Correlation between copy number variation genes (focal events) and selected clinical features

Thyroid Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1X63K9Q

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 29 focal events and 15 clinical features across 475 patients, 14 significant findings detected with Q value < 0.25.

DEL PEAK 2(2P23.1) MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
DEL PEAK 3(2Q35) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.
DEL PEAK 6(6Q22.31) MUTATION ANALYSIS cnv correlated to 'Time to Death'.
DEL PEAK 9(8P23.2) MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
DEL PEAK 10(8P22) MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
DEL PEAK 11(8P12) MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
DEL PEAK 12(8Q24.22) MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
DEL PEAK 13(9Q21.13) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE'.
DEL PEAK 16(11P15.1) MUTATION ANALYSIS cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.
DEL PEAK 24(18Q22.2) MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
DEL PEAK 34(XQ22.3) MUTATION ANALYSIS cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 29 focal events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 14 significant findings detected.


		Clinical Features	Time to Death	AGE	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RADIATIONEXPOSURE	EXTRATHYROIDAL EXTENSION	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES	MULTIFOCALITY	TUMOR SIZE
	nCNV (%)	nWild-Type	logrank test	t-test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	t-test	Fisher's exact test	t-test
DEL PEAK 3(2Q35) MUTATION ANALYSIS	11 (2%)	464	0.0467 (1.00)	0.0587 (1.00)	0.000198 (0.0835)	0.624 (1.00)	0.00731 (1.00)	0.0323 (1.00)	0.49 (1.00)	0.0157 (1.00)	1 (1.00)	0.343 (1.00)	0.531 (1.00)	0.207 (1.00)	3.83e-25 (1.66e-22)	1 (1.00)	0.202 (1.00)
DEL PEAK 16(11P15 1) MUTATION ANALYSIS	7 (1%)	468	0.00188 (0.776)	0.000502 (0.211)	2.17e-07 (9.24e-05)	0.189 (1.00)	0.449 (1.00)	0.0928 (1.00)	0.0155 (1.00)	0.827 (1.00)	0.19 (1.00)	1 (1.00)	0.536 (1.00)	0.504 (1.00)	0.0804 (1.00)	0.708 (1.00)	0.0349 (1.00)
DEL PEAK 34(XQ22 3) MUTATION ANALYSIS	4 (1%)	471	0.748 (1.00)	0.0809 (1.00)	1.57e-06 (0.000667)	0.056 (1.00)	0.123 (1.00)	0.103 (1.00)	0.0577 (1.00)	1 (1.00)	1 (1.00)	0.117 (1.00)	0.636 (1.00)	0.298 (1.00)	4.19e-25 (1.81e-22)	1 (1.00)	0.863 (1.00)
DEL PEAK 2(2P23 1) MUTATION ANALYSIS	12 (3%)	463	0.702 (1.00)	0.657 (1.00)	0.015 (1.00)	0.887 (1.00)	0.0201 (1.00)	0.0258 (1.00)	0.524 (1.00)	0.00464 (1.00)	1 (1.00)	1 (1.00)	0.0913 (1.00)	0.509 (1.00)	2.53e-09 (1.08e-06)	0.779 (1.00)	0.879 (1.00)
DEL PEAK 6(6Q22 31) MUTATION ANALYSIS	6 (1%)	469	9.71e-05 (0.0411)	0.0478 (1.00)	0.185 (1.00)	0.904 (1.00)	0.372 (1.00)	0.0169 (1.00)	0.19 (1.00)	0.789 (1.00)	0.165 (1.00)	0.188 (1.00)	0.348 (1.00)	0.682 (1.00)	0.002 (0.823)	0.691 (1.00)	0.0497 (1.00)
