full Table Description of clustering approach #62: '11q loss mutation analysis'

Cluster Labels | 11Q LOSS MUTATED | 11Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 609 | 3954

'11q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.05e-44 (Chi-square test), Q value = 3.1e-41

Table S304. Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
11Q LOSS MUTATED | 29 | 56 | 211 | 27 | 37 | 61 | 8 | 54 | 0 | 101 | 0 | 23
11Q LOSS WILD-TYPE | 96 | 488 | 635 | 385 | 410 | 258 | 485 | 608 | 2 | 447 | 2 | 136

Figure S242. Get High-res Image Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'11q loss mutation analysis' versus 'GENDER'

P value = 5.76e-05 (Fisher's exact test), Q value = 0.074

Table S305. Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
11Q LOSS MUTATED | 429 | 180
11Q LOSS WILD-TYPE | 2452 | 1502

Figure S243. Get High-res Image Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'11q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.7e-22 (Chi-square test), Q value = 6.9e-19

Table S306. Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
11Q LOSS MUTATED | 25 | 2 | 16 | 61 | 8 | 1 | 5 | 10 | 0 | 0 | 2 | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 33 | 5 | 0 | 17 | 5 | 101 | 16 | 0 | 3
11Q LOSS WILD-TYPE | 331 | 52 | 334 | 258 | 485 | 9 | 70 | 195 | 7 | 3 | 13 | 1 | 3 | 2 | 11 | 1 | 1 | 1 | 2 | 282 | 13 | 7 | 126 | 8 | 451 | 63 | 1 | 17

Figure S244. Get High-res Image Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'11q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 1.04e-05 (Chi-square test), Q value = 0.014

Table S307. Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
11Q LOSS MUTATED | 43 | 46 | 119 | 51
11Q LOSS WILD-TYPE | 669 | 452 | 762 | 372

Figure S245. Get High-res Image Clustering Approach #62: '11q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #63: '12p loss mutation analysis'

Table S308. Get Full Table Description of clustering approach #63: '12p loss mutation analysis'

Cluster Labels | 12P LOSS MUTATED | 12P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 256 | 4307

'12p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.2e-07 (Chi-square test), Q value = 3e-04

Table S309. Clustering Approach #63: '12p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
12P LOSS MUTATED | 6 | 47 | 62 | 21 | 18 | 11 | 2 | 33 | 0 | 44 | 0 | 12
12P LOSS WILD-TYPE | 119 | 497 | 784 | 391 | 429 | 308 | 491 | 629 | 2 | 504 | 2 | 147

Figure S246. Get High-res Image Clustering Approach #63: '12p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'12p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.32e-10 (Chi-square test), Q value = 1.9e-07

Table S310. Clustering Approach #63: '12p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
12P LOSS MUTATED | 21 | 0 | 6 | 11 | 2 | 0 | 6 | 18 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 4 | 1 | 0 | 12 | 0 | 44 | 11 | 0 | 2
12P LOSS WILD-TYPE | 335 | 54 | 344 | 308 | 491 | 10 | 69 | 187 | 7 | 3 | 13 | 2 | 3 | 2 | 11 | 1 | 1 | 1 | 1 | 311 | 17 | 7 | 131 | 13 | 508 | 68 | 1 | 18

Figure S247. Get High-res Image Clustering Approach #63: '12p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #64: '12q loss mutation analysis'

Table S311. Get Full Table Description of clustering approach #64: '12q loss mutation analysis'

Cluster Labels | 12Q LOSS MUTATED | 12Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 237 | 4326

'12q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.31e-16 (Chi-square test), Q value = 4.8e-13

Table S312. Clustering Approach #64: '12q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
12Q LOSS MUTATED | 8 | 45 | 48 | 20 | 12 | 7 | 2 | 21 | 0 | 64 | 0 | 10
12Q LOSS WILD-TYPE | 117 | 499 | 798 | 392 | 435 | 312 | 491 | 641 | 2 | 484 | 2 | 149

Figure S248. Get High-res Image Clustering Approach #64: '12q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'12q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.04e-16 (Chi-square test), Q value = 1e-12

Table S313. Clustering Approach #64: '12q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
12Q LOSS MUTATED | 20 | 0 | 4 | 7 | 2 | 0 | 6 | 10 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 2 | 1 | 0 | 10 | 0 | 64 | 7 | 0 | 1
12Q LOSS WILD-TYPE | 336 | 54 | 346 | 312 | 491 | 10 | 69 | 195 | 7 | 3 | 14 | 2 | 3 | 2 | 12 | 1 | 1 | 1 | 1 | 313 | 17 | 7 | 133 | 13 | 488 | 72 | 1 | 19

Figure S249. Get High-res Image Clustering Approach #64: '12q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #65: '13q loss mutation analysis'

Table S314. Get Full Table Description of clustering approach #65: '13q loss mutation analysis'

Cluster Labels | 13Q LOSS MUTATED | 13Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 1007 | 3556

'13q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.7e-88 (Chi-square test), Q value = 1.2e-84

Table S315. Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
13Q LOSS MUTATED | 18 | 148 | 248 | 7 | 52 | 61 | 33 | 194 | 1 | 238 | 2 | 5
13Q LOSS WILD-TYPE | 107 | 396 | 598 | 405 | 395 | 258 | 460 | 468 | 1 | 310 | 0 | 154

