SNP6 Copy number analysis (GISTIC2)
Sarcoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1C827RR
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1C827RR
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.20 (Firehose task version: 126).

Summary

There were 127 tumor samples used in this analysis: 12 significant arm-level results, 17 significant focal amplifications, and 37 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 17 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
12q15 | 5.3431e-56 | 5.3431e-56 | chr12:69178021-69244387 | 1
1q24.3 | 7.0489e-15 | 7.0489e-15 | chr1:172019584-172206659 | 6
17p12 | 6.872e-08 | 6.872e-08 | chr17:11702856-15565257 | 25
6q24.3 | 3.9825e-07 | 3.9825e-07 | chr6:148810209-149693709 | 4
1p32.1 | 8.2855e-07 | 8.2855e-07 | chr1:58611919-59952427 | 8
5p15.33 | 0.0019208 | 0.0019208 | chr5:1019815-1300024 | 6
19q12 | 0.0020378 | 0.0020378 | chr19:30245403-30326293 | 1
6p21.1 | 0.0027446 | 0.0027446 | chr6:42316793-42577711 | 2
11q22.2 | 0.004862 | 0.004862 | chr11:101789694-102572619 | 9
19p13.2 | 0.0066591 | 0.0066591 | chr19:9780258-10329244 | 19
Xq21.1 | 0.022036 | 0.022036 | chrX:80178943-85674259 | 15
12p13.32 | 0.028294 | 0.028294 | chr12:4747451-5507248 | 6
3p11.2 | 0.029098 | 0.029098 | chr3:85487213-93734670 | 13
Xp21.1 | 0.079127 | 0.079127 | chrX:1-62179667 | 395
8q21.12 | 0.10178 | 0.10178 | chr8:74064911-90343200 | 61
20q12 | 0.15462 | 0.15462 | chr20:37374217-40360023 | 12
7p21.3 | 0.16545 | 0.16545 | chr7:4818271-11029669 | 52

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q15.

Table S1. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MDM2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q24.3.

Table S2. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-199a-2
DNM3
MIR199A2
MIR214
MIR3120
DNM3OS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p12.

Table S3. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MAP2K4
hsa-mir-548h-3
hsa-mir-744
COX10
DNAH9
PMP22
ZNF18
ARHGAP44
HS3ST3B1
HS3ST3A1
TRIM16
ELAC2
TEKT3
MGC12916
MYOCD
CDRT7
CDRT15P1
CDRT15
FAM18B2
FLJ34690
CDRT4
CDRT1
MIR744
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q24.3.

Table S4. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
UST
TAB2
SASH1
LOC100128176

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p32.1.

Table S5. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
JUN
DAB1
TACSTD2
FGGY
MYSM1
OMA1
HSD52
LOC100131060

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

Table S6. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
MIR4635

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q12.

Table S7. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

Table S8. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
UBR2
TRERF1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.2.

Table S9. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BIRC3
BIRC2
MMP7
MMP20
YAP1
KIAA1377
MMP27
C11orf70
TMEM123

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.2.

Table S10. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DNMT1
P2RY11
PIN1
EIF3G
COL5A3
RDH8
ZNF562
FBXL12
C19orf66
PPAN
UBL5
ANGPTL6
OLFM2
ZNF846
C3P1
SNORD105
PPAN-P2RY11
ZNF812
SNORD105B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq21.1.

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-361
hsa-mir-548i-4
CHM
CYLC1
POU3F4
SH3BGRL
ZNF711
RPS6KA6
HMGN5
POF1B
DACH2
APOOL
HDX
SATL1
UBE2DNL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

Table S12. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
KCNA1
KCNA5
KCNA6
NDUFA9
AKAP3
GALNT8

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p11.2.

Table S13. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
EPHA3
HTR1F
POU1F1
PROS1
CGGBP1
CHMP2B
ZNF654
ARL13B
CADM2
C3orf38
VGLL3
STX19
MIR4795

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp21.1.