DEL PEAK 9(8P23 2) MUTATION ANALYSIS	4 (1%)	471	0.867 (1.00)	0.998 (1.00)	0.188 (1.00)	1 (1.00)	0.248 (1.00)	0.373 (1.00)	0.0577 (1.00)	0.472 (1.00)	1 (1.00)	1 (1.00)	0.636 (1.00)	1 (1.00)	4.19e-25 (1.81e-22)	1 (1.00)	0.879 (1.00)
DEL PEAK 10(8P22) MUTATION ANALYSIS	4 (1%)	471	0.867 (1.00)	0.998 (1.00)	0.188 (1.00)	1 (1.00)	0.248 (1.00)	0.373 (1.00)	0.0577 (1.00)	0.472 (1.00)	1 (1.00)	1 (1.00)	0.636 (1.00)	1 (1.00)	4.19e-25 (1.81e-22)	1 (1.00)	0.879 (1.00)
DEL PEAK 11(8P12) MUTATION ANALYSIS	4 (1%)	471	0.867 (1.00)	0.998 (1.00)	0.188 (1.00)	1 (1.00)	0.248 (1.00)	0.373 (1.00)	0.0577 (1.00)	0.472 (1.00)	1 (1.00)	1 (1.00)	0.636 (1.00)	1 (1.00)	4.19e-25 (1.81e-22)	1 (1.00)	0.879 (1.00)
DEL PEAK 12(8Q24 22) MUTATION ANALYSIS	7 (1%)	468	0.837 (1.00)	0.376 (1.00)	0.105 (1.00)	0.784 (1.00)	0.061 (1.00)	0.739 (1.00)	0.0155 (1.00)	0.16 (1.00)	1 (1.00)	1 (1.00)	0.75 (1.00)	0.504 (1.00)	4.1e-25 (1.77e-22)	1 (1.00)	0.335 (1.00)
DEL PEAK 13(9Q21 13) MUTATION ANALYSIS	19 (4%)	456	0.0702 (1.00)	0.0091 (1.00)	5.93e-11 (2.54e-08)	0.314 (1.00)	0.8 (1.00)	0.0319 (1.00)	0.117 (1.00)	0.673 (1.00)	0.44 (1.00)	0.534 (1.00)	0.0686 (1.00)	0.741 (1.00)	0.418 (1.00)	0.817 (1.00)	0.168 (1.00)
DEL PEAK 24(18Q22 2) MUTATION ANALYSIS	5 (1%)	470	0.703 (1.00)	0.278 (1.00)	0.312 (1.00)	0.179 (1.00)	0.623 (1.00)	0.688 (1.00)	1 (1.00)	0.579 (1.00)	1 (1.00)	1 (1.00)	0.438 (1.00)	1 (1.00)	6.71e-05 (0.0284)	0.38 (1.00)	0.317 (1.00)
AMP PEAK 1(XQ22 3) MUTATION ANALYSIS	15 (3%)	460	0.345 (1.00)	0.398 (1.00)	0.0116 (1.00)	0.717 (1.00)	0.575 (1.00)	0.454 (1.00)	0.0148 (1.00)	0.576 (1.00)	1 (1.00)	1 (1.00)	0.0123 (1.00)	1 (1.00)	0.826 (1.00)	0.302 (1.00)	0.936 (1.00)
DEL PEAK 4(5P15 2) MUTATION ANALYSIS	4 (1%)	471	0.916 (1.00)	0.239 (1.00)	0.719 (1.00)	0.623 (1.00)	0.623 (1.00)	0.189 (1.00)	0.577 (1.00)	0.0311 (1.00)	1 (1.00)	1 (1.00)	0.403 (1.00)	0.06 (1.00)	0.182 (1.00)	0.338 (1.00)	0.273 (1.00)
DEL PEAK 8(7Q34) MUTATION ANALYSIS	4 (1%)	471	0.758 (1.00)	0.81 (1.00)	0.795 (1.00)	0.547 (1.00)	0.623 (1.00)	1 (1.00)	1 (1.00)	0.129 (1.00)	1 (1.00)	1 (1.00)	0.636 (1.00)	1 (1.00)	0.23 (1.00)	0.628 (1.00)	0.191 (1.00)
DEL PEAK 14(10Q21 2) MUTATION ANALYSIS	11 (2%)	464	0.633 (1.00)	0.997 (1.00)	0.943 (1.00)	0.84 (1.00)	0.338 (1.00)	0.628 (1.00)	0.49 (1.00)	0.52 (1.00)	0.283 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.489 (1.00)	0.524 (1.00)	0.141 (1.00)
DEL PEAK 15(10Q23 31) MUTATION ANALYSIS	11 (2%)	464	0.626 (1.00)	0.0266 (1.00)	0.00878 (1.00)	0.804 (1.00)	0.0201 (1.00)	0.154 (1.00)	0.168 (1.00)	0.25 (1.00)	1 (1.00)	1 (1.00)	0.821 (1.00)	0.696 (1.00)	0.00127 (0.528)	1 (1.00)	0.0225 (1.00)
DEL PEAK 17(13Q12 3) MUTATION ANALYSIS	14 (3%)	461	0.36 (1.00)	0.00165 (0.684)	0.0732 (1.00)	0.676 (1.00)	0.14 (1.00)	0.114 (1.00)	0.06 (1.00)	0.507 (1.00)	0.346 (1.00)	0.00108 (0.452)	0.858 (1.00)	0.63 (1.00)	0.062 (1.00)	0.427 (1.00)	0.493 (1.00)