Figure S250. Get High-res Image Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'13q loss mutation analysis' versus 'GENDER'

P value = 1.22e-06 (Fisher's exact test), Q value = 0.0016

Table S316. Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
13Q LOSS MUTATED | 701 | 306
13Q LOSS WILD-TYPE | 2180 | 1376

Figure S251. Get High-res Image Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'13q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.53e-83 (Chi-square test), Q value = 2.4e-80

Table S317. Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
13Q LOSS MUTATED | 6 | 1 | 30 | 61 | 33 | 6 | 15 | 47 | 0 | 0 | 5 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 116 | 3 | 1 | 4 | 1 | 241 | 19 | 0 | 6
13Q LOSS WILD-TYPE | 350 | 53 | 320 | 258 | 460 | 4 | 60 | 158 | 7 | 3 | 10 | 1 | 2 | 2 | 12 | 1 | 1 | 1 | 1 | 199 | 15 | 6 | 139 | 12 | 311 | 60 | 1 | 14

Figure S252. Get High-res Image Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'13q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 9.98e-12 (Chi-square test), Q value = 1.4e-08

Table S318. Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
13Q LOSS MUTATED | 66 | 136 | 52 | 37
13Q LOSS WILD-TYPE | 400 | 496 | 642 | 172

Figure S253. Get High-res Image Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'13q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 1.38e-08 (Chi-square test), Q value = 1.9e-05

Table S319. Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
13Q LOSS MUTATED | 112 | 85 | 243 | 90
13Q LOSS WILD-TYPE | 600 | 413 | 638 | 333

Figure S254. Get High-res Image Clustering Approach #65: '13q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #66: '14q loss mutation analysis'

Table S320. Get Full Table Description of clustering approach #66: '14q loss mutation analysis'

Cluster Labels | 14Q LOSS MUTATED | 14Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 866 | 3697

'14q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.77e-38 (Chi-square test), Q value = 2.7e-35

Table S321. Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
14Q LOSS MUTATED | 19 | 123 | 120 | 94 | 39 | 17 | 159 | 89 | 0 | 155 | 0 | 49
14Q LOSS WILD-TYPE | 106 | 421 | 726 | 318 | 408 | 302 | 334 | 573 | 2 | 393 | 2 | 110

Figure S255. Get High-res Image Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'14q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.06e-38 (Chi-square test), Q value = 1.6e-35

Table S322. Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
14Q LOSS MUTATED | 91 | 3 | 13 | 17 | 159 | 2 | 7 | 14 | 0 | 0 | 3 | 1 | 0 | 1 | 2 | 0 | 0 | 1 | 0 | 58 | 3 | 0 | 49 | 0 | 155 | 23 | 0 | 2
14Q LOSS WILD-TYPE | 265 | 51 | 337 | 302 | 334 | 8 | 68 | 191 | 7 | 3 | 12 | 1 | 3 | 1 | 11 | 1 | 1 | 0 | 2 | 257 | 15 | 7 | 94 | 13 | 397 | 56 | 1 | 18

Figure S256. Get High-res Image Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'14q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 2.02e-07 (Chi-square test), Q value = 0.00028

Table S323. Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
14Q LOSS MUTATED | 101 | 108 | 177 | 18
14Q LOSS WILD-TYPE | 365 | 524 | 517 | 191

Figure S257. Get High-res Image Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'14q loss mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000151 (Chi-square test), Q value = 0.19

Table S324. Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
14Q LOSS MUTATED | 214 | 82 | 30 | 0
14Q LOSS WILD-TYPE | 853 | 271 | 252 | 11

Figure S258. Get High-res Image Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'14q loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 5.75e-05 (Chi-square test), Q value = 0.074

Table S325. Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
14Q LOSS MUTATED | 317 | 54 | 3 | 0 | 17
14Q LOSS WILD-TYPE | 1107 | 114 | 6 | 3 | 148

Figure S259. Get High-res Image Clustering Approach #66: '14q loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

Clustering Approach #67: '15q loss mutation analysis'

Table S326. Get Full Table Description of clustering approach #67: '15q loss mutation analysis'

Cluster Labels | 15Q LOSS MUTATED | 15Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 803 | 3760

'15q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.19e-60 (Chi-square test), Q value = 5e-57

Table S327. Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
15Q LOSS MUTATED | 15 | 73 | 151 | 99 | 64 | 23 | 12 | 103 | 1 | 202 | 2 | 55
15Q LOSS WILD-TYPE | 110 | 471 | 695 | 313 | 383 | 296 | 481 | 559 | 1 | 346 | 0 | 104

Figure S260. Get High-res Image Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'15q loss mutation analysis' versus 'GENDER'

P value = 1.96e-12 (Fisher's exact test), Q value = 2.8e-09

Table S328. Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
15Q LOSS MUTATED | 593 | 210
15Q LOSS WILD-TYPE | 2288 | 1472

Figure S261. Get High-res Image Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'15q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.38e-63 (Chi-square test), Q value = 5.3e-60

