Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 20 peak regions and 6 molecular subtypes across 191 patients, 38 significant findings detected with Q value < 0.25.

Amp Peak 1(1p33) cnvs correlated to 'CN_CNMF'.
Amp Peak 2(1q43) cnvs correlated to 'METHLYATION_CNMF'.
Amp Peak 3(11q23.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 4(13q31.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(20q11.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(21q22.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 2(3p13) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 4(5q31.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 5(7p12.1) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 6(7q32.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 7(7q34) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 10(12p13.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 12(16q23.1) cnvs correlated to 'CN_CNMF'.
Del Peak 13(17p13.2) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Del Peak 14(17q11.2) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 15(18p11.21) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 16(20q13.13) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 20 regions and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 38 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Chi-square test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 4(5q31 2)	18 (9%)	173	6.32e-15 (7.27e-13)	5.31e-07 (5.62e-05)	0.0053 (0.397)	0.0923 (1.00)	0.00131 (0.117)	0.000764 (0.0702)
Del Peak 5(7p12 1)	16 (8%)	175	2.4e-07 (2.64e-05)	1.06e-05 (0.00108)	0.00179 (0.152)	0.00272 (0.217)	0.0046 (0.349)	0.0037 (0.285)
Del Peak 6(7q32 3)	23 (12%)	168	8.78e-07 (9.22e-05)	1.44e-05 (0.00145)	0.0384 (1.00)	0.022 (1.00)	0.000422 (0.0401)	0.000296 (0.0284)
Del Peak 7(7q34)	24 (13%)	167	2.83e-06 (0.000295)	3.61e-06 (0.000372)	0.0221 (1.00)	0.0212 (1.00)	9.94e-05 (0.00965)	8.56e-05 (0.00839)
Del Peak 2(3p13)	9 (5%)	182	0.00179 (0.152)	0.0384 (1.00)	0.0349 (1.00)	0.718 (1.00)	0.00258 (0.209)	0.00208 (0.173)
Del Peak 13(17p13 2)	15 (8%)	176	1.68e-14 (1.91e-12)	2.27e-05 (0.00225)	0.0113 (0.754)	0.0211 (1.00)	0.0476 (1.00)	0.00175 (0.15)
Amp Peak 3(11q23 3)	17 (9%)	174	4.87e-33 (5.7e-31)	0.00119 (0.107)	0.373 (1.00)	0.784 (1.00)	1 (1.00)	0.847 (1.00)
Amp Peak 6(21q22 2)	14 (7%)	177	9.35e-32 (1.08e-29)	0.000948 (0.0862)	0.00336 (0.265)	0.337 (1.00)	0.0107 (0.726)	0.0185 (1.00)
Del Peak 10(12p13 2)	10 (5%)	181	8.25e-13 (9.33e-11)	0.0022 (0.18)	0.197 (1.00)	0.167 (1.00)	0.0962 (1.00)	0.0241 (1.00)
Del Peak 14(17q11 2)	13 (7%)	178	1.72e-05 (0.00172)	0.00138 (0.12)	0.156 (1.00)	0.222 (1.00)	0.154 (1.00)	0.0093 (0.657)
Del Peak 15(18p11 21)	9 (5%)	182	4.63e-07 (5e-05)	0.000742 (0.069)	0.381 (1.00)	0.718 (1.00)	0.149 (1.00)	0.0974 (1.00)
Amp Peak 1(1p33)	7 (4%)	184	4.86e-07 (5.2e-05)	0.00924 (0.657)	0.124 (1.00)	0.665 (1.00)	0.111 (1.00)	0.238 (1.00)
Amp Peak 2(1q43)	7 (4%)	184	0.0063 (0.466)	0.000527 (0.0496)	0.373 (1.00)	0.425 (1.00)	0.323 (1.00)	0.171 (1.00)
Amp Peak 4(13q31 3)	7 (4%)	184	1.96e-10 (2.2e-08)	0.00924 (0.657)	0.0668 (1.00)	0.0965 (1.00)	0.682 (1.00)	0.2 (1.00)
Amp Peak 5(20q11 21)	3 (2%)	188	0.00135 (0.119)	0.101 (1.00)		0.55 (1.00)
Del Peak 12(16q23 1)	9 (5%)	182	2.61e-07 (2.84e-05)	0.0121 (0.798)	0.332 (1.00)	1 (1.00)	0.0529 (1.00)	0.0822 (1.00)
Del Peak 16(20q13 13)	4 (2%)	187	9.73e-10 (1.08e-07)	0.0302 (1.00)	0.786 (1.00)	1 (1.00)	0.213 (1.00)	0.227 (1.00)
Del Peak 3(3q26 31)	3 (2%)	188	0.00355 (0.277)	0.101 (1.00)	0.786 (1.00)	1 (1.00)	0.0841 (1.00)	0.094 (1.00)
Del Peak 9(9q21 32)	5 (3%)	186	0.63 (1.00)	0.731 (1.00)	0.176 (1.00)	0.664 (1.00)	0.138 (1.00)	0.115 (1.00)
Del Peak 11(12q21 33)	3 (2%)	188	0.057 (1.00)	0.529 (1.00)	0.186 (1.00)	0.552 (1.00)	0.00913 (0.657)	0.00841 (0.614)