Table S14. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GATA1
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
CRLF2
P2RY8
hsa-let-7f-2
hsa-mir-502
hsa-mir-222
hsa-mir-548f-5
hsa-mir-1308
hsa-mir-651
NR0B1
ALAS2
AMELX
SLC25A6
SHROOM2
ARAF
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT
BMX
CACNA1F
S100G
CLCN4
CLCN5
CSF2RA
CYBB
DDX3X
DMD
EIF1AX
EIF2S3
ELK1
FANCB
FGD1
FIGF
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
GK
GLRA2
GPM6B
GPR34
GRPR
HSD17B10
HCCS
ERAS
IL3RA
KAL1
KCND1
PRICKLE3
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOA
MAOB
CD99
MID1
NDP
NHS
GPR143
TBC1D25
OTC
CDK16
PDHA1
PDK3
CFP
PFKFB1
PHEX
PHKA2
PIGA
PLP2
POLA1
PPEF1
PRKX
PRPS2
PRRG1
RBBP7
RBM3
RP2
RPGR
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SHOX
SMS
SSX5
CDKL5
SUV39H1
SYN1
SYP
TBL1X
DYNLT3
TIMP1
TSPAN7
TMSB4X
TRO
UBA1
SLC35A2
XG
XK
ZFX
ZNF182
ZNF41
ZNF157
ZXDA
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
USP11
USP9X
RBM10
SMC1A
SRPX
UXT
OFD1
PIR
INE2
INE1
CASK
ASMTL
PAGE1
AKAP4
AP1S2
GYG2
RGN
REPS2
ZBED1
BMP15
MED14
RAB9A
PCYT1B
MAGED1
XAGE2
XAGE1D
PAGE4
FRMPD4
PHF16
HDAC6
HUWE1
PQBP1
GPR64
ATP6AP2
SSX3
TIMM17B
RRAGB
SCML2
PRDX4
EBP
RAI2
MAGED2
MSL3
PIM2
IL1RAPL1
WDR45
PRAF2
CA5B
KLF8
CNKSR2
IQSEC2
PHF8
ACOT9
SMPX
GSPT2
FTSJ1
CXorf27
MXRA5
EGFL6
VCX
GAGE12I
GAGE2E
GPR82
GPKOW
APEX2
PCSK1N
PPP2R3B
CCDC22
MAGEH1
FAM156A
UBQLN2
SH3KBP1
FOXP3
TLR7
TLR8
MBTPS2
VCX2
VCX3A
FTHL17
GPR173
SPIN2A
NDUFB11
GNL3L
BCOR
FAM120C
GEMIN8
NUDT11
PLCXD1
OTUD5
ZNF673
TXLNG
WWC3
CTPS2
CHST7
GRIPAP1
ZNF630
TMEM27
SHROOM4
NLGN4X
MID1IP1
ACE2
NYX
DUSP21
TSPYL2
WDR13
PORCN
WNK3
APOO
CXorf36
MAGIX
ASMTL-AS1
CXorf21
EFHC2
KLHL15
PPP1R2P9
MAGED4B
TMEM47
SLC9A7
CCNB3
PPP1R3F
CCDC120
TSR2
FAM104B
PAGE5
ATXN3L
SLC38A5
SYAP1
SYTL5
BEND2
DGKK
FUNDC1
PTCHD1
SMEK3P
MAGEB10
DCAF8L1
VENTXP1
MAGEB16
FOXR2
PAGE3
ASB11
ASB9
ZNF645
LOC158572
FAAH2
ZXDB
FAM47A
MOSPD2
RIBC1
MAGEB6
USP51
CXorf38
DDX53
SPIN3
FAM47B
CXorf22
FAM48B2
TCEANC
ARX
XAGE3
XAGE5
NUDT10
FAM9A
FAM9B
FAM9C
PAGE2
DHRSX
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX8
PPP2R3B-AS1
LOC286442
CXorf59
MAGEB18
CA5BP1
ZNF81
ITIH6
LANCL3
LOC347411
DCAF8L2
ARSH
TLR8-AS1
MAP3K15
SPACA5
USP27X
CENPVL1
PAGE2B
LOC389906
CXXC1P1
GLOD5
CD99P1
LOC401588
YY2
MIRLET7F2
MIR188
MIR221
MIR222
MIR98
VCX3B
LOC441495
FAM47C
UQCRBP1
SPIN2B
SPANXN5
SSX4B
LOC550643
MIR362
MIR500A
MIR501
MIR502
ZNF674
GAGE10
GAGE2B
GAGE13
GAGE12G
CXorf30
XAGE1C
XAGE1E
XAGE1A
XAGE1B
SCARNA23
SNORA11
MIR532
MIR651
MIR660
CXorf31
SSX2B
FAM156B
MAGED4
XAGE2B
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
LOC729609
GAGE12F
LOC100093698
GAGE8
SNORA11C
SNORA11D
SNORA11E
CXorf28
FAM48B1
LOC100132163
GAGE12D
XGPY2
LOC100132831
LOC100133123
LOC100133957
SCARNA9L
LOC100288814
LINC00102
MIR500B
MTRNR2L10
MIR23C
MIR3690
LOC100509575
PIR-FIGF
MIR4769
MIR4536-1
MIR4768
MIR4770
MIR4767

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q21.12.

Table S15. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3149
hsa-mir-2052
CA1
CA2
CA3
E2F5
FABP4
FABP5
HNF4G
IL7
IMPA1
MMP16
PMP2
PKIA
PEX2
RPL7
TCEB1
TPD52
CPNE3
WWP1
STMN2
HEY1
LY96
STAU2
MRPS28
PI15
ZC2HC1A
FAM82B
GDAP1
CNGB3
TMEM70
UBE2W
PAG1
JPH1
SNX16
ZBTB10
ZFAND1
ZFHX4
CRISPLD1
LRRCC1
PSKH2
CHMP4C
DCAF4L2
RALYL
RDH10
SLC7A13
CNBD1
ATP6V0D2
REXO1L1
SLC10A5
CA13
C8orf59
FLJ39080
ZNF704
FABP9
FABP12
LOC100128126
LOC100130301
LOC100192378
REXO1L2P
MIR2052

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q12.

Table S16. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TOP1
MAFB
PLCG1
ZHX3
PPP1R16B
DHX35
LPIN3
ACTR5
FAM83D
CHD6
EMILIN3
LOC339568

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p21.3.

Table S17. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PMS2
hsa-mir-589
ACTB
ICA1
NDUFA4
RAC1
RPA3
FSCN1
ZNF12
AIMP2
CYTH3
PHF14
KIAA0415
KDELR2
WIPI2
EIF2AK1
NXPH1
CCZ1
MIOS
RNF216
ZNF853
ZDHHC4
RADIL
PAPOLB
C1GALT1
RBAK
C7orf26
FBXL18
USP42
TNRC18
C7orf70
GLCCI1
PER4
MMD2
DAGLB
CCZ1B
SLC29A4
RSPH10B
COL28A1
LOC389458
GRID2IP
ZNF815
RNF216P1
PMS2CL
ZNF890P
OCM
MIR589
RSPH10B2
LOC729852
LOC100131257
RBAK-LOC389458
MIR4656