Table S329. Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
15Q LOSS MUTATED | 95 | 4 | 27 | 23 | 12 | 1 | 10 | 47 | 0 | 0 | 3 | 0 | 2 | 0 | 5 | 0 | 0 | 1 | 1 | 33 | 6 | 0 | 50 | 4 | 205 | 31 | 0 | 5
15Q LOSS WILD-TYPE | 261 | 50 | 323 | 296 | 481 | 9 | 65 | 158 | 7 | 3 | 12 | 2 | 1 | 2 | 8 | 1 | 1 | 0 | 1 | 282 | 12 | 7 | 93 | 9 | 347 | 48 | 1 | 15

Figure S262. Get High-res Image Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'15q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 1.85e-06 (Chi-square test), Q value = 0.0025

Table S330. Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
15Q LOSS MUTATED | 41 | 83 | 138 | 29
15Q LOSS WILD-TYPE | 425 | 549 | 556 | 180

Figure S263. Get High-res Image Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'15q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 3.04e-14 (Chi-square test), Q value = 4.4e-11

Table S331. Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
15Q LOSS MUTATED | 74 | 97 | 234 | 81
15Q LOSS WILD-TYPE | 638 | 401 | 647 | 342

Figure S264. Get High-res Image Clustering Approach #67: '15q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #68: '16p loss mutation analysis'

Table S332. Get Full Table Description of clustering approach #68: '16p loss mutation analysis'

Cluster Labels | 16P LOSS MUTATED | 16P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 499 | 4064

'16p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.63e-173 (Chi-square test), Q value = 5.8e-170

Table S333. Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
16P LOSS MUTATED | 14 | 30 | 47 | 7 | 57 | 12 | 2 | 72 | 2 | 248 | 1 | 7
16P LOSS WILD-TYPE | 111 | 514 | 799 | 405 | 390 | 307 | 491 | 590 | 0 | 300 | 1 | 152

Figure S265. Get High-res Image Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'16p loss mutation analysis' versus 'GENDER'

P value = 8.69e-20 (Fisher's exact test), Q value = 1.3e-16

Table S334. Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
16P LOSS MUTATED | 404 | 95
16P LOSS WILD-TYPE | 2477 | 1587

Figure S266. Get High-res Image Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'16p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.47e-134 (Chi-square test), Q value = 2.3e-131

Table S335. Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
16P LOSS MUTATED | 5 | 2 | 24 | 12 | 2 | 1 | 5 | 14 | 0 | 0 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 46 | 5 | 1 | 5 | 1 | 251 | 28 | 0 | 1
16P LOSS WILD-TYPE | 351 | 52 | 326 | 307 | 491 | 9 | 70 | 191 | 7 | 3 | 14 | 1 | 2 | 2 | 12 | 1 | 1 | 1 | 1 | 269 | 13 | 6 | 138 | 12 | 301 | 51 | 1 | 19

Figure S267. Get High-res Image Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'16p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 9.54e-28 (Chi-square test), Q value = 1.4e-24

Table S336. Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
16P LOSS MUTATED | 46 | 32 | 209 | 57
16P LOSS WILD-TYPE | 666 | 466 | 672 | 366

Figure S268. Get High-res Image Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'16p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.42e-06 (Fisher's exact test), Q value = 0.0046

Table S337. Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
16P LOSS MUTATED | 54 | 445
16P LOSS WILD-TYPE | 772 | 3292

Figure S269. Get High-res Image Clustering Approach #68: '16p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #69: '16q loss mutation analysis'

Table S338. Get Full Table Description of clustering approach #69: '16q loss mutation analysis'

Cluster Labels | 16Q LOSS MUTATED | 16Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 1000 | 3563

'16q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.19e-229 (Chi-square test), Q value = 1.9e-226

Table S339. Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
16Q LOSS MUTATED | 15 | 45 | 351 | 5 | 94 | 24 | 5 | 104 | 1 | 344 | 2 | 10
16Q LOSS WILD-TYPE | 110 | 499 | 495 | 407 | 353 | 295 | 488 | 558 | 1 | 204 | 0 | 149

Figure S270. Get High-res Image Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'16q loss mutation analysis' versus 'GENDER'

P value = 7.3e-72 (Fisher's exact test), Q value = 1.1e-68

Table S340. Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
16Q LOSS MUTATED | 860 | 140
16Q LOSS WILD-TYPE | 2021 | 1542

Figure S271. Get High-res Image Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'16q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.95e-195 (Chi-square test), Q value = 3.1e-192

Table S341. Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
16Q LOSS MUTATED | 3 | 2 | 45 | 24 | 5 | 3 | 9 | 24 | 0 | 0 | 3 | 2 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 59 | 6 | 1 | 8 | 1 | 347 | 43 | 0 | 4
16Q LOSS WILD-TYPE | 353 | 52 | 305 | 295 | 488 | 7 | 66 | 181 | 7 | 3 | 12 | 0 | 2 | 2 | 12 | 1 | 1 | 1 | 1 | 256 | 12 | 6 | 135 | 12 | 205 | 36 | 1 | 16

Figure S272. Get High-res Image Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'16q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 1.01e-06 (Chi-square test), Q value = 0.0014

Table S342. Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
16Q LOSS MUTATED | 29 | 71 | 26 | 11
16Q LOSS WILD-TYPE | 437 | 561 | 668 | 198

Figure S273. Get High-res Image Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'16q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 3.38e-42 (Chi-square test), Q value = 5.1e-39

Table S343. Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
16Q LOSS MUTATED | 69 | 44 | 295 | 69
16Q LOSS WILD-TYPE | 643 | 454 | 586 | 354