DEL PEAK 18(13Q21 31) MUTATION ANALYSIS	15 (3%)	460	0.36 (1.00)	0.0619 (1.00)	0.653 (1.00)	0.771 (1.00)	0.0874 (1.00)	0.231 (1.00)	0.0787 (1.00)	0.511 (1.00)	0.0681 (1.00)	0.00108 (0.452)	0.752 (1.00)	0.654 (1.00)	0.00156 (0.649)	0.119 (1.00)	0.653 (1.00)
DEL PEAK 19(15Q25 3) MUTATION ANALYSIS	7 (1%)	468	0.687 (1.00)	0.666 (1.00)	0.105 (1.00)	0.269 (1.00)	0.122 (1.00)	0.0181 (1.00)	0.682 (1.00)	0.0304 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.737 (1.00)	0.25 (1.00)	0.708 (1.00)	0.397 (1.00)
DEL PEAK 21(16Q23 3) MUTATION ANALYSIS	5 (1%)	470	0.748 (1.00)	0.0803 (1.00)	0.0298 (1.00)	0.0713 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.0813 (1.00)	1 (1.00)	0.188 (1.00)	0.0312 (1.00)	0.223 (1.00)	0.725 (1.00)	0.665 (1.00)	0.904 (1.00)
DEL PEAK 22(17P13 1) MUTATION ANALYSIS	7 (1%)	468	0.597 (1.00)	0.701 (1.00)	0.517 (1.00)	0.132 (1.00)	0.449 (1.00)	0.335 (1.00)	0.682 (1.00)	0.16 (1.00)	0.0156 (1.00)	0.254 (1.00)	0.176 (1.00)	0.737 (1.00)	0.929 (1.00)	1 (1.00)	0.0909 (1.00)
DEL PEAK 23(18P11 21) MUTATION ANALYSIS	4 (1%)	471	0.754 (1.00)	0.555 (1.00)	0.188 (1.00)	0.334 (1.00)	1 (1.00)	0.373 (1.00)	1 (1.00)	0.472 (1.00)	1 (1.00)	1 (1.00)	0.636 (1.00)	1 (1.00)	0.002 (0.823)	0.628 (1.00)	0.24 (1.00)
DEL PEAK 25(19P13 2) MUTATION ANALYSIS	6 (1%)	469	0.00116 (0.484)	0.0554 (1.00)	0.57 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.19 (1.00)	1 (1.00)	1 (1.00)	0.0212 (1.00)	0.736 (1.00)	0.0988 (1.00)		0.691 (1.00)	0.00552 (1.00)
DEL PEAK 28(21Q21 1) MUTATION ANALYSIS	9 (2%)	466	0.843 (1.00)	0.0667 (1.00)	0.00754 (1.00)	0.278 (1.00)	1 (1.00)	0.59 (1.00)	0.704 (1.00)	0.763 (1.00)	1 (1.00)	1 (1.00)	0.605 (1.00)	0.365 (1.00)	0.895 (1.00)	0.313 (1.00)	0.64 (1.00)
DEL PEAK 29(22Q13 1) MUTATION ANALYSIS	82 (17%)	393	0.607 (1.00)	0.847 (1.00)	0.675 (1.00)	0.378 (1.00)	0.255 (1.00)	0.503 (1.00)	0.494 (1.00)	0.262 (1.00)	0.481 (1.00)	0.331 (1.00)	0.113 (1.00)	0.536 (1.00)	0.244 (1.00)	0.14 (1.00)	0.899 (1.00)
DEL PEAK 30(22Q13 2) MUTATION ANALYSIS	82 (17%)	393	0.607 (1.00)	0.847 (1.00)	0.675 (1.00)	0.378 (1.00)	0.255 (1.00)	0.503 (1.00)	0.494 (1.00)	0.262 (1.00)	0.481 (1.00)	0.331 (1.00)	0.113 (1.00)	0.536 (1.00)	0.244 (1.00)	0.14 (1.00)	0.899 (1.00)
DEL PEAK 31(22Q13 31) MUTATION ANALYSIS	82 (17%)	393	0.607 (1.00)	0.847 (1.00)	0.675 (1.00)	0.378 (1.00)	0.255 (1.00)	0.503 (1.00)	0.494 (1.00)	0.262 (1.00)	0.481 (1.00)	0.331 (1.00)	0.113 (1.00)	0.536 (1.00)	0.244 (1.00)	0.14 (1.00)	0.899 (1.00)
DEL PEAK 32(22Q13 32) MUTATION ANALYSIS	83 (17%)	392	0.604 (1.00)	0.889 (1.00)	0.677 (1.00)	0.36 (1.00)	0.208 (1.00)	0.628 (1.00)	0.584 (1.00)	0.191 (1.00)	0.481 (1.00)	0.333 (1.00)	0.103 (1.00)	0.536 (1.00)	0.212 (1.00)	0.111 (1.00)	0.899 (1.00)
DEL PEAK 33(XQ22 1) MUTATION ANALYSIS	6 (1%)	469	0.722 (1.00)	0.204 (1.00)	0.000795 (0.334)	0.206 (1.00)	0.685 (1.00)	0.182 (1.00)	0.0439 (1.00)	1 (1.00)	1 (1.00)	0.188 (1.00)	0.348 (1.00)	0.293 (1.00)	0.812 (1.00)	0.421 (1.00)	0.483 (1.00)