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 37 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
13q14.2 | 7.1213e-23 | 7.1213e-23 | chr13:48833767-49064807 | 2
17p13.1 | 1.4428e-19 | 2.8971e-12 | chr17:7549751-7593565 | 2
Xq21.1 | 1.209e-12 | 4.2871e-12 | chrX:76710176-77102528 | 1
1p36.32 | 9.3749e-12 | 9.3749e-12 | chr1:1-6847369 | 137
19q13.43 | 8.8385e-09 | 8.8385e-09 | chr19:58400307-59128983 | 34
19p13.3 | 3.9887e-08 | 4.1199e-08 | chr19:1-390340 | 9
11q24.3 | 4.9394e-08 | 4.851e-08 | chr11:126870419-129248060 | 9
9p21.3 | 9.9772e-13 | 5.5258e-08 | chr9:21865498-22448737 | 4
10p15.3 | 1.2643e-07 | 1.2643e-07 | chr10:1-857150 | 4
2q37.3 | 1.5956e-13 | 8.3093e-07 | chr2:242162274-243199373 | 17
4q35.1 | 3.3657e-06 | 3.3316e-06 | chr4:178911874-191154276 | 64
11p15.5 | 3.2864e-06 | 3.3316e-06 | chr11:1-564126 | 24
17q25.3 | 1.0972e-06 | 6.8942e-06 | chr17:80443432-80617015 | 2
10q23.31 | 3.355e-05 | 3.1939e-05 | chr10:89313008-90348818 | 6
1q43 | 9.1136e-05 | 9.1136e-05 | chr1:205176004-249250621 | 370
9q34.3 | 0.00059282 | 0.00061654 | chr9:134611545-141213431 | 167
2q37.3 | 8.3587e-12 | 0.0011381 | chr2:231267644-243199373 | 153
8p23.3 | 0.0036932 | 0.0038145 | chr8:1-6262191 | 15
14q24.1 | 0.0044464 | 0.0044174 | chr14:68275375-69288431 | 2
12p13.1 | 0.0053819 | 0.008007 | chr12:1-19287837 | 258
9p24.3 | 3.5614e-06 | 0.0082698 | chr9:1-2018113 | 11
17q11.2 | 0.0012097 | 0.0088065 | chr17:29326736-30180957 | 11
6p24.3 | 0.012802 | 0.013299 | chr6:1-26019211 | 142
17p13.3 | 4.2774e-05 | 0.013299 | chr17:1-7610950 | 215
7q36.3 | 0.014991 | 0.014991 | chr7:150775658-159138663 | 56
21q22.3 | 0.016435 | 0.015961 | chr21:47427840-47609222 | 3
6q14.1 | 0.024128 | 0.024779 | chr6:57206486-134142659 | 302
2p25.3 | 0.025373 | 0.026355 | chr2:1-29284772 | 195
16q12.1 | 0.029168 | 0.028513 | chr16:31772318-55368634 | 61
Xq27.1 | 0.026355 | 0.052915 | chrX:114822917-151807257 | 260
12p11.1 | 0.046404 | 0.07469 | chr12:29934306-62867654 | 370
21q11.2 | 0.082539 | 0.079802 | chr21:1-23095995 | 41
22q13.31 | 0.085305 | 0.085469 | chr22:45018949-51304566 | 86
3p21.31 | 0.086396 | 0.086396 | chr3:41280645-66121046 | 307
Xp22.32 | 0.13384 | 0.13579 | chrX:1-17461904 | 99
3q25.1 | 0.14771 | 0.14307 | chr3:103942997-198022430 | 626
5q23.3 | 0.15989 | 0.16161 | chr5:113830803-180915260 | 581

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

Table S18. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

Table S19. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TP53
ATP1B2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.1.

Table S20. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATRX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

Table S21. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
CDK11B
DFFB
DVL1
MEGF6
GABRD
GNB1
ZBTB48
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
RER1
ACOT7
ICMT
CHD5
NOC2L
OR4F3
ARHGEF16
SSU72
WRAP73
SDF4
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
DNAJC11
AJAP1
TP73-AS1
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
OR4F5
NOL9
LINC00115
MORN1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
C1orf170
KIAA1751
THAP3
LOC115110
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
LOC148413
PHF13
CCDC27
CALML6
C1orf86
ATAD3C
LOC254099
TTLL10
NPHP4
FAM41C
LOC284661
C1orf174
KLHL17
TMEM240
TMEM52
AGRN
GPR153
FAM132A
HES5
LOC388588
RNF207
HES3
RNF223
MIR200A
MIR200B
FLJ42875
ANKRD65
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
FAM138A
WASH7P
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR4251
MIR4252
MIR4689
MIR4417

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.43.

Table S22. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF256
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
ZSCAN18
MGC2752
ZNF329
ZNF606
ZBTB45
ZNF837
C19orf18
ZNF418
ZNF417
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
A1BG-AS1
LOC646862
LOC100128398
LOC100131691
MIR4754

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.3.

Table S23. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-1302-11
PPAP2C
THEG
MIER2
OR4F17
WASH5P
FLJ45445
FAM138F
FAM138A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

Table S24. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FLI1
ETS1
KCNJ1
KCNJ5
ARHGAP32
TP53AIP1
C11orf45
KIRREL3-AS3
LOC100507392

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.3.

Table S25. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

Table S26. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZMYND11
DIP2C
TUBB8
C10orf108

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

Table S27. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3133
BOK
DTYMK
HDLBP
SEPT2
PDCD1
FARP2
STK25
ATG4B
THAP4
GAL3ST2
ING5
NEU4
CXXC11
D2HGDH
LOC728323
BOK-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

Table S28. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DUX4
hsa-mir-1305
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ZFP42
ENPP6
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

Table S29. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
HRAS
PSMD13
RNH1
RASSF7
IFITM1
IFITM3
IFITM2
PKP3
SIRT3
BET1L
SIGIRR
RIC8A
ATHL1
PTDSS2
ODF3
LRRC56
SCGB1C1
NLRP6
C11orf35
ANO9
B4GALNT4
IFITM5
LOC653486
LOC100133161

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q25.3.

Table S30. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FOXK2
WDR45L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.31.

Table S31. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PTEN
PAPSS2
RNLS
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

Table S32. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ELK4
FH
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
AVPR1B
C4BPA
C4BPB
CAPN2
CD34
CENPF
CHML
LYST
CHRM3
CR1
CR1L
CR2
CTSE
CD55
EIF2D
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PLXNA2
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
HIST3H3
GNPAT
DYRK3
CDC42BPA
DEGS1
KMO
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GGPS1
IKBKE
TMEM63A
TOMM20
URB2
CEP170
TMCC2
LPGAT1
AKT3
BPNT1
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
IL24
DUSP10
COG2
RBM34
FBXO28
SRGAP2
ABCB10
OPN3
RAB3GAP2
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
PPPDE1
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
HHAT
ENAH
NUP133
RCOR3
SERTAD4
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
NUAK2
RASSF5
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
LOC148696
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
PGBD2
OR2L13
OR14A16
LOC284576
LOC284578
LOC284581
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR194-1
MIR205
MIR215
MIR29B2
MIR29C
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
DUSP5P
C1orf133
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
SNORA36B
SNORA16B
LOC728463
FAM72A
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.3.