Figure S274. Get High-res Image Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'16q loss mutation analysis' versus 'COMPLETENESS.OF.RESECTION'

P value = 1.07e-05 (Chi-square test), Q value = 0.014

Table S344. Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

nPatients | R0 | R1 | R2 | RX
--- | --- | --- | --- | ---
ALL | 1171 | 69 | 59 | 77
16Q LOSS MUTATED | 141 | 23 | 9 | 11
16Q LOSS WILD-TYPE | 1030 | 46 | 50 | 66

Figure S275. Get High-res Image Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

'16q loss mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.99e-06 (Chi-square test), Q value = 0.013

Table S345. Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
16Q LOSS MUTATED | 32 | 30 | 1 | 7 | 131 | 67 | 4 | 48 | 10 | 16 | 12 | 0 | 7
16Q LOSS WILD-TYPE | 40 | 32 | 6 | 36 | 156 | 119 | 38 | 76 | 15 | 25 | 47 | 1 | 9

Figure S276. Get High-res Image Clustering Approach #69: '16q loss mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #70: '17p loss mutation analysis'

Table S346. Get Full Table Description of clustering approach #70: '17p loss mutation analysis'

Cluster Labels | 17P LOSS MUTATED | 17P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 1418 | 3145

'17p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.2e-195 (Chi-square test), Q value = 3.5e-192

Table S347. Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
17P LOSS MUTATED | 35 | 38 | 352 | 162 | 86 | 41 | 24 | 187 | 1 | 403 | 1 | 85
17P LOSS WILD-TYPE | 90 | 506 | 494 | 250 | 361 | 278 | 469 | 475 | 1 | 145 | 1 | 74

Figure S277. Get High-res Image Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'17p loss mutation analysis' versus 'GENDER'

P value = 1.96e-32 (Fisher's exact test), Q value = 2.9e-29

Table S348. Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
17P LOSS MUTATED | 1071 | 347
17P LOSS WILD-TYPE | 1810 | 1335

Figure S278. Get High-res Image Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'17p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.37e-162 (Chi-square test), Q value = 8.5e-159

Table S349. Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
17P LOSS MUTATED | 155 | 7 | 33 | 41 | 24 | 2 | 15 | 54 | 3 | 1 | 2 | 1 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 104 | 8 | 2 | 78 | 6 | 405 | 45 | 0 | 0
17P LOSS WILD-TYPE | 201 | 47 | 317 | 278 | 469 | 8 | 60 | 151 | 4 | 2 | 13 | 1 | 2 | 2 | 12 | 1 | 1 | 0 | 2 | 211 | 10 | 5 | 65 | 7 | 147 | 34 | 1 | 20

Figure S279. Get High-res Image Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'PATHOLOGY.T'

P value = 2.22e-07 (Chi-square test), Q value = 3e-04

Table S350. Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
17P LOSS MUTATED | 75 | 164 | 212 | 43
17P LOSS WILD-TYPE | 391 | 468 | 482 | 166

Figure S280. Get High-res Image Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'17p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 2.74e-31 (Chi-square test), Q value = 4.1e-28

Table S351. Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
17P LOSS MUTATED | 154 | 162 | 440 | 133
17P LOSS WILD-TYPE | 558 | 336 | 441 | 290

Figure S281. Get High-res Image Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'17p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.23e-23 (Fisher's exact test), Q value = 4.8e-20

Table S352. Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
17P LOSS MUTATED | 142 | 1276
17P LOSS WILD-TYPE | 684 | 2461

Figure S282. Get High-res Image Clustering Approach #70: '17p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #71: '17q loss mutation analysis'

Table S353. Get Full Table Description of clustering approach #71: '17q loss mutation analysis'

Cluster Labels | 17Q LOSS MUTATED | 17Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 629 | 3934

'17q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.79e-204 (Chi-square test), Q value = 1.6e-200

Table S354. Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
17Q LOSS MUTATED | 6 | 25 | 134 | 35 | 57 | 5 | 12 | 32 | 1 | 301 | 1 | 20
17Q LOSS WILD-TYPE | 119 | 519 | 712 | 377 | 390 | 314 | 481 | 630 | 1 | 247 | 1 | 139

Figure S283. Get High-res Image Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'17q loss mutation analysis' versus 'GENDER'

P value = 8.72e-49 (Fisher's exact test), Q value = 1.3e-45

Table S355. Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
17Q LOSS MUTATED | 551 | 78
17Q LOSS WILD-TYPE | 2330 | 1604

Figure S284. Get High-res Image Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'17q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.38e-170 (Chi-square test), Q value = 2.2e-167

Table S356. Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
17Q LOSS MUTATED | 33 | 2 | 29 | 5 | 12 | 0 | 3 | 9 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 18 | 6 | 0 | 17 | 2 | 303 | 22 | 0 | 0
17Q LOSS WILD-TYPE | 323 | 52 | 321 | 314 | 481 | 10 | 72 | 196 | 7 | 3 | 15 | 2 | 2 | 2 | 12 | 1 | 1 | 1 | 2 | 297 | 12 | 7 | 126 | 11 | 249 | 57 | 1 | 20

Figure S285. Get High-res Image Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'17q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 2.14e-45 (Chi-square test), Q value = 3.3e-42

Table S357. Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
17Q LOSS MUTATED | 36 | 41 | 262 | 62
17Q LOSS WILD-TYPE | 676 | 457 | 619 | 361

