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

Thymoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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 (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C14X5729

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 12 focal events and 8 clinical features across 123 patients, 27 significant findings detected with Q value < 0.25.

del_2q37.1 cnv correlated to 'TUMOR_TISSUE_SITE' and 'ETHNICITY'.
del_3p22.2 cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
del_6p25.2 cnv correlated to 'Time to Death', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_6q21 cnv correlated to 'Time to Death', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_7q36.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
del_9p21.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
del_9q22.33 cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.
del_11q22.1 cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_19p13.11 cnv correlated to 'YEARS_TO_BIRTH', 'TUMOR_TISSUE_SITE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_22q12.1 cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_22q13.32 cnv correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 12 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 27 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	TUMOR TISSUE SITE	GENDER	RADIATION THERAPY	HISTOLOGICAL TYPE	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-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
del 19p13 11	5 (4%)	118	0.675 (0.887)	0.0628 (0.249)	0.0699 (0.249)	0.193 (0.515)	1 (1.00)	7e-05 (0.00336)	1 (1.00)	0.0535 (0.233)
del 6p25 2	26 (21%)	97	0.00445 (0.061)	0.718 (0.906)	1 (1.00)	1 (1.00)	0.645 (0.88)	0.0035 (0.0587)	0.277 (0.605)	0.0236 (0.119)
del 6q21	20 (16%)	103	0.0579 (0.242)	0.187 (0.514)	0.379 (0.714)	0.626 (0.88)	0.609 (0.88)	0.00011 (0.00352)	0.502 (0.803)	0.00593 (0.0633)
del 11q22 1	7 (6%)	116	0.439 (0.745)	0.014 (0.0843)	0.178 (0.514)	0.442 (0.745)	0.229 (0.538)	0.00586 (0.0633)	0.705 (0.903)	0.0118 (0.077)
del 22q12 1	19 (15%)	104	0.37 (0.71)	0.0102 (0.077)	0.128 (0.41)	0.455 (0.753)	0.797 (0.968)	0.0686 (0.249)	0.87 (1.00)	0.00777 (0.0745)
del 22q13 32	15 (12%)	108	0.763 (0.952)	0.0284 (0.136)	0.0947 (0.325)	0.411 (0.745)	0.144 (0.446)	0.00925 (0.077)	1 (1.00)	0.0199 (0.106)
del 2q37 1	5 (4%)	118	0.625 (0.88)	0.333 (0.665)	0.0699 (0.249)	1 (1.00)	0.66 (0.88)	0.434 (0.745)	0.304 (0.635)	0.00367 (0.0587)
del 3p22 2	14 (11%)	109	0.199 (0.516)	0.656 (0.88)	0.187 (0.514)	1 (1.00)	0.552 (0.841)	0.012 (0.077)	1 (1.00)	0.0113 (0.077)
del 9q22 33	3 (2%)	120	0.000332 (0.00796)	0.329 (0.665)	0.528 (0.817)	1 (1.00)	0.268 (0.599)	0.0155 (0.0878)	1 (1.00)	0.23 (0.538)
del 7q36 3	3 (2%)	120	0.777 (0.957)	0.62 (0.88)	0.528 (0.817)	0.607 (0.88)	0.268 (0.599)	0.0459 (0.21)	1 (1.00)	0.23 (0.538)
del 9p21 3	11 (9%)	112	0.471 (0.766)	0.122 (0.403)	0.705 (0.903)	0.35 (0.686)	1 (1.00)	1e-05 (0.00096)	1 (1.00)	0.225 (0.538)
del 10q26 3	6 (5%)	117	0.172 (0.514)	0.845 (1.00)	1 (1.00)	0.425 (0.745)	1 (1.00)	0.296 (0.631)	0.65 (0.88)	0.411 (0.745)

'del_2q37.1' versus 'TUMOR_TISSUE_SITE'

P value = 0.0699 (Fisher's exact test), Q value = 0.25

Table S1. Gene #1: 'del_2q37.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	ANTERIOR MEDIASTINUM	THYMUS
ALL	27	96
DEL PEAK 1(2Q37.1) MUTATED	3	2
DEL PEAK 1(2Q37.1) WILD-TYPE	24	94

Figure S1. Get High-res Image Gene #1: 'del_2q37.1' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_2q37.1' versus 'ETHNICITY'

P value = 0.00367 (Fisher's exact test), Q value = 0.059

Table S2. Gene #1: 'del_2q37.1' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 1(2Q37.1) MUTATED	3	2
DEL PEAK 1(2Q37.1) WILD-TYPE	6	98

Figure S2. Get High-res Image Gene #1: 'del_2q37.1' versus Clinical Feature #8: 'ETHNICITY'

'del_3p22.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.012 (Fisher's exact test), Q value = 0.077

Table S3. Gene #2: 'del_3p22.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 2(3P22.2) MUTATED	0	2	0	6	4	2
DEL PEAK 2(3P22.2) WILD-TYPE	17	36	15	24	8	9

Figure S3. Get High-res Image Gene #2: 'del_3p22.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_3p22.2' versus 'ETHNICITY'