Table S33. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NOTCH1
RALGDS
TSC1
BRD3
hsa-mir-602
hsa-mir-4292
hsa-mir-126
ABCA2
ABO
C8G
CACNA1B
ENTPD2
CEL
CELP
COL5A1
DBH
SARDH
FCN1
FCN2
FUT7
GRIN1
LCN1
PAEP
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
CLIC3
GTF3C5
GTF3C4
MED27
ADAMTSL2
PPP1R26
SEC16A
TUBB4B
UBAC1
OLFM1
AGPAT2
SDCCAG3
NOXA1
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
SETX
PMPCA
COBRA1
NELF
GPSM1
DKFZP434A062
GBGT1
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
FBXW5
C9orf167
EXD3
C9orf86
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
CARD9
DDX31
MRPL41
EHMT1
NTNG2
KIAA1984
SNHG7
TMEM141
C9orf37
SAPCD2
C9orf69
UAP1L1
ARRDC1
WDR85
TMEM203
ZMYND19
NACC2
C9orf116
LCN8
FAM69B
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LINC00094
LCN12
C9orf142
TPRN
GLT6D1
PNPLA7
C9orf169
ENTPD8
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
LCN10
C9orf173
NRARP
FAM163B
FLJ40292
TUBBP5
RNF224
SNORA17
SNORA43
MIR602
RNF208
DNLZ
LOC100128593
LOC100129722
LOC100130954
LOC100131193
FAM157B
RNU6ATAC
LOC100289341
MIR4292
MIR3621
MIR3689A
MIR3689B
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

Table S34. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
HTR2B
INPP5D
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SNORD20
SAG
SP100
SPP2
DGKD
PER2
LRRFIP1
GPR55
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
C2orf54
ARMC9
EFHD1
ILKAP
ITM2C
ING5
MGC16025
B3GNT7
AGAP1
TWIST2
DIS3L2
NEU4
SPATA3
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LOC151475
LINC00471
LOC151484
MSL3P1
C2orf57
TIGD1
LOC200772
C2orf72
CXXC11
DUSP28
ESPNL
ECEL1P2
LOC348761
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR4269
UBE2F-SCLY
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

Table S35. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53
MIR596

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.1.

Table S36. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZFP36L1
RAD51B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CCND2
ETV6
KDM5A
ZNF384
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
KCNA1
KCNA5
KCNA6
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NINJ2
NOP2
NTF3
OLR1
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
SCNN1A
SLC2A3
SLC6A12
SLC6A13
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
CSDA
DYRK4
GPRC5A
CD163
GDF3
CLSTN3
NCAPD2
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
RAD51AP1
KLRAP1
TSPAN9
STRAP
PRR4
PHB2
KLRK1
ERC1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
PRMT8
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
WNK1
BCL2L14
ADIPOR2
RERGL
PLBD1
NANOG
DUSP16
WNT5B
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
CCDC77
ACRBP
SPSB2
EFCAB4B
RERG
PLCZ1
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
FBXL14
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf53
DCP1B
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
B4GALNT3
CLEC9A
C12orf36
LOC283440
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
LOC574538
POU5F1P3
LOC642846
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
LOC100271702
LOC100288778
LOC100292680
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
MIR3649
LOC100506314
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.3.

Table S38. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-1302-9
DMRT1
FOXD4
DMRT2
KANK1
CBWD1
DMRT3
DOCK8
C9orf66
FAM138C
WASH1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NF1
hsa-mir-365-2
EVI2A
EVI2B
OMG
RAB11FIP4
MIR193A
MIR365B
MIR4724
MIR4733
MIR4725

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.3.

Table S40. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IRF4
DEK
hsa-mir-548a-1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
GPLD1
HIST1H1A
HIVEP1
ID4
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SLC17A1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
ALDH5A1
CMAHP
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
FAM65B
KIAA0319
NUP153
RANBP9
SLC17A4
SLC17A2
ECI2
TRIM38
CAP2
SCGN
FARS2
SLC17A3
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
GMNN
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
TMEM14C
TDP2
GFOD1
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
MUTED
CCDC90A
KIF13A
TXNDC5
C6orf62
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
PIP5K1P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
RNF144B
HIST1H2BA
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
KAAG1
NHLRC1
HIST1H2APS1
PSMG4
DKFZP686I15217
FLJ23152
LINC00340
C6orf201
ERVFRD-1
PPP1R3G
MIR548A1
HULC
LOC729177
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4639
MIR4645

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.3.

Table S41. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TP53
USP6
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ACADVL
ALOX12
ALOX12P2
ALOX15
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DPH1
DVL2
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
HIC1
ITGAE
MNT
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RPA1
SHBG
SLC2A4
SOX15
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
TNFSF13
TNFSF12
TM4SF5
RABEP1
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
GABARAP
NLRP1
RAP1GAP2
CAMTA2
ZZEF1
KIAA0664
SMG6
WSCD1
CTDNEP1
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
GPR172B
WRAP53
RNMTL1
VPS53
C17orf85
TSR1
DHX33
PLSCR3
NLGN2
ZBTB4
CXCL16
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
PITPNM3
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
NEURL4
ZNF594
SPATA22
TXNDC17
MIR22HG
SAT2
SMYD4
OVCA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
RTN4RL1
KCTD11
TRPV3
SLC16A11
FBXO39
SLC16A13
C17orf74
SPNS3
C17orf61
BCL6B
LOC284009
VMO1
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
OR3A4P
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
SNORA48
SNORD10
OR1D4
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
C17orf107
LOC100130950
DBIL5P
MIR1253
LOC100306951
MIR3183
LOC100506388
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4520A
MIR4520B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

Table S42. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MLL3
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
DPP6
EN2
GBX1
MNX1
HTR5A
INSIG1
PTPRN2
RHEB
SHH
SMARCD3
VIPR2
XRCC2
UBE3C
DNAJB6
ABCF2
PAXIP1
PRKAG2
NUB1
CHPF2
NCAPG2
WDR60
ACTR3B
ESYT2
GALNT11
LMBR1
LINC00244
NOM1
TMUB1
AGAP3
C7orf13
ASB10
RNF32
LOC154822
CRYGN
RBM33
GALNTL5
LOC202781
FABP5P3
CNPY1
LOC285889
WDR86
MIR153-2
LOC645249
MIR595
MIR671
LOC100128264
LOC100128822
LOC100131176
LOC100132707
MIR3907
LOC100505483
LOC100506585

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

Table S43. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
COL6A2
FTCD
C21orf56

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.1.

