Correlation between copy number variation genes (focal events) and molecular subtypes

Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)

17 October 2014 | analyses__2014_10_17

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1C24V92

Overview

Introduction

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

Summary

Testing the association between copy number variation 20 focal events and 6 molecular subtypes across 191 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p33 cnv correlated to 'CN_CNMF'.
amp_11q23.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_21q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
del_3p13 cnv correlated to 'CN_CNMF'.
del_5q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_7q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_12p13.2 cnv correlated to 'CN_CNMF'.
del_12q21.33 cnv correlated to 'CN_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF'.
del_17p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'CN_CNMF'.
del_18p11.21 cnv 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 focal events and 6 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 36 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	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 5q31 2	18 (9%)	173	1e-05 (0.00116)	9e-05 (0.00909)	0.00534 (0.406)	0.00084 (0.0764)	0.00077 (0.0716)	0.0013 (0.112)
del 7q34	24 (13%)	167	1e-05 (0.00116)	6e-05 (0.00618)	0.0215 (1.00)	1e-05 (0.00116)	0.0008 (0.0736)	0.00055 (0.0533)
del 7q34	24 (13%)	167	1e-05 (0.00116)	6e-05 (0.00618)	0.0216 (1.00)	2e-05 (0.00216)	0.00092 (0.0819)	0.00056 (0.0538)
del 7p12 1	16 (8%)	175	0.00019 (0.019)	0.00062 (0.0589)	0.00186 (0.154)	5e-05 (0.0052)	0.00614 (0.454)	0.00639 (0.46)
del 17p13 2	15 (8%)	176	1e-05 (0.00116)	0.00085 (0.0765)	0.0114 (0.767)	0.0002 (0.0198)	0.0865 (1.00)	0.00116 (0.102)
amp 21q22 2	14 (7%)	177	1e-05 (0.00116)	0.00214 (0.175)	0.00327 (0.262)	0.0361 (1.00)	0.00167 (0.14)	0.0673 (1.00)
amp 11q23 3	17 (9%)	174	1e-05 (0.00116)	2e-05 (0.00216)	0.373 (1.00)	0.201 (1.00)	0.746 (1.00)	0.187 (1.00)
amp 1p33	7 (4%)	184	0.00049 (0.048)	0.0116 (0.767)	0.125 (1.00)	0.13 (1.00)	0.00951 (0.656)	0.0492 (1.00)
amp 19p13 2	6 (3%)	185	0.0029 (0.235)	0.555 (1.00)	0.857 (1.00)	0.632 (1.00)	0.895 (1.00)	1 (1.00)
del 3p13	8 (4%)	183	0.00072 (0.0677)	0.297 (1.00)	0.0676 (1.00)	0.236 (1.00)	0.0365 (1.00)	0.0478 (1.00)
del 12p13 2	10 (5%)	181	2e-05 (0.00216)	0.00519 (0.4)	0.199 (1.00)	0.0723 (1.00)	0.0697 (1.00)	0.00959 (0.656)
del 12q21 33	3 (2%)	188	0.00135 (0.115)	0.304 (1.00)	0.187 (1.00)	0.587 (1.00)	0.00843 (0.59)	0.006 (0.45)
del 16q23 1	9 (5%)	182	0.00121 (0.105)	0.149 (1.00)	0.33 (1.00)	0.494 (1.00)	0.043 (1.00)	0.0657 (1.00)
del 17q11 2	13 (7%)	178	1e-05 (0.00116)	0.0224 (1.00)	0.156 (1.00)	0.00661 (0.469)	0.136 (1.00)	0.0035 (0.273)
del 18p11 21	9 (5%)	182	2e-05 (0.00216)	0.0178 (1.00)	0.382 (1.00)	0.335 (1.00)	0.213 (1.00)	0.0311 (1.00)
amp 1q43	7 (4%)	184	0.00338 (0.267)	0.0124 (0.808)	0.377 (1.00)	0.0364 (1.00)	0.137 (1.00)	0.015 (0.944)
amp 13q31 3	7 (4%)	184	0.0807 (1.00)	0.0124 (0.808)	0.067 (1.00)	0.0364 (1.00)	0.737 (1.00)	0.0566 (1.00)
amp 20q11 21	3 (2%)	188	0.00618 (0.454)	0.267 (1.00)
del 9q21 32	5 (3%)	186	0.236 (1.00)	0.516 (1.00)	0.176 (1.00)	0.602 (1.00)	0.182 (1.00)	0.105 (1.00)
del 20q13 13	4 (2%)	187	0.0288 (1.00)	0.148 (1.00)	0.787 (1.00)	0.588 (1.00)	0.126 (1.00)	0.411 (1.00)