P value = 0.0113 (Fisher's exact test), Q value = 0.077

Table S4. Gene #2: 'del_3p22.2' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 2(3P22.2) MUTATED	4	9
DEL PEAK 2(3P22.2) WILD-TYPE	5	91

Figure S4. Get High-res Image Gene #2: 'del_3p22.2' versus Clinical Feature #8: 'ETHNICITY'

'del_6p25.2' versus 'Time to Death'

P value = 0.00445 (logrank test), Q value = 0.061

Table S5. Gene #3: 'del_6p25.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	122	9	0.5 - 150.0 (40.6)
DEL PEAK 3(6P25.2) MUTATED	25	5	4.1 - 120.4 (31.9)
DEL PEAK 3(6P25.2) WILD-TYPE	97	4	0.5 - 150.0 (42.1)

Figure S5. Get High-res Image Gene #3: 'del_6p25.2' versus Clinical Feature #1: 'Time to Death'

'del_6p25.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0035 (Fisher's exact test), Q value = 0.059

Table S6. Gene #3: 'del_6p25.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 3(6P25.2) MUTATED	2	5	0	8	5	6
DEL PEAK 3(6P25.2) WILD-TYPE	15	33	15	22	7	5

Figure S6. Get High-res Image Gene #3: 'del_6p25.2' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6p25.2' versus 'ETHNICITY'

P value = 0.0236 (Fisher's exact test), Q value = 0.12

Table S7. Gene #3: 'del_6p25.2' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 3(6P25.2) MUTATED	5	19
DEL PEAK 3(6P25.2) WILD-TYPE	4	81

Figure S7. Get High-res Image Gene #3: 'del_6p25.2' versus Clinical Feature #8: 'ETHNICITY'

'del_6q21' versus 'Time to Death'

P value = 0.0579 (logrank test), Q value = 0.24

Table S8. Gene #4: 'del_6q21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	122	9	0.5 - 150.0 (40.6)
DEL PEAK 4(6Q21) MUTATED	20	3	10.4 - 97.4 (30.0)
DEL PEAK 4(6Q21) WILD-TYPE	102	6	0.5 - 150.0 (41.7)

Figure S8. Get High-res Image Gene #4: 'del_6q21' versus Clinical Feature #1: 'Time to Death'

'del_6q21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0035

Table S9. Gene #4: 'del_6q21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 4(6Q21) MUTATED	0	2	0	8	5	5
DEL PEAK 4(6Q21) WILD-TYPE	17	36	15	22	7	6

Figure S9. Get High-res Image Gene #4: 'del_6q21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_6q21' versus 'ETHNICITY'

P value = 0.00593 (Fisher's exact test), Q value = 0.063

Table S10. Gene #4: 'del_6q21' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 4(6Q21) MUTATED	5	13
DEL PEAK 4(6Q21) WILD-TYPE	4	87

Figure S10. Get High-res Image Gene #4: 'del_6q21' versus Clinical Feature #8: 'ETHNICITY'

'del_7q36.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0459 (Fisher's exact test), Q value = 0.21

Table S11. Gene #5: 'del_7q36.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 5(7Q36.3) MUTATED	0	0	0	1	0	2
DEL PEAK 5(7Q36.3) WILD-TYPE	17	38	15	29	12	9

Figure S11. Get High-res Image Gene #5: 'del_7q36.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00096

Table S12. Gene #6: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 6(9P21.3) MUTATED	1	1	0	0	2	7
DEL PEAK 6(9P21.3) WILD-TYPE	16	37	15	30	10	4

Figure S12. Get High-res Image Gene #6: 'del_9p21.3' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_9q22.33' versus 'Time to Death'

P value = 0.000332 (logrank test), Q value = 0.008

Table S13. Gene #7: 'del_9q22.33' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	122	9	0.5 - 150.0 (40.6)
DEL PEAK 7(9Q22.33) MUTATED	3	1	5.9 - 21.1 (21.1)
DEL PEAK 7(9Q22.33) WILD-TYPE	119	8	0.5 - 150.0 (42.1)

Figure S13. Get High-res Image Gene #7: 'del_9q22.33' versus Clinical Feature #1: 'Time to Death'

'del_9q22.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0155 (Fisher's exact test), Q value = 0.088

Table S14. Gene #7: 'del_9q22.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 7(9Q22.33) MUTATED	1	0	0	0	0	2
DEL PEAK 7(9Q22.33) WILD-TYPE	16	38	15	30	12	9

Figure S14. Get High-res Image Gene #7: 'del_9q22.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_11q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.014 (Wilcoxon-test), Q value = 0.084

Table S15. Gene #9: 'del_11q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	122	58.3 (13.0)
DEL PEAK 9(11Q22.1) MUTATED	7	44.4 (16.5)
DEL PEAK 9(11Q22.1) WILD-TYPE	115	59.1 (12.4)

Figure S15. Get High-res Image Gene #9: 'del_11q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00586 (Fisher's exact test), Q value = 0.063

Table S16. Gene #9: 'del_11q22.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 9(11Q22.1) MUTATED	0	0	0	4	3	0
DEL PEAK 9(11Q22.1) WILD-TYPE	17	38	15	26	9	11