'DEL PEAK 2(2P23.1) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.53e-09 (t-test), Q value = 1.1e-06

Table S1. Gene #2: 'DEL PEAK 2(2P23.1) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 2(2P23.1) MUTATED	10	0.3 (0.9)
DEL PEAK 2(2P23.1) WILD-TYPE	369	3.7 (6.3)

Figure S1. Get High-res Image Gene #2: 'DEL PEAK 2(2P23.1) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 3(2Q35) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000198 (Chi-square test), Q value = 0.083

Table S2. Gene #3: 'DEL PEAK 3(2Q35) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	270	49	106	2	41	5
DEL PEAK 3(2Q35) MUTATED	3	6	2	0	0	0
DEL PEAK 3(2Q35) WILD-TYPE	267	43	104	2	41	5

Figure S2. Get High-res Image Gene #3: 'DEL PEAK 3(2Q35) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 3(2Q35) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.83e-25 (t-test), Q value = 1.7e-22

Table S3. Gene #3: 'DEL PEAK 3(2Q35) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 3(2Q35) MUTATED	8	0.0 (0.0)
DEL PEAK 3(2Q35) WILD-TYPE	371	3.6 (6.3)

Figure S3. Get High-res Image Gene #3: 'DEL PEAK 3(2Q35) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 6(6Q22.31) MUTATION STATUS' versus 'Time to Death'

P value = 9.71e-05 (logrank test), Q value = 0.041

Table S4. Gene #5: 'DEL PEAK 6(6Q22.31) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	470	13	0.0 - 158.8 (14.2)
DEL PEAK 6(6Q22.31) MUTATED	5	2	1.6 - 54.1 (33.6)
DEL PEAK 6(6Q22.31) WILD-TYPE	465	11	0.0 - 158.8 (14.0)

Figure S4. Get High-res Image Gene #5: 'DEL PEAK 6(6Q22.31) MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'DEL PEAK 9(8P23.2) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 1.8e-22

Table S5. Gene #7: 'DEL PEAK 9(8P23.2) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 9(8P23.2) MUTATED	4	0.0 (0.0)
DEL PEAK 9(8P23.2) WILD-TYPE	375	3.6 (6.3)

Figure S5. Get High-res Image Gene #7: 'DEL PEAK 9(8P23.2) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 10(8P22) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 1.8e-22