Table S44. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PRDM1
ROS1
STL
GOPC
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
AIM1
AMD1
ARG1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
FABP7
FOXO3
FRK
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
HSF2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
ME1
MYO6
NT5E
ENPP1
ENPP3
PGM3
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
RNY4
RPS12
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
PTP4A1
STX7
DDO
SNX3
RNGTT
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
TBX18
TAAR2
TAAR3
HMGN3
MED23
FHL5
AKAP7
ATG5
KIAA0408
ZBTB24
SNAP91
FIG4
CASP8AP2
TRDN
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
SMPDL3A
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
PHF3
HEY2
ORC3
BRD7P3
MTO1
ASF1A
PNISR
IBTK
MOXD1
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
HDDC2
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
LGSN
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
ECHDC1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
SERINC1
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
TRMT11
SMAP1
C6orf164
POPDC3
MICAL1
OR2A4
OGFRL1
FAM184A
MANEA
LINC00472
KHDC1
GPR63
SPACA1
RNF146
TAAR8
SH3BGRL2
ARMC2
RPF2
L3MBTL3
MCHR2
FAXC
GJA10
RTN4IP1
RSPO3
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
ARHGAP18
GTF3C6
MRAP2
RWDD2A
KLHL32
TMEM200A
MB21D1
NUS1
C6orf192
SLC16A10
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
NCOA7
HINT3
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
SAMD3
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
KHDRBS2
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
MMS22L
FAM26E
MCM9
SCML4
LINC00326
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
TAAR6
DPPA5
RSPH4A
EYS
C6orf58
GUSBP4
GJB7
SNHG5
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
THEMIS
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
LOC100507203
LOC100507254
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.3.

Table S45. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ADCY3
APOB
RHOB
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
FOSL2
FTH1P3
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
PPP1CB
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
MRPL33
BRE
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
GPN1
MAPRE3
SLC4A1AP
EFR3B
MYT1L
WDR43
LPIN1
PUM2
NTSR2
IFT172
SH3YL1
SNORD53
TRIB2
GRHL1
NRBP1
ITSN2
TRAPPC12
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
TRMT61B
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
RBKS
HS1BP3
FNDC4
COLEC11
CENPO
CCDC121
SMC6
NOL10
C2orf44
FAM49A
C2orf16
ZNF512
ABHD1
EPT1
RSAD2
CCDC164
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
PLB1
FAM84A
GDF7
GPR113
FAM179A
UBXN2A
CYS1
KRTCAP3
SPDYA
ATP6V1C2
RNASEH1
FAM150B
DNAJC5G
IAH1
FLJ33534
C2orf70
C2orf53
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
PFN4
LOC375190
LOC386597
MFSD2B
PTRHD1
LOC400940
LINC00487
FLJ12334
FAM110C
LOC645949
C2orf84
SNORD92
LOC727982
RAD51AP2
DNAJC27-AS1
LOC730811
OST4
MIR1301
LOC100302650
SNORA80B
MIR4261
MIR4263
MIR3125
MIR4262
LOC100505624
LOC100505716
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q12.1.

Table S46. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CYLD
hsa-mir-3181
hsa-mir-1826
ADCY7
CBLN1
PHKB
RBL2
SALL1
SIAH1
N4BP1
IRX5
DNAJA2
ZNF267
ZNF423
RPGRIP1L
ORC6
TP53TG3
TOX3
BRD7
HEATR3
VPS35
NOD2
PAPD5
AKTIP
FTO
IRX6
IRX3
SHCBP1
CHD9
ITFG1
NETO2
LONP2
GPT2
ABCC11
NKD1
MYLK3
ABCC12
C16orf78
ANKRD26P1
SNX20
LOC146481
CNEP1R1
LOC283914
SLC6A10P
C16orf87
LOC388276
LOC390705
FLJ26245
HERC2P4
UBE2MP1
LOC643714
LOC643802
CRNDE
LINC00273
TP53TG3C
LOC729264
TP53TG3B
LOC100130700
LOC100505619
LOC100507577
MIR548AE2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq27.1.

Table S47. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ELF4
GPC3
hsa-mir-105-2
hsa-mir-452
hsa-mir-4330
hsa-mir-2114
hsa-mir-514-3
hsa-mir-513c
hsa-mir-891a
hsa-mir-891b
hsa-mir-320d-2
hsa-mir-505
hsa-mir-504
hsa-mir-934
hsa-mir-424
hsa-mir-106a
hsa-mir-220a
hsa-mir-766
hsa-mir-1277
AGTR2
SLC25A5
XIAP
BRS3
CD40LG
CDR1
CNGA2
F9
GPC4
FGF13
FHL1
FMR1
AFF2
GABRA3
GABRE
GLUD2
GRIA3
HMGB3
HPRT1
IDS
IGSF1
IL13RA1
LAMP2
SH2D1A
MAGEA4
MAGEA5
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MCF2
MTM1
NDUFA1
OCRL
PLS3
RPL39
SMARCA1
SOX3
SRD5A1P1
UBE2A
XPNPEP2
ZIC3
ZNF75D
RNF113A
CUL4B
MTMR1
APLN
FAM127A
SLC25A14
AIFM1
CXorf1
GPR50
RAB33A
ARHGEF6
MAGEC1
ZBTB33
MAMLD1
ODZ1
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
PGRMC1
SLC6A14
SEPT6
ATP1B4
LDOC1
FAM127B
SNORA69
SNORD61
RBMX
HTATSF1
MCTS1
C1GALT1C1
SPANXA1
ZDHHC9
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
WDR44
CXorf48
FAM70A
SAGE1
ZNF280C
MBNL3
FAM45B
NKRF
MOSPD1
THOC2
KIAA1210
RAP2C
BCORL1
CXorf56
SPANXD
SPANXC
UPF3B
PRRG3
NKAP
MAP7D3
LONRF3
GPR101
CD99L2
USP26
PHF6
RHOXF2
TMEM185A
SLITRK2
MGC16121
FATE1
HS6ST2
FRMD7
KLHL13
CXorf40A
MMGT1
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
GPR112
ACTRT1
GPR119
DOCK11
FMR1NB
LOC158696
ARHGAP36
AKAP14
RHOXF1
NKAPP1
FAM122B
FAM122C
ZCCHC12
SPANXE
SPANXF1
CXorf61
SLC25A43
DDX26B
ZNF449
VMA21
CT47A11
ATP11C
RP1-177G6.2
LOC286467
DCAF12L2
SOWAHD
OR13H1
CCDC160
CXorf66
UBE2NL
LINC00086
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
SPANXN1
SPANXN2
MIR424
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR452
MIR450A2
MIR503
MIR504
MIR505
MIR506
MIR507
MIR508
MIR509-1
MIR510
MIR514A1
MIR514A2
MIR514A3
SPANXA2-OT1
CT47B1
CXorf69
LINC00087
CT47A7
MIR542
RHOXF2B
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
SPANXB1
SPANXA2
CT45A2
MIR767
MIR766
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129520
LOC100129662
HSFX2
CXorf64
LOC100131434
CXorf51B
SPANXB2
LOC100272228
MIR320D2
MIR1277
SLC25A5-AS1
MIR2114
MIR514B
MIR4330
HSFX1
LOC100506757
CT47A12
MAGEA10-MAGEA5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p11.1.