Figure S286. Get High-res Image Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'17q loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.1e-08 (Fisher's exact test), Q value = 2.9e-05

Table S358. Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
17Q LOSS MUTATED | 66 | 563
17Q LOSS WILD-TYPE | 760 | 3174

Figure S287. Get High-res Image Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'17q loss mutation analysis' versus 'COMPLETENESS.OF.RESECTION'

P value = 8.95e-05 (Chi-square test), Q value = 0.11

Table S359. Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

nPatients | R0 | R1 | R2 | RX
--- | --- | --- | --- | ---
ALL | 1171 | 69 | 59 | 77
17Q LOSS MUTATED | 102 | 17 | 6 | 12
17Q LOSS WILD-TYPE | 1069 | 52 | 53 | 65

Figure S288. Get High-res Image Clustering Approach #71: '17q loss mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

Clustering Approach #72: '18p loss mutation analysis'

Table S360. Get Full Table Description of clustering approach #72: '18p loss mutation analysis'

Cluster Labels | 18P LOSS MUTATED | 18P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 931 | 3632

'18p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.86e-147 (Chi-square test), Q value = 2.9e-144

Table S361. Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
18P LOSS MUTATED | 18 | 50 | 168 | 212 | 28 | 27 | 46 | 91 | 1 | 175 | 0 | 112
18P LOSS WILD-TYPE | 107 | 494 | 678 | 200 | 419 | 292 | 447 | 571 | 1 | 373 | 2 | 47

Figure S289. Get High-res Image Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.74e-130 (Chi-square test), Q value = 2.7e-127

Table S362. Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
18P LOSS MUTATED | 204 | 7 | 16 | 27 | 46 | 2 | 15 | 30 | 0 | 0 | 3 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 0 | 34 | 5 | 3 | 107 | 5 | 176 | 7 | 0 | 4
18P LOSS WILD-TYPE | 152 | 47 | 334 | 292 | 447 | 8 | 60 | 175 | 7 | 3 | 12 | 2 | 1 | 2 | 11 | 1 | 1 | 1 | 2 | 281 | 13 | 4 | 36 | 8 | 376 | 72 | 1 | 16

Figure S290. Get High-res Image Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'18p loss mutation analysis' versus 'PATHOLOGY.T'

P value = 1.75e-26 (Chi-square test), Q value = 2.6e-23

Table S363. Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
18P LOSS MUTATED | 44 | 131 | 258 | 54
18P LOSS WILD-TYPE | 422 | 501 | 436 | 155

Figure S291. Get High-res Image Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'18p loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 4.8e-09 (Chi-square test), Q value = 6.7e-06

Table S364. Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
18P LOSS MUTATED | 336 | 73 | 7 | 0 | 42
18P LOSS WILD-TYPE | 1088 | 95 | 2 | 3 | 123

Figure S292. Get High-res Image Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'18p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 5e-12 (Chi-square test), Q value = 7.1e-09

Table S365. Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
18P LOSS MUTATED | 110 | 139 | 274 | 120
18P LOSS WILD-TYPE | 602 | 359 | 607 | 303

Figure S293. Get High-res Image Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'18p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.81e-12 (Fisher's exact test), Q value = 6.8e-09

Table S366. Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
18P LOSS MUTATED | 99 | 832
18P LOSS WILD-TYPE | 727 | 2905

Figure S294. Get High-res Image Clustering Approach #72: '18p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #73: '18q loss mutation analysis'

Table S367. Get Full Table Description of clustering approach #73: '18q loss mutation analysis'

Cluster Labels | 18Q LOSS MUTATED | 18Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 1126 | 3437

'18q loss mutation analysis' versus 'AGE'

P value = 3.22e-05 (t-test), Q value = 0.042

Table S368. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
18Q LOSS MUTATED | 1109 | 63.2 (12.2)
18Q LOSS WILD-TYPE | 3398 | 61.4 (12.7)

Figure S295. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'18q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.45e-148 (Chi-square test), Q value = 1e-144

Table S369. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
18Q LOSS MUTATED | 31 | 43 | 168 | 226 | 41 | 85 | 48 | 139 | 1 | 217 | 0 | 123
18Q LOSS WILD-TYPE | 94 | 501 | 678 | 186 | 406 | 234 | 445 | 523 | 1 | 331 | 2 | 36

Figure S296. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'18q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.9e-112 (Chi-square test), Q value = 3e-109

Table S370. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
18Q LOSS MUTATED | 215 | 10 | 20 | 85 | 48 | 3 | 23 | 42 | 0 | 0 | 5 | 1 | 2 | 1 | 1 | 1 | 0 | 0 | 0 | 57 | 6 | 3 | 113 | 9 | 218 | 15 | 0 | 5
18Q LOSS WILD-TYPE | 141 | 44 | 330 | 234 | 445 | 7 | 52 | 163 | 7 | 3 | 10 | 1 | 1 | 1 | 12 | 0 | 1 | 1 | 2 | 258 | 12 | 4 | 30 | 4 | 334 | 64 | 1 | 15

Figure S297. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'18q loss mutation analysis' versus 'PATHOLOGY.T'

P value = 3.09e-24 (Chi-square test), Q value = 4.6e-21

Table S371. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
18Q LOSS MUTATED | 67 | 177 | 298 | 77
18Q LOSS WILD-TYPE | 399 | 455 | 396 | 132