Table S6. Gene #8: 'DEL PEAK 10(8P22) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 10(8P22) MUTATED	4	0.0 (0.0)
DEL PEAK 10(8P22) WILD-TYPE	375	3.6 (6.3)

Figure S6. Get High-res Image Gene #8: 'DEL PEAK 10(8P22) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 11(8P12) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 1.8e-22

Table S7. Gene #9: 'DEL PEAK 11(8P12) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 11(8P12) MUTATED	4	0.0 (0.0)
DEL PEAK 11(8P12) WILD-TYPE	375	3.6 (6.3)

Figure S7. Get High-res Image Gene #9: 'DEL PEAK 11(8P12) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 12(8Q24.22) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.1e-25 (t-test), Q value = 1.8e-22

Table S8. Gene #10: 'DEL PEAK 12(8Q24.22) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 12(8Q24.22) MUTATED	5	0.0 (0.0)
DEL PEAK 12(8Q24.22) WILD-TYPE	374	3.6 (6.3)

Figure S8. Get High-res Image Gene #10: 'DEL PEAK 12(8Q24.22) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 13(9Q21.13) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.93e-11 (Chi-square test), Q value = 2.5e-08

Table S9. Gene #11: 'DEL PEAK 13(9Q21.13) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	270	49	106	2	41	5
DEL PEAK 13(9Q21.13) MUTATED	6	5	3	2	3	0
DEL PEAK 13(9Q21.13) WILD-TYPE	264	44	103	0	38	5

Figure S9. Get High-res Image Gene #11: 'DEL PEAK 13(9Q21.13) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 16(11P15.1) MUTATION STATUS' versus 'AGE'

P value = 0.000502 (t-test), Q value = 0.21

Table S10. Gene #14: 'DEL PEAK 16(11P15.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	475	47.0 (15.5)
DEL PEAK 16(11P15.1) MUTATED	7	68.1 (8.7)
DEL PEAK 16(11P15.1) WILD-TYPE	468	46.7 (15.4)

Figure S10. Get High-res Image Gene #14: 'DEL PEAK 16(11P15.1) MUTATION STATUS' versus Clinical Feature #2: 'AGE'

'DEL PEAK 16(11P15.1) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.17e-07 (Chi-square test), Q value = 9.2e-05

Table S11. Gene #14: 'DEL PEAK 16(11P15.1) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	270	49	106	2	41	5
DEL PEAK 16(11P15.1) MUTATED	1	1	4	1	0	0
DEL PEAK 16(11P15.1) WILD-TYPE	269	48	102	1	41	5

Figure S11. Get High-res Image Gene #14: 'DEL PEAK 16(11P15.1) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 24(18Q22.2) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.71e-05 (t-test), Q value = 0.028

Table S12. Gene #21: 'DEL PEAK 24(18Q22.2) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 24(18Q22.2) MUTATED	5	0.4 (0.9)
DEL PEAK 24(18Q22.2) WILD-TYPE	374	3.6 (6.3)

Figure S12. Get High-res Image Gene #21: 'DEL PEAK 24(18Q22.2) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'DEL PEAK 34(XQ22.3) MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.57e-06 (Chi-square test), Q value = 0.00067

Table S13. Gene #29: 'DEL PEAK 34(XQ22.3) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	270	49	106	2	41	5
DEL PEAK 34(XQ22.3) MUTATED	0	4	0	0	0	0
DEL PEAK 34(XQ22.3) WILD-TYPE	270	45	106	2	41	5

Figure S13. Get High-res Image Gene #29: 'DEL PEAK 34(XQ22.3) MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'DEL PEAK 34(XQ22.3) MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.19e-25 (t-test), Q value = 1.8e-22

Table S14. Gene #29: 'DEL PEAK 34(XQ22.3) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	379	3.6 (6.2)
DEL PEAK 34(XQ22.3) MUTATED	4	0.0 (0.0)
DEL PEAK 34(XQ22.3) WILD-TYPE	375	3.6 (6.3)

Figure S14. Get High-res Image Gene #29: 'DEL PEAK 34(XQ22.3) MUTATION STATUS' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = THCA-TP.clin.merged.picked.txt
Number of patients = 475
Number of significantly focal cnvs = 29
Number of selected clinical features = 15
Exclude genes that fewer than K tumors have mutations, 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 tumors with and without gene mutations 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 or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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