'Amp Peak 1(1p33) mutation analysis' versus 'CN_CNMF'

P value = 4.86e-07 (Chi-square test), Q value = 5.2e-05

Table S1. Gene #1: 'Amp Peak 1(1p33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 1(1P33) MUTATED	0	3	0	4	0
AMP PEAK 1(1P33) WILD-TYPE	142	12	15	14	1

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(1p33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 2(1q43) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000527 (Chi-square test), Q value = 0.05

Table S2. Gene #2: 'Amp Peak 2(1q43) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
AMP PEAK 2(1Q43) MUTATED	0	0	0	0	7	0
AMP PEAK 2(1Q43) WILD-TYPE	46	18	26	36	39	13

Figure S2. Get High-res Image Gene #2: 'Amp Peak 2(1q43) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 3(11q23.3) mutation analysis' versus 'CN_CNMF'

P value = 4.87e-33 (Chi-square test), Q value = 5.7e-31

Table S3. Gene #3: 'Amp Peak 3(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 3(11Q23.3) MUTATED	0	14	0	2	1
AMP PEAK 3(11Q23.3) WILD-TYPE	142	1	15	16	0

Figure S3. Get High-res Image Gene #3: 'Amp Peak 3(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 3(11q23.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00119 (Chi-square test), Q value = 0.11

Table S4. Gene #3: 'Amp Peak 3(11q23.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
AMP PEAK 3(11Q23.3) MUTATED	0	0	3	1	10	3
AMP PEAK 3(11Q23.3) WILD-TYPE	46	18	23	35	36	10

Figure S4. Get High-res Image Gene #3: 'Amp Peak 3(11q23.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 4(13q31.3) mutation analysis' versus 'CN_CNMF'

P value = 1.96e-10 (Chi-square test), Q value = 2.2e-08

Table S5. Gene #4: 'Amp Peak 4(13q31.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 4(13Q31.3) MUTATED	0	1	0	6	0
AMP PEAK 4(13Q31.3) WILD-TYPE	142	14	15	12	1

Figure S5. Get High-res Image Gene #4: 'Amp Peak 4(13q31.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(20q11.21) mutation analysis' versus 'CN_CNMF'

P value = 0.00135 (Chi-square test), Q value = 0.12

Table S6. Gene #5: 'Amp Peak 5(20q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 5(20Q11.21) MUTATED	0	0	2	1	0
AMP PEAK 5(20Q11.21) WILD-TYPE	142	15	13	17	1

Figure S6. Get High-res Image Gene #5: 'Amp Peak 5(20q11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(21q22.2) mutation analysis' versus 'CN_CNMF'