Figure S298. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'18q loss mutation analysis' versus 'PATHOLOGY.N'

P value = 8.37e-07 (Chi-square test), Q value = 0.0011

Table S372. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
18Q LOSS MUTATED | 311 | 148 | 121 | 4
18Q LOSS WILD-TYPE | 756 | 205 | 161 | 7

Figure S299. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'18q loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 2.29e-05 (Chi-square test), Q value = 0.03

Table S373. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
18Q LOSS MUTATED | 408 | 73 | 7 | 0 | 54
18Q LOSS WILD-TYPE | 1016 | 95 | 2 | 3 | 111

Figure S300. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'18q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 5.26e-14 (Chi-square test), Q value = 7.5e-11

Table S374. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
18Q LOSS MUTATED | 146 | 182 | 328 | 160
18Q LOSS WILD-TYPE | 566 | 316 | 553 | 263

Figure S301. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'18q loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.46e-19 (Fisher's exact test), Q value = 3.6e-16

Table S375. Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
18Q LOSS MUTATED | 108 | 1018
18Q LOSS WILD-TYPE | 718 | 2719

Figure S302. Get High-res Image Clustering Approach #73: '18q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #74: '19p loss mutation analysis'

Table S376. Get Full Table Description of clustering approach #74: '19p loss mutation analysis'

Cluster Labels | 19P LOSS MUTATED | 19P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 446 | 4117

'19p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.43e-67 (Chi-square test), Q value = 1e-63

Table S377. Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
19P LOSS MUTATED | 8 | 17 | 66 | 16 | 30 | 23 | 4 | 137 | 1 | 137 | 0 | 7
19P LOSS WILD-TYPE | 117 | 527 | 780 | 396 | 417 | 296 | 489 | 525 | 1 | 411 | 2 | 152

Figure S303. Get High-res Image Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'19p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.63e-51 (Chi-square test), Q value = 5.6e-48

Table S378. Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
19P LOSS MUTATED | 15 | 1 | 10 | 23 | 4 | 2 | 24 | 47 | 0 | 0 | 5 | 0 | 1 | 1 | 3 | 0 | 0 | 1 | 1 | 50 | 2 | 2 | 6 | 0 | 138 | 18 | 0 | 2
19P LOSS WILD-TYPE | 341 | 53 | 340 | 296 | 489 | 8 | 51 | 158 | 7 | 3 | 10 | 2 | 2 | 1 | 10 | 1 | 1 | 0 | 1 | 265 | 16 | 5 | 137 | 13 | 414 | 61 | 1 | 18

Figure S304. Get High-res Image Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'19p loss mutation analysis' versus 'PATHOLOGY.T'

P value = 2.22e-07 (Chi-square test), Q value = 3e-04

Table S379. Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
19P LOSS MUTATED | 37 | 90 | 36 | 22
19P LOSS WILD-TYPE | 429 | 542 | 658 | 187

Figure S305. Get High-res Image Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'19p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 3.85e-06 (Chi-square test), Q value = 0.0051

Table S380. Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
19P LOSS MUTATED | 71 | 54 | 154 | 41
19P LOSS WILD-TYPE | 641 | 444 | 727 | 382

Figure S306. Get High-res Image Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'19p loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.75e-06 (Fisher's exact test), Q value = 0.0037

Table S381. Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
19P LOSS MUTATED | 46 | 400
19P LOSS WILD-TYPE | 780 | 3337

Figure S307. Get High-res Image Clustering Approach #74: '19p loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #75: '19q loss mutation analysis'

Table S382. Get Full Table Description of clustering approach #75: '19q loss mutation analysis'

Cluster Labels | 19Q LOSS MUTATED | 19Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 362 | 4201

'19q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.1e-64 (Chi-square test), Q value = 7.9e-61

Table S383. Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
19Q LOSS MUTATED | 3 | 22 | 51 | 14 | 23 | 17 | 1 | 86 | 1 | 137 | 0 | 7
19Q LOSS WILD-TYPE | 122 | 522 | 795 | 398 | 424 | 302 | 492 | 576 | 1 | 411 | 2 | 152

Figure S308. Get High-res Image Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'19q loss mutation analysis' versus 'GENDER'

P value = 5.16e-07 (Fisher's exact test), Q value = 7e-04

Table S384. Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
19Q LOSS MUTATED | 272 | 90
19Q LOSS WILD-TYPE | 2609 | 1592

Figure S309. Get High-res Image Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'19q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.28e-50 (Chi-square test), Q value = 2e-47

Table S385. Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
19Q LOSS MUTATED | 13 | 1 | 9 | 17 | 1 | 2 | 13 | 27 | 0 | 0 | 2 | 0 | 0 | 0 | 3 | 1 | 0 | 1 | 2 | 34 | 2 | 1 | 6 | 0 | 138 | 12 | 0 | 3
19Q LOSS WILD-TYPE | 343 | 53 | 341 | 302 | 492 | 8 | 62 | 178 | 7 | 3 | 13 | 2 | 3 | 2 | 10 | 0 | 1 | 0 | 0 | 281 | 16 | 6 | 137 | 13 | 414 | 67 | 1 | 17

Figure S310. Get High-res Image Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'19q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 8.01e-10 (Chi-square test), Q value = 1.1e-06