'amp_1p33' versus 'CN_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.048

Table S1. Gene #1: 'amp_1p33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
AMP PEAK 1(1P33) MUTATED	1	3	3	0
AMP PEAK 1(1P33) WILD-TYPE	147	11	24	2

Figure S1. Get High-res Image Gene #1: 'amp_1p33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S2. Gene #3: 'amp_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
AMP PEAK 3(11Q23.3) MUTATED	0	14	3	0
AMP PEAK 3(11Q23.3) WILD-TYPE	148	0	24	2

Figure S2. Get High-res Image Gene #3: 'amp_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q23.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S3. Gene #3: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
AMP PEAK 3(11Q23.3) MUTATED	0	0	12	4	1
AMP PEAK 3(11Q23.3) WILD-TYPE	46	44	49	10	19

Figure S3. Get High-res Image Gene #3: 'amp_11q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'CN_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.23

Table S4. Gene #5: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
AMP PEAK 5(19P13.2) MUTATED	1	1	4	0
AMP PEAK 5(19P13.2) WILD-TYPE	147	13	23	2

Figure S4. Get High-res Image Gene #5: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S5. Gene #7: 'amp_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
AMP PEAK 7(21Q22.2) MUTATED	0	0	14	0
AMP PEAK 7(21Q22.2) WILD-TYPE	148	14	13	2

Figure S5. Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_21q22.2' versus 'METHLYATION_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.18

Table S6. Gene #7: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
AMP PEAK 7(21Q22.2) MUTATED	1	0	11	0	1
AMP PEAK 7(21Q22.2) WILD-TYPE	45	44	50	14	19

Figure S6. Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_21q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.14

Table S7. Gene #7: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
AMP PEAK 7(21Q22.2) MUTATED	1	4	7	0
AMP PEAK 7(21Q22.2) WILD-TYPE	57	33	34	43

Figure S7. Get High-res Image Gene #7: 'amp_21q22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.068

Table S8. Gene #8: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 2(3P13) MUTATED	2	0	6	0
DEL PEAK 2(3P13) WILD-TYPE	146	14	21	2

Figure S8. Get High-res Image Gene #8: 'del_3p13' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S9. Gene #9: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 3(5Q31.2) MUTATED	1	1	15	1
DEL PEAK 3(5Q31.2) WILD-TYPE	147	13	12	1

Figure S9. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q31.2' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0091

Table S10. Gene #9: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 3(5Q31.2) MUTATED	1	0	15	0	2
DEL PEAK 3(5Q31.2) WILD-TYPE	45	44	46	14	18

Figure S10. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.076

Table S11. Gene #9: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	16	13	14	55	26	42
DEL PEAK 3(5Q31.2) MUTATED	0	0	0	14	0	2
DEL PEAK 3(5Q31.2) WILD-TYPE	16	13	14	41	26	40

Figure S11. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.072

Table S12. Gene #9: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
DEL PEAK 3(5Q31.2) MUTATED	1	10	3	3
DEL PEAK 3(5Q31.2) WILD-TYPE	57	27	38	40

Figure S12. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.11

Table S13. Gene #9: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	34	78
DEL PEAK 3(5Q31.2) MUTATED	1	8	8
DEL PEAK 3(5Q31.2) WILD-TYPE	66	26	70

Figure S13. Get High-res Image Gene #9: 'del_5q31.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7p12.1' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.019

Table S14. Gene #10: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 4(7P12.1) MUTATED	7	0	8	1
DEL PEAK 4(7P12.1) WILD-TYPE	141	14	19	1

Figure S14. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7p12.1' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.059

Table S15. Gene #10: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 4(7P12.1) MUTATED	1	0	13	1	1
DEL PEAK 4(7P12.1) WILD-TYPE	45	44	48	13	19

Figure S15. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.15

Table S16. Gene #10: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	52	44
DEL PEAK 4(7P12.1) MUTATED	12	0	3
DEL PEAK 4(7P12.1) WILD-TYPE	58	52	41

Figure S16. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0052

Table S17. Gene #10: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	16	13	14	55	26	42
DEL PEAK 4(7P12.1) MUTATED	0	0	0	15	0	0
DEL PEAK 4(7P12.1) WILD-TYPE	16	13	14	40	26	42

Figure S17. Get High-res Image Gene #10: 'del_7p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S18. Gene #11: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 5(7Q34) MUTATED	9	2	11	2
DEL PEAK 5(7Q34) WILD-TYPE	139	12	16	0