P value = 9.35e-32 (Chi-square test), Q value = 1.1e-29

Table S7. Gene #6: 'Amp Peak 6(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
AMP PEAK 6(21Q22.2) MUTATED	0	0	13	1	0
AMP PEAK 6(21Q22.2) WILD-TYPE	142	15	2	17	1

Figure S7. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(21q22.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000948 (Chi-square test), Q value = 0.086

Table S8. Gene #6: 'Amp Peak 6(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
AMP PEAK 6(21Q22.2) MUTATED	1	0	1	1	10	0
AMP PEAK 6(21Q22.2) WILD-TYPE	45	18	25	35	36	13

Figure S8. Get High-res Image Gene #6: 'Amp Peak 6(21q22.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 2(3p13) mutation analysis' versus 'CN_CNMF'

P value = 0.00179 (Chi-square test), Q value = 0.15

Table S9. Gene #7: 'Del Peak 2(3p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 2(3P13) MUTATED	2	1	3	3	0
DEL PEAK 2(3P13) WILD-TYPE	140	14	12	15	1

Figure S9. Get High-res Image Gene #7: 'Del Peak 2(3p13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(3p13) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00258 (Fisher's exact test), Q value = 0.21

Table S10. Gene #7: 'Del Peak 2(3p13) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	38	57
DEL PEAK 2(3P13) MUTATED	0	5	3
DEL PEAK 2(3P13) WILD-TYPE	83	33	54

Figure S10. Get High-res Image Gene #7: 'Del Peak 2(3p13) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 2(3p13) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00208 (Fisher's exact test), Q value = 0.17

Table S11. Gene #7: 'Del Peak 2(3p13) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	79	62
DEL PEAK 2(3P13) MUTATED	5	0	3
DEL PEAK 2(3P13) WILD-TYPE	32	79	59

Figure S11. Get High-res Image Gene #7: 'Del Peak 2(3p13) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 4(5q31.2) mutation analysis' versus 'CN_CNMF'

P value = 6.32e-15 (Chi-square test), Q value = 7.3e-13

Table S12. Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 4(5Q31.2) MUTATED	1	1	7	8	1
DEL PEAK 4(5Q31.2) WILD-TYPE	141	14	8	10	0

Figure S12. Get High-res Image Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 4(5q31.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 5.31e-07 (Chi-square test), Q value = 5.6e-05

Table S13. Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 4(5Q31.2) MUTATED	1	0	0	2	15	0
DEL PEAK 4(5Q31.2) WILD-TYPE	45	18	26	34	31	13

Figure S13. Get High-res Image Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 4(5q31.2) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.12

Table S14. Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	38	57
DEL PEAK 4(5Q31.2) MUTATED	4	10	3
DEL PEAK 4(5Q31.2) WILD-TYPE	79	28	54

Figure S14. Get High-res Image Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 4(5q31.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000764 (Fisher's exact test), Q value = 0.07

Table S15. Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	79	62
DEL PEAK 4(5Q31.2) MUTATED	10	3	4
DEL PEAK 4(5Q31.2) WILD-TYPE	27	76	58

Figure S15. Get High-res Image Gene #9: 'Del Peak 4(5q31.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 5(7p12.1) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-07 (Chi-square test), Q value = 2.6e-05

Table S16. Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 5(7P12.1) MUTATED	7	1	0	7	1
DEL PEAK 5(7P12.1) WILD-TYPE	135	14	15	11	0

Figure S16. Get High-res Image Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 5(7p12.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.06e-05 (Chi-square test), Q value = 0.0011

Table S17. Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 5(7P12.1) MUTATED	1	0	1	0	13	1
DEL PEAK 5(7P12.1) WILD-TYPE	45	18	25	36	33	12

Figure S17. Get High-res Image Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 5(7p12.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.15

Table S18. Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	52	44
DEL PEAK 5(7P12.1) MUTATED	12	0	3
DEL PEAK 5(7P12.1) WILD-TYPE	58	52	41

Figure S18. Get High-res Image Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #3: 'MRNASEQ_CNMF'

'Del Peak 5(7p12.1) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.22

Table S19. Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	110	56
DEL PEAK 5(7P12.1) MUTATED	15	0
DEL PEAK 5(7P12.1) WILD-TYPE	95	56