Table S386. Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
19Q LOSS MUTATED | 48 | 37 | 139 | 34
19Q LOSS WILD-TYPE | 664 | 461 | 742 | 389

Figure S311. Get High-res Image Clustering Approach #75: '19q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #76: '20p loss mutation analysis'

Table S387. Get Full Table Description of clustering approach #76: '20p loss mutation analysis'

Cluster Labels | 20P LOSS MUTATED | 20P LOSS WILD-TYPE
--- | --- | ---
Number of samples | 253 | 4310

'20p loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.02e-10 (Chi-square test), Q value = 1.4e-07

Table S388. Clustering Approach #76: '20p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
20P LOSS MUTATED | 3 | 12 | 48 | 33 | 15 | 21 | 6 | 60 | 0 | 35 | 0 | 19
20P LOSS WILD-TYPE | 122 | 532 | 798 | 379 | 432 | 298 | 487 | 602 | 2 | 513 | 2 | 140

Figure S312. Get High-res Image Clustering Approach #76: '20p loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.75e-09 (Chi-square test), Q value = 8e-06

Table S389. Clustering Approach #76: '20p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
20P LOSS MUTATED | 31 | 2 | 7 | 21 | 6 | 1 | 11 | 28 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 16 | 1 | 1 | 17 | 2 | 35 | 7 | 0 | 0
20P LOSS WILD-TYPE | 325 | 52 | 343 | 298 | 487 | 9 | 64 | 177 | 7 | 3 | 14 | 2 | 2 | 2 | 13 | 1 | 1 | 1 | 1 | 299 | 17 | 6 | 126 | 11 | 517 | 72 | 1 | 20

Figure S313. Get High-res Image Clustering Approach #76: '20p loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #77: '20q loss mutation analysis'

Table S390. Get Full Table Description of clustering approach #77: '20q loss mutation analysis'

Cluster Labels | 20Q LOSS MUTATED | 20Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 108 | 4455

'20q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.63e-09 (Chi-square test), Q value = 1.3e-05

Table S391. Clustering Approach #77: '20q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
20Q LOSS MUTATED | 1 | 11 | 22 | 2 | 5 | 10 | 0 | 36 | 0 | 21 | 0 | 0
20Q LOSS WILD-TYPE | 124 | 533 | 824 | 410 | 442 | 309 | 493 | 626 | 2 | 527 | 2 | 159

Figure S314. Get High-res Image Clustering Approach #77: '20q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'20q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.42e-07 (Chi-square test), Q value = 0.0011

Table S392. Clustering Approach #77: '20q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
20Q LOSS MUTATED | 2 | 0 | 3 | 10 | 0 | 0 | 6 | 10 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 17 | 1 | 1 | 0 | 0 | 21 | 1 | 0 | 1
20Q LOSS WILD-TYPE | 354 | 54 | 347 | 309 | 493 | 10 | 69 | 195 | 7 | 3 | 14 | 2 | 2 | 2 | 13 | 1 | 1 | 1 | 2 | 298 | 17 | 6 | 143 | 13 | 531 | 78 | 1 | 19

Figure S315. Get High-res Image Clustering Approach #77: '20q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #78: '21q loss mutation analysis'

Table S393. Get Full Table Description of clustering approach #78: '21q loss mutation analysis'

Cluster Labels | 21Q LOSS MUTATED | 21Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 647 | 3916

'21q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.1e-46 (Chi-square test), Q value = 3.2e-43

Table S394. Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
21Q LOSS MUTATED | 13 | 27 | 80 | 71 | 26 | 58 | 33 | 143 | 0 | 151 | 0 | 44
21Q LOSS WILD-TYPE | 112 | 517 | 766 | 341 | 421 | 261 | 460 | 519 | 2 | 397 | 2 | 115

Figure S316. Get High-res Image Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'21q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.61e-27 (Chi-square test), Q value = 2.4e-24

Table S395. Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
21Q LOSS MUTATED | 67 | 4 | 10 | 58 | 33 | 3 | 11 | 27 | 2 | 0 | 1 | 0 | 1 | 0 | 3 | 1 | 0 | 0 | 1 | 93 | 3 | 0 | 40 | 2 | 151 | 13 | 0 | 2
21Q LOSS WILD-TYPE | 289 | 50 | 340 | 261 | 460 | 7 | 64 | 178 | 5 | 3 | 14 | 2 | 2 | 2 | 10 | 0 | 1 | 1 | 1 | 222 | 15 | 7 | 103 | 11 | 401 | 66 | 1 | 18

Figure S317. Get High-res Image Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'21q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 5.65e-06 (Chi-square test), Q value = 0.0075

Table S396. Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
21Q LOSS MUTATED | 115 | 78 | 219 | 74
21Q LOSS WILD-TYPE | 597 | 420 | 662 | 349

Figure S318. Get High-res Image Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'21q loss mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.08e-07 (Fisher's exact test), Q value = 0.00015

Table S397. Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
21Q LOSS MUTATED | 71 | 576
21Q LOSS WILD-TYPE | 755 | 3161

Figure S319. Get High-res Image Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'21q loss mutation analysis' versus 'STOPPEDSMOKINGYEAR'

