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

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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