Table S48. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATF1
CDK4
DDIT3
HOXC11
HOXC13
NACA
MLL2
hsa-mir-26a-2
hsa-mir-616
hsa-mir-1228
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
APOF
AQP2
AQP5
AQP6
ARF3
ATP5B
ATP5G2
BICD1
CACNB3
CCNT1
CD63
CDK2
CNTN1
COL2A1
CS
CYP27B1
DGKA
DDX11
EIF4B
CELA1
ERBB3
B4GALNT1
BLOC1S1
GLI1
GPD1
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
LRP1
MARS
METTL1
MIP
MMP19
MYL6
MYO1A
NAB2
NELL2
NFE2
SLC11A2
PA2G4
PCBP2
PDE1B
PFDN5
PFKM
PKP2
POU6F1
PPP1R1A
PRIM1
PRKAG1
PRPH
TWF1
RAB5B
RARG
RBMS2
RDH5
RNY5
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
PMEL
SMARCC2
SMARCD1
SP1
STAT2
STAT6
SUOX
TAC3
TARBP2
TMBIM6
TFCP2
VDR
WNT1
WNT10B
MAP3K12
TUBA1A
AAAS
SOAT2
RDH16
NPFF
HSD17B6
ENDOU
TIMELESS
KRT75
SCAF11
SLC16A7
DDX23
SLC4A8
ESPL1
DAZAP2
KIAA0748
ZBTB39
PAN2
USP15
TROAP
DNM1L
TSFM
CTDSP2
YAF2
RNF41
GDF11
CNPY2
TUBA1B
RAPGEF3
MCRS1
IPO8
DCTN2
AVIL
PTGES3
OS9
ATF7
BAZ2A
GALNT6
NXPH4
GPR182
COPZ1
R3HDM2
FAIM2
DDN
TMEM194A
ESYT1
TENC1
KCNH3
CBX5
ANP32D
SMUG1
PRPF40B
METTL7A
LETMD1
METTL21B
ZNF385A
SNORD59A
GLS2
RND1
ORMDL2
RACGAP1
SENP1
PDZRN4
DHH
PLEKHA8P1
YARS2
IRAK4
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
IL23A
HDAC7
GPR84
SLC38A2
PRR13
KANSL2
SLC38A4
C12orf35
KIF21A
SLC48A1
LMBR1L
NDUFA4L2
SMAGP
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
FAM60A
C12orf10
C12orf44
ARHGAP9
IKZF4
SLC26A10
SPATS2
CAPRIN2
TMEM106C
OBFC2B
RPAP3
PIP4K2C
FLJ13224
DNAJC22
ADAMTS20
SLC38A1
CSRNP2
PUS7L
INHBE
RACGAP1P
FAM186B
TMEM117
WIBG
SARNP
TUBA1C
ZC3H10
ALG10
SPRYD3
MFSD5
C12orf62
DNAJC14
ZCRB1
CCDC65
LACRT
FMNL3
CERS5
XRCC6BP1
FAM113B
MARCH9
COQ10A
KRT71
LARP4
SLC2A13
MBD6
ARHGEF25
AGAP2
DCD
MUCL1
LRRK2
FAM186A
OR10P1
SDR9C7
LRIG3
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
FGD4
ASB8
MYL6B
KRT72
PRICKLE1
BCDIN3D
ALG10B
CPNE8
KRT80
DENND5B
GRASP
KRT78
AMN1
DTX3
METTL7B
ANO6
ARID2
STAC3
METTL20
OR6C74
OR6C3
LOC255411
LOC283332
LOC283335
ZNF740
OR6C6
ANKRD52
SLC39A5
SPRYD4
LOC283403
LOC283404
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
FAM19A2
SYT10
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
AMIGO2
KRT77
C12orf68
OR6C1
OR6C75
OR6C76
OR6C70
LOC400027
LOC400043
FIGNL2
OR6C65
OR6C68
MIR196A2
MIR26A2
H3F3C
DBX2
FLJ12825
TMEM198B
TSPAN11
OR9K2
MIR148B
HIGD1C
GLYCAM1
HNRNPA1P10
SNORA2A
SNORA2B
SNORA34
SNORD59B
MIR615
HOTAIR
LOC100130776
LOC100233209
LOC100240734
LOC100240735
LOC100286844
LOC100287314
MIR1228
MIR1293
MIR1291
LOC100335030
LOC100506660
LOC100506844
BLOC1S1-RDH5
MIR4701
MIR3198-2
MIR4698
LOC100652999

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

Table S49. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
POTED
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

Table S50. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.31.

Table S51. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FHIT
BAP1
SETD2
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
CDC25A
CISH
CCR1
CCR3
CCR5
CCBP2
COL7A1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
NKTR
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
HESX1
BSN
LIMD1
CCRL2
SEC22C
RRP9
MAGI1
CACNA2D2
VPRBP
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CSPG5
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
RAD54L2
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
NDUFAF3
PTPN23
DNAH1
HIGD1A
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
ABHD5
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
ULK4
FEZF2
ANO10
DALRD3
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZNF167
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
SELK
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
ABHD14B
C3orf39
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
ZNF501
GPR62
FAM3D
LYZL4
KBTBD5
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
CCDC12
CCDC13
PRICKLE2
C3orf67
KCTD6
KLHDC8B
DNAH12
PDE12
FAM116A
ALS2CL
TMIE
FBXW12
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
CCDC36
PRSS42
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR138-1
MIR191
TMEM89
IQCF6
C3orf78
MIR425
LOC644714
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
MIR548A2
MIR564
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
NRADDP
LOC100132146
BSN-AS2
PRSS46
LOC100287879
MIR1226
MIR711
MIR4271
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4443
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.32.