P value = 5.24e-05 (t-test), Q value = 0.068

Table S398. Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 568 | 1995.2 (13.5)
21Q LOSS MUTATED | 112 | 1999.2 (10.8)
21Q LOSS WILD-TYPE | 456 | 1994.2 (13.9)

Figure S320. Get High-res Image Clustering Approach #78: '21q loss mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

Clustering Approach #79: '22q loss mutation analysis'

Table S399. Get Full Table Description of clustering approach #79: '22q loss mutation analysis'

Cluster Labels | 22Q LOSS MUTATED | 22Q LOSS WILD-TYPE
--- | --- | ---
Number of samples | 1165 | 3398

'22q loss mutation analysis' versus 'Time to Death'

P value = 5.47e-05 (logrank test), Q value = 0.071

Table S400. Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
22Q LOSS MUTATED | 1090 | 427 | 0.0 - 224.0 (16.1)
22Q LOSS WILD-TYPE | 3206 | 974 | 0.0 - 223.4 (14.2)

Figure S321. Get High-res Image Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'22q loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.28e-167 (Chi-square test), Q value = 3.6e-164

Table S401. Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
22Q LOSS MUTATED | 23 | 146 | 287 | 80 | 72 | 24 | 11 | 106 | 1 | 373 | 1 | 40
22Q LOSS WILD-TYPE | 102 | 398 | 559 | 332 | 375 | 295 | 482 | 556 | 1 | 175 | 1 | 119

Figure S322. Get High-res Image Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'22q loss mutation analysis' versus 'GENDER'

P value = 5.59e-34 (Fisher's exact test), Q value = 8.4e-31

Table S402. Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
22Q LOSS MUTATED | 904 | 261
22Q LOSS WILD-TYPE | 1977 | 1421

Figure S323. Get High-res Image Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'22q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.78e-170 (Chi-square test), Q value = 1.4e-166

Table S403. Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
22Q LOSS MUTATED | 79 | 1 | 36 | 24 | 11 | 4 | 15 | 44 | 1 | 0 | 5 | 0 | 1 | 0 | 2 | 1 | 0 | 1 | 1 | 30 | 6 | 1 | 36 | 4 | 375 | 30 | 0 | 6
22Q LOSS WILD-TYPE | 277 | 53 | 314 | 295 | 482 | 6 | 60 | 161 | 6 | 3 | 10 | 2 | 2 | 2 | 11 | 0 | 1 | 0 | 1 | 285 | 12 | 6 | 107 | 9 | 177 | 49 | 1 | 14

Figure S324. Get High-res Image Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'22q loss mutation analysis' versus 'TUMOR.STAGE'

P value = 3.92e-53 (Chi-square test), Q value = 6e-50

Table S404. Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
22Q LOSS MUTATED | 75 | 83 | 374 | 89
22Q LOSS WILD-TYPE | 637 | 415 | 507 | 334

Figure S325. Get High-res Image Clustering Approach #79: '22q loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #80: 'Xq loss mutation analysis'

Table S405. Get Full Table Description of clustering approach #80: 'Xq loss mutation analysis'

Cluster Labels | XQ LOSS MUTATED | XQ LOSS WILD-TYPE
--- | --- | ---
Number of samples | 200 | 4363

'Xq loss mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.04e-48 (Chi-square test), Q value = 7.7e-45

Table S406. Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
XQ LOSS MUTATED | 2 | 10 | 30 | 5 | 13 | 8 | 11 | 21 | 1 | 93 | 0 | 5
XQ LOSS WILD-TYPE | 123 | 534 | 816 | 407 | 434 | 311 | 482 | 641 | 1 | 455 | 2 | 154

Figure S326. Get High-res Image Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Xq loss mutation analysis' versus 'GENDER'

P value = 4.06e-07 (Fisher's exact test), Q value = 0.00055

Table S407. Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
XQ LOSS MUTATED | 159 | 41
XQ LOSS WILD-TYPE | 2722 | 1641

Figure S327. Get High-res Image Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #4: 'GENDER'

'Xq loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.42e-35 (Chi-square test), Q value = 8.2e-32

Table S408. Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
XQ LOSS MUTATED | 4 | 1 | 6 | 8 | 11 | 1 | 1 | 7 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 10 | 1 | 0 | 5 | 0 | 94 | 6 | 0 | 0
XQ LOSS WILD-TYPE | 352 | 53 | 344 | 311 | 482 | 9 | 74 | 198 | 7 | 3 | 15 | 1 | 3 | 2 | 13 | 1 | 1 | 0 | 2 | 305 | 17 | 7 | 138 | 13 | 458 | 73 | 1 | 20

Figure S328. Get High-res Image Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Xq loss mutation analysis' versus 'TUMOR.STAGE'

P value = 2.78e-10 (Chi-square test), Q value = 3.9e-07

Table S409. Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
XQ LOSS MUTATED | 21 | 14 | 87 | 20
XQ LOSS WILD-TYPE | 691 | 484 | 794 | 403

Figure S329. Get High-res Image Clustering Approach #80: 'Xq loss mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Methods & Data
Input

- Cluster data file = broad_values_by_arm.mutsig.cluster.txt

- Clinical data file = PANCAN12-TP.clin.merged.picked.txt

- Number of patients = 4563

- Number of clustering approaches = 80

- Number of selected clinical features = 21

- Exclude small clusters that include fewer than K patients, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary clinical features, two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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