Figure S16. Get High-res Image Gene #9: 'del_11q22.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_11q22.1' versus 'ETHNICITY'

P value = 0.0118 (Fisher's exact test), Q value = 0.077

Table S17. Gene #9: 'del_11q22.1' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 9(11Q22.1) MUTATED	3	4
DEL PEAK 9(11Q22.1) WILD-TYPE	6	96

Figure S17. Get High-res Image Gene #9: 'del_11q22.1' versus Clinical Feature #8: 'ETHNICITY'

'del_19p13.11' versus 'YEARS_TO_BIRTH'

P value = 0.0628 (Wilcoxon-test), Q value = 0.25

Table S18. Gene #10: 'del_19p13.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	122	58.3 (13.0)
DEL PEAK 10(19P13.11) MUTATED	5	68.2 (4.0)
DEL PEAK 10(19P13.11) WILD-TYPE	117	57.8 (13.1)

Figure S18. Get High-res Image Gene #10: 'del_19p13.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19p13.11' versus 'TUMOR_TISSUE_SITE'

P value = 0.0699 (Fisher's exact test), Q value = 0.25

Table S19. Gene #10: 'del_19p13.11' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients	ANTERIOR MEDIASTINUM	THYMUS
ALL	27	96
DEL PEAK 10(19P13.11) MUTATED	3	2
DEL PEAK 10(19P13.11) WILD-TYPE	24	94

Figure S19. Get High-res Image Gene #10: 'del_19p13.11' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'del_19p13.11' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0034

Table S20. Gene #10: 'del_19p13.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 10(19P13.11) MUTATED	0	0	0	0	1	4
DEL PEAK 10(19P13.11) WILD-TYPE	17	38	15	30	11	7

Figure S20. Get High-res Image Gene #10: 'del_19p13.11' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_19p13.11' versus 'ETHNICITY'

P value = 0.0535 (Fisher's exact test), Q value = 0.23

Table S21. Gene #10: 'del_19p13.11' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 10(19P13.11) MUTATED	2	3
DEL PEAK 10(19P13.11) WILD-TYPE	7	97

Figure S21. Get High-res Image Gene #10: 'del_19p13.11' versus Clinical Feature #8: 'ETHNICITY'

'del_22q12.1' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.077

Table S22. Gene #11: 'del_22q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	122	58.3 (13.0)
DEL PEAK 11(22Q12.1) MUTATED	18	65.3 (11.3)
DEL PEAK 11(22Q12.1) WILD-TYPE	104	57.0 (12.9)

Figure S22. Get High-res Image Gene #11: 'del_22q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q12.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0686 (Fisher's exact test), Q value = 0.25

Table S23. Gene #11: 'del_22q12.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 11(22Q12.1) MUTATED	5	6	0	2	3	3
DEL PEAK 11(22Q12.1) WILD-TYPE	12	32	15	28	9	8

Figure S23. Get High-res Image Gene #11: 'del_22q12.1' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_22q12.1' versus 'ETHNICITY'

P value = 0.00777 (Fisher's exact test), Q value = 0.075

Table S24. Gene #11: 'del_22q12.1' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 11(22Q12.1) MUTATED	5	14
DEL PEAK 11(22Q12.1) WILD-TYPE	4	86

Figure S24. Get High-res Image Gene #11: 'del_22q12.1' versus Clinical Feature #8: 'ETHNICITY'

'del_22q13.32' versus 'YEARS_TO_BIRTH'

P value = 0.0284 (Wilcoxon-test), Q value = 0.14

Table S25. Gene #12: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	122	58.3 (13.0)
DEL PEAK 12(22Q13.32) MUTATED	15	64.7 (11.2)
DEL PEAK 12(22Q13.32) WILD-TYPE	107	57.4 (13.0)

Figure S25. Get High-res Image Gene #12: 'del_22q13.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 0.00925 (Fisher's exact test), Q value = 0.077

Table S26. Gene #12: 'del_22q13.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients	THYMOMA; TYPE A	THYMOMA; TYPE AB	THYMOMA; TYPE B1	THYMOMA; TYPE B2	THYMOMA; TYPE B3	THYMOMA; TYPE C
ALL	17	38	15	30	12	11
DEL PEAK 12(22Q13.32) MUTATED	2	3	0	2	3	5
DEL PEAK 12(22Q13.32) WILD-TYPE	15	35	15	28	9	6

Figure S26. Get High-res Image Gene #12: 'del_22q13.32' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'ETHNICITY'

P value = 0.0199 (Fisher's exact test), Q value = 0.11

Table S27. Gene #12: 'del_22q13.32' versus Clinical Feature #8: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	9	100
DEL PEAK 12(22Q13.32) MUTATED	4	11
DEL PEAK 12(22Q13.32) WILD-TYPE	5	89

Figure S27. Get High-res Image Gene #12: 'del_22q13.32' versus Clinical Feature #8: 'ETHNICITY'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/19781936/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THYM-TP/19775615/THYM-TP.merged_data.txt
Number of patients = 123
Number of significantly focal cnvs = 12
Number of selected clinical features = 8
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

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] 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)

[3] 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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