Table S52. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CRLF2
P2RY8
hsa-mir-651
AMELX
SLC25A6
SHROOM2
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT
BMX
S100G
CLCN4
CSF2RA
FANCB
FIGF
GLRA2
GPM6B
GRPR
HCCS
IL3RA
KAL1
CD99
MID1
GPR143
PIGA
PRKX
PRPS2
RBBP7
TRAPPC2
SHOX
TBL1X
TMSB4X
XG
GTPBP6
HDHD1
AKAP17A
PNPLA4
ZRSR2
OFD1
PIR
INE2
ASMTL
AP1S2
GYG2
REPS2
ZBED1
RAB9A
FRMPD4
MSL3
CA5B
MXRA5
EGFL6
VCX
PPP2R3B
TLR7
TLR8
VCX2
VCX3A
GEMIN8
PLCXD1
TXLNG
WWC3
CTPS2
TMEM27
NLGN4X
ACE2
ASMTL-AS1
ATXN3L
SYAP1
ASB11
ASB9
MOSPD2
TCEANC
FAM9A
FAM9B
FAM9C
DHRSX
PPP2R3B-AS1
CA5BP1
ARSH
TLR8-AS1
LOC389906
CD99P1
VCX3B
MIR651
LOC100093698
CXorf28
XGPY2
LOC100133123
LOC100288814
LINC00102
MIR3690
PIR-FIGF
MIR4768
MIR4770
MIR4767

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q25.1.

Table S53. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BCL6
FOXL2
CBLB
EIF4A2
ETV5
GATA2
LPP
MLF1
PIK3CA
RPN1
SOX2
TFRC
GMPS
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
AADAC
ACPP
ACTL6A
ADCY5
ADPRH
AGTR1
AHSG
ALCAM
APOD
ATP1B3
ATP6V1A
ATR
BCHE
BDH1
CASR
CD80
CD86
CD47
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
CRYGS
CSTA
DGKG
DLG1
DRD3
DVL3
ECT2
EHHADH
EIF4G1
EPHB1
EPHB3
MECOM
FGF12
GAP43
GHSR
GOLGB1
GP5
GP9
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRG
HES1
IL1RAP
IL12A
ITGB5
KNG1
KPNA1
KPNA4
LSAMP
TM4SF1
MBNL1
MCM2
MFI2
MME
CD200
MUC4
MYLK
NCK1
NDUFB4
NDUFB5
OPA1
CLDN11
P2RY1
PAK2
PCCB
PCYT1A
PFN2
SERPINI1
SERPINI2
PIK3CB
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
POLR2H
PPP1R2
PPP2R3A
PRKCI
MASP1
PSMD2
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
RPL35A
RYK
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC15A2
SLCO2A1
HLTF
SSR3
SST
TERC
TF
TFDP2
THPO
SEC62
TM4SF4
TRH
TRPC1
UPK1B
UMPS
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
FXR1
SOX14
BFSP2
RUVBL1
TP63
CHRD
B4GALT4
B3GALNT1
SNX4
TNFSF10
NR1I2
EIF2B5
MBD4
H1FX
USP13
KALRN
CLDN1
MAP3K13
SLC33A1
COPB2
ADIPOQ
CHST2
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
KIAA0226
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
COX17
TNK2
ALG3
CD96
KCNMB2
STAG1
IGF2BP2
CLDN16
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
FSTL1
MRPL3
PDCD10
RNF13
MGLL
MRAS
COPG
SLITRK3
NLGN1
NCBP2
MYH15
PLCH1
TMCC1
TNIK
MCF2L2
PLXND1
ATP11B
DNAJC13
U2SURP
VPS8
C3orf27
ACAP2
ANAPC13
ARMC8
C3orf17
WWTR1
PVRL3
TIPARP
UBXN7
ARHGEF26
ZBTB20
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
MORC1
SERP1
GOLIM4
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
SCHIP1
PIK3R4
PODXL2
TRAT1
NMD3
COMMD2
A4GNT
DBR1
ZNF639
CLDN18
TIMMDC1
RSRC1
PLA1A
AMOTL2
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
P2RY13
IL20RB
GPR87
DCUN1D1
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
KLHL24
SIDT1
SLC41A3
PIGX
SLC35A5
IFT57
MSL2
TBCCD1
FAIM
SLC25A36
DPPA4
LEPREL1
TMEM39A
ABCF3
LSG1
ABHD10
PARL
CDV3
MFN1
YEATS2
IFT122
WDR52
EAF2
MYNN
EIF5A2
MUC13
SUCNR1
MCCC1
LXN
C3orf37
MRPS22
POGLUT1
BBX
CCNL1
PLSCR2
PLSCR4
HRASLS
MRPL47
ISY1
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
KIAA1524
SLC7A14
SRPRB
SENP2
GNB4
BPESC1
EEFSEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZMAT3
ATG3
MFSD1
CCDC14
FNDC3B
P2RY12
TMEM108
ZXDC
ZBED2
ATP13A3
HSPBAP1
C3orf52
VEPH1
QTRTD1
TBL1XR1
ZBBX
LRRC31
CCDC48
NEK11
UBA5
MAP6D1
PHC3
C3orf36
ARL14
NAA50
PIGZ
CEP63
CEP70
ABTB1
TMEM22
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
ZIC4
ACAD11
IQCG
ATP13A4
FYTTD1
CHCHD6
HPS3
ARPM1
SLC12A8
RETNLB
CCDC54
MGC2889
LRCH3
DIRC2
CEP19
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
LOC90246
C3orf25
TMEM41A
BOC
SPSB4
ACPL2
TMEM44
EGFEM1P
CAMK2N2
TXNRD3
OSBPL11
LRRC58
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
CPNE4
CCDC58
DNAJC19
OTOL1
FAM131A
CD200R1
ZDHHC19
LRRC15
FAM43A
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
GRK7
TMEM207
RTP1
RPL32P3
H1FOO
PISRT1
TTC14
DTX3L
LOC151658
PPM1L
WDR49
LRRC34
DPPA2
CCDC80
BTLA
MB21D2
XXYLT1
ROPN1B
C3orf22
C3orf55
C3orf79
CCDC50
PYDC2
SPICE1
NUDT16P1
LOC152217
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
RNF168
CHST13
KBTBD12
DHX36
HTR3C
DZIP1L
ALG1L
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
PTPLB
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
LOC253573
NAALADL2
ZDHHC23
NUP210P1
TCTEX1D2
C3orf43
SDHAP1
COL6A5
GK5
PLCXD2
GCET2
UTS2D
LSAMP-AS3
SLC9A9
LOC285205
DNAJB8-AS1
HTR3E
RABL3
IGSF10
C3orf33
SLC9A10
C3orf70
TPRG1
ILDR1
TRIM59
TRIM42
RAB43
CCDC39
KY
LOC339874
LOC339894
LOC339926
LPP-AS2
H1FX-AS1
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
CCDC37
NPHP3-AS1
ANKRD18DP
NMNAT3
LRRC33
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
MIR198
ARGFX
SNORD2
SNORA4
ALG1L2
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
SNORA81
SNORD66
MIR551B
MIR567
MIR568
MIR569
MIR570
SDHAP2
FAM157A
FAM86HP
PRR23A
LOC730091
LOC100125556
MIR922
MIR944
LOC100128023
WWTR1-AS1
LOC100128164
LOC100129550
ZBTB20-AS1
LOC100131551
LOC100131635
SNAR-I
MIR1224
TIPARP-AS1
LOC100289361
MIR1248
MIR1280
MIR548I1
LOC100302640
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100505687
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
LOC100507032
MFI2-AS1
LOC100507086
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
NPHP3-ACAD11
ISY1-RAB43
TM4SF19-TCTEX1D2
MIR4796
MIR4797
MIR4788
MIR4789
MIR4446