Figure S19. Get High-res Image Gene #10: 'Del Peak 5(7p12.1) mutation analysis' versus Clinical Feature #4: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 6(7q32.3) mutation analysis' versus 'CN_CNMF'

P value = 8.78e-07 (Chi-square test), Q value = 9.2e-05

Table S20. Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 6(7Q32.3) MUTATED	7	3	5	7	1
DEL PEAK 6(7Q32.3) WILD-TYPE	135	12	10	11	0

Figure S20. Get High-res Image Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 6(7q32.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.44e-05 (Chi-square test), Q value = 0.0015

Table S21. Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 6(7Q32.3) MUTATED	1	1	2	1	16	2
DEL PEAK 6(7Q32.3) WILD-TYPE	45	17	24	35	30	11

Figure S21. Get High-res Image Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 6(7q32.3) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000422 (Fisher's exact test), Q value = 0.04

Table S22. Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	38	57
DEL PEAK 6(7Q32.3) MUTATED	4	12	6
DEL PEAK 6(7Q32.3) WILD-TYPE	79	26	51

Figure S22. Get High-res Image Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 6(7q32.3) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000296 (Fisher's exact test), Q value = 0.028

Table S23. Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	79	62
DEL PEAK 6(7Q32.3) MUTATED	12	4	6
DEL PEAK 6(7Q32.3) WILD-TYPE	25	75	56

Figure S23. Get High-res Image Gene #11: 'Del Peak 6(7q32.3) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 7(7q34) mutation analysis' versus 'CN_CNMF'

P value = 2.83e-06 (Chi-square test), Q value = 0.00029

Table S24. Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 7(7Q34) MUTATED	8	3	5	7	1
DEL PEAK 7(7Q34) WILD-TYPE	134	12	10	11	0

Figure S24. Get High-res Image Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 7(7q34) mutation analysis' versus 'METHLYATION_CNMF'

P value = 3.61e-06 (Chi-square test), Q value = 0.00037

Table S25. Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 7(7Q34) MUTATED	1	1	2	1	17	2
DEL PEAK 7(7Q34) WILD-TYPE	45	17	24	35	29	11

Figure S25. Get High-res Image Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 7(7q34) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 9.94e-05 (Fisher's exact test), Q value = 0.0096

Table S26. Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	83	38	57
DEL PEAK 7(7Q34) MUTATED	4	13	6
DEL PEAK 7(7Q34) WILD-TYPE	79	25	51

Figure S26. Get High-res Image Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #5: 'MIRSEQ_CNMF'

'Del Peak 7(7q34) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8.56e-05 (Fisher's exact test), Q value = 0.0084

Table S27. Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	79	62
DEL PEAK 7(7Q34) MUTATED	13	4	6
DEL PEAK 7(7Q34) WILD-TYPE	24	75	56

Figure S27. Get High-res Image Gene #12: 'Del Peak 7(7q34) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 10(12p13.2) mutation analysis' versus 'CN_CNMF'

P value = 8.25e-13 (Chi-square test), Q value = 9.3e-11

Table S28. Gene #14: 'Del Peak 10(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 10(12P13.2) MUTATED	1	1	0	8	0
DEL PEAK 10(12P13.2) WILD-TYPE	141	14	15	10	1

Figure S28. Get High-res Image Gene #14: 'Del Peak 10(12p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(12p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.0022 (Chi-square test), Q value = 0.18

Table S29. Gene #14: 'Del Peak 10(12p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 10(12P13.2) MUTATED	0	0	0	1	8	1
DEL PEAK 10(12P13.2) WILD-TYPE	46	18	26	35	38	12

Figure S29. Get High-res Image Gene #14: 'Del Peak 10(12p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 12(16q23.1) mutation analysis' versus 'CN_CNMF'

P value = 2.61e-07 (Chi-square test), Q value = 2.8e-05

Table S30. Gene #16: 'Del Peak 12(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 12(16Q23.1) MUTATED	2	1	1	4	1
DEL PEAK 12(16Q23.1) WILD-TYPE	140	14	14	14	0

