Correlation between copy number variations of arm-level result and selected clinical features
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.

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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