Figure S18. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0062

Table S19. Gene #11: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 5(7Q34) MUTATED	1	1	18	2	2
DEL PEAK 5(7Q34) WILD-TYPE	45	43	43	12	18

Figure S19. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S20. Gene #11: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	16	13	14	55	26	42
DEL PEAK 5(7Q34) MUTATED	1	1	0	18	0	0
DEL PEAK 5(7Q34) WILD-TYPE	15	12	14	37	26	42

Figure S20. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.074

Table S21. Gene #11: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
DEL PEAK 5(7Q34) MUTATED	2	12	5	4
DEL PEAK 5(7Q34) WILD-TYPE	56	25	36	39

Figure S21. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.053

Table S22. Gene #11: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	34	78
DEL PEAK 5(7Q34) MUTATED	2	10	11
DEL PEAK 5(7Q34) WILD-TYPE	65	24	67

Figure S22. Get High-res Image Gene #11: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S23. Gene #12: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 6(7Q34) MUTATED	9	2	11	2
DEL PEAK 6(7Q34) WILD-TYPE	139	12	16	0

Figure S23. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q34' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0062

Table S24. Gene #12: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 6(7Q34) MUTATED	1	1	18	2	2
DEL PEAK 6(7Q34) WILD-TYPE	45	43	43	12	18

Figure S24. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S25. Gene #12: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	16	13	14	55	26	42
DEL PEAK 6(7Q34) MUTATED	1	1	0	18	0	0
DEL PEAK 6(7Q34) WILD-TYPE	15	12	14	37	26	42

Figure S25. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q34' versus 'MIRSEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.082

Table S26. Gene #12: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	58	37	41	43
DEL PEAK 6(7Q34) MUTATED	2	12	5	4
DEL PEAK 6(7Q34) WILD-TYPE	56	25	36	39

Figure S26. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.054

Table S27. Gene #12: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	34	78
DEL PEAK 6(7Q34) MUTATED	2	10	11
DEL PEAK 6(7Q34) WILD-TYPE	65	24	67

Figure S27. Get High-res Image Gene #12: 'del_7q34' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S28. Gene #14: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 10(12P13.2) MUTATED	2	0	7	1
DEL PEAK 10(12P13.2) WILD-TYPE	146	14	20	1

Figure S28. Get High-res Image Gene #14: 'del_12p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q21.33' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.11

Table S29. Gene #15: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 11(12Q21.33) MUTATED	0	0	2	1
DEL PEAK 11(12Q21.33) WILD-TYPE	148	14	25	1

Figure S29. Get High-res Image Gene #15: 'del_12q21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.11

Table S30. Gene #16: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 12(16Q23.1) MUTATED	3	0	6	0
DEL PEAK 12(16Q23.1) WILD-TYPE	145	14	21	2

Figure S30. Get High-res Image Gene #16: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S31. Gene #17: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 13(17P13.2) MUTATED	0	0	15	0
DEL PEAK 13(17P13.2) WILD-TYPE	148	14	12	2

Figure S31. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.076

Table S32. Gene #17: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	46	44	61	14	20
DEL PEAK 13(17P13.2) MUTATED	0	1	12	0	2
DEL PEAK 13(17P13.2) WILD-TYPE	46	43	49	14	18

Figure S32. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.02

Table S33. Gene #17: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	16	13	14	55	26	42
DEL PEAK 13(17P13.2) MUTATED	0	0	0	14	0	1
DEL PEAK 13(17P13.2) WILD-TYPE	16	13	14	41	26	41

Figure S33. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.1

Table S34. Gene #17: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	67	34	78
DEL PEAK 13(17P13.2) MUTATED	0	5	10
DEL PEAK 13(17P13.2) WILD-TYPE	67	29	68

Figure S34. Get High-res Image Gene #17: 'del_17p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0012

Table S35. Gene #18: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 14(17Q11.2) MUTATED	2	2	9	0
DEL PEAK 14(17Q11.2) WILD-TYPE	146	12	18	2

Figure S35. Get High-res Image Gene #18: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18p11.21' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0022

Table S36. Gene #19: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	14	27	2
DEL PEAK 15(18P11.21) MUTATED	1	0	8	0
DEL PEAK 15(18P11.21) WILD-TYPE	147	14	19	2

Figure S36. Get High-res Image Gene #19: 'del_18p11.21' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = LAML-TB.transferedmergedcluster.txt
Number of patients = 191
Number of significantly focal cnvs = 20
Number of molecular subtypes = 6
Exclude genes that fewer than K tumors have alterations, K = 3

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] 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)

[2] 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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