Figure S30. Get High-res Image Gene #16: 'Del Peak 12(16q23.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(17p13.2) mutation analysis' versus 'CN_CNMF'

P value = 1.68e-14 (Chi-square test), Q value = 1.9e-12

Table S31. Gene #17: 'Del Peak 13(17p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 13(17P13.2) MUTATED	0	1	5	8	1
DEL PEAK 13(17P13.2) WILD-TYPE	142	14	10	10	0

Figure S31. Get High-res Image Gene #17: 'Del Peak 13(17p13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(17p13.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 2.27e-05 (Chi-square test), Q value = 0.0022

Table S32. Gene #17: 'Del Peak 13(17p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 13(17P13.2) MUTATED	0	0	0	3	12	0
DEL PEAK 13(17P13.2) WILD-TYPE	46	18	26	33	34	13

Figure S32. Get High-res Image Gene #17: 'Del Peak 13(17p13.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 13(17p13.2) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00175 (Fisher's exact test), Q value = 0.15

Table S33. Gene #17: 'Del Peak 13(17p13.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	79	62
DEL PEAK 13(17P13.2) MUTATED	7	1	7
DEL PEAK 13(17P13.2) WILD-TYPE	30	78	55

Figure S33. Get High-res Image Gene #17: 'Del Peak 13(17p13.2) mutation analysis' versus Clinical Feature #6: 'MIRSEQ_CHIERARCHICAL'

'Del Peak 14(17q11.2) mutation analysis' versus 'CN_CNMF'

P value = 1.72e-05 (Chi-square test), Q value = 0.0017

Table S34. Gene #18: 'Del Peak 14(17q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 14(17Q11.2) MUTATED	2	3	3	5	0
DEL PEAK 14(17Q11.2) WILD-TYPE	140	12	12	13	1

Figure S34. Get High-res Image Gene #18: 'Del Peak 14(17q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(17q11.2) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.00138 (Chi-square test), Q value = 0.12

Table S35. Gene #18: 'Del Peak 14(17q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 14(17Q11.2) MUTATED	0	0	0	4	9	0
DEL PEAK 14(17Q11.2) WILD-TYPE	46	18	26	32	37	13

Figure S35. Get High-res Image Gene #18: 'Del Peak 14(17q11.2) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 15(18p11.21) mutation analysis' versus 'CN_CNMF'

P value = 4.63e-07 (Chi-square test), Q value = 5e-05

Table S36. Gene #19: 'Del Peak 15(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 15(18P11.21) MUTATED	1	0	3	5	0
DEL PEAK 15(18P11.21) WILD-TYPE	141	15	12	13	1

Figure S36. Get High-res Image Gene #19: 'Del Peak 15(18p11.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(18p11.21) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000742 (Chi-square test), Q value = 0.069

Table S37. Gene #19: 'Del Peak 15(18p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	46	18	26	36	46	13
DEL PEAK 15(18P11.21) MUTATED	0	0	0	1	8	0
DEL PEAK 15(18P11.21) WILD-TYPE	46	18	26	35	38	13

Figure S37. Get High-res Image Gene #19: 'Del Peak 15(18p11.21) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 16(20q13.13) mutation analysis' versus 'CN_CNMF'

P value = 9.73e-10 (Chi-square test), Q value = 1.1e-07

Table S38. Gene #20: 'Del Peak 16(20q13.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	142	15	15	18	1
DEL PEAK 16(20Q13.13) MUTATED	0	0	4	0	0
DEL PEAK 16(20Q13.13) WILD-TYPE	142	15	11	18	1

Figure S38. Get High-res Image Gene #20: 'Del Peak 16(20q13.13) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = LAML-TB.transferedmergedcluster.txt
Number of patients = 191
Number of copy number variation regions = 20
Number of molecular subtypes = 6
Exclude regions that fewer than K tumors have alterations, K = 3

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.

References

[1] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[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)

[4] GISTIC_version2

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