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q23.3.

Table S54. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDO1
CDX1
AP3S1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
NKX2-5
CTNNA1
DBN1
DMXL1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HINT1
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
LCP2
LECT2
LMNB1
LOX
LTC4S
SMAD5
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SNX2
SPARC
SPINK1
SPOCK1
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
ATG12
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
LYRM7
TRIM41
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
ZNF474
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
SRFBP1
LOC153469
ZMAT2
BTNL9
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
AQPEP
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
DTWD2
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
TICAM2
DND1
C5orf25
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
LOC644100
FLJ33630
CCNI2
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728342
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
VTRNA2-1
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505841
LOC100507387
MIR4633
MIR4634
MIR4461
MIR4460
MIR4638
MIR378E
LOC100859930

Arm-level results

Table 3. Get Full Table Arm-level significance table - 12 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.22 | 0.615 | 0.829 | 0.17 | -0.562 | 0.94
1q | 1955 | 0.22 | 0.488 | 0.834 | 0.18 | -0.475 | 0.94
2p | 924 | 0.10 | -3.05 | 1 | 0.34 | 2.41 | 0.0294
2q | 1556 | 0.07 | -3.46 | 1 | 0.26 | 1.04 | 0.397
3p | 1062 | 0.10 | -3.25 | 1 | 0.23 | -0.195 | 0.924
3q | 1139 | 0.11 | -2.83 | 1 | 0.26 | 0.589 | 0.654
4p | 489 | 0.21 | -1.1 | 1 | 0.23 | -0.757 | 0.94
4q | 1049 | 0.17 | -1.71 | 1 | 0.23 | -0.288 | 0.94
5p | 270 | 0.35 | 2.02 | 0.371 | 0.16 | -2.29 | 0.997
5q | 1427 | 0.29 | 1.68 | 0.371 | 0.18 | -1.06 | 0.973
6p | 1173 | 0.23 | -0.0415 | 1 | 0.27 | 0.846 | 0.497
6q | 839 | 0.21 | -0.877 | 1 | 0.17 | -1.75 | 0.997
7p | 641 | 0.32 | 1.49 | 0.455 | 0.22 | -0.885 | 0.955
7q | 1277 | 0.26 | 0.779 | 0.772 | 0.20 | -0.661 | 0.94
8p | 580 | 0.27 | 0.227 | 0.965 | 0.26 | 0.0586 | 0.829
8q | 859 | 0.28 | 0.755 | 0.772 | 0.20 | -1.16 | 0.973
9p | 422 | 0.22 | -0.907 | 1 | 0.41 | 3.53 | 0.00117
9q | 1113 | 0.28 | 0.91 | 0.772 | 0.29 | 1.26 | 0.297
10p | 409 | 0.14 | -2.25 | 1 | 0.50 | 5.68 | 5.36e-08
10q | 1268 | 0.08 | -2.7 | 1 | 0.55 | 8.36 | 0
11p | 862 | 0.10 | -3.13 | 1 | 0.38 | 3.34 | 0.00212
11q | 1515 | 0.08 | -3.15 | 1 | 0.33 | 2.98 | 0.00581
12p | 575 | 0.13 | -2.78 | 1 | 0.26 | 0.135 | 0.813
12q | 1447 | 0.07 | -3.61 | 1 | 0.24 | 0.483 | 0.683
13q | 654 | 0.10 | -2.85 | 1 | 0.54 | 7.14 | 7.12e-12
14q | 1341 | 0.27 | 0.887 | 0.772 | 0.36 | 3.19 | 0.00317
15q | 1355 | 0.30 | 1.78 | 0.371 | 0.21 | -0.382 | 0.94
16p | 872 | 0.20 | -1.12 | 1 | 0.32 | 1.82 | 0.114
16q | 702 | 0.08 | -3.12 | 1 | 0.53 | 7.12 | 7.12e-12
17p | 683 | 0.24 | -0.308 | 1 | 0.26 | 0.204 | 0.813
17q | 1592 | 0.21 | -0.287 | 1 | 0.24 | 0.455 | 0.683
18p | 143 | 0.21 | -1.51 | 1 | 0.28 | 0.133 | 0.813
18q | 446 | 0.15 | -2.36 | 1 | 0.32 | 1.35 | 0.273
19p | 995 | 0.26 | 0.497 | 0.834 | 0.16 | -1.8 | 0.997
19q | 1709 | 0.22 | 0.234 | 0.965 | 0.18 | -0.707 | 0.94
20p | 355 | 0.30 | 0.733 | 0.772 | 0.24 | -0.592 | 0.94
20q | 753 | 0.34 | 2.13 | 0.371 | 0.12 | -2.72 | 0.997
21q | 509 | 0.29 | 0.78 | 0.772 | 0.26 | -0.0561 | 0.871
22q | 921 | 0.33 | 1.87 | 0.371 | 0.40 | 3.55 | 0.00117
Xq | 1312 | 0.12 | -2.14 | 1 | 0.46 | 5.92 | 1.57e-08

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

- Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SARC-TP/5949541/GDAC_MergeDataFiles_5954231/SARC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 127 Input Tumor Samples.

Tumor Sample Names
TCGA-DX-A1KU-01A-32D-A24M-01
TCGA-DX-A1KW-01A-22D-A24M-01
TCGA-DX-A1KX-01A-22D-A24M-01
TCGA-DX-A1KY-01A-11D-A24M-01
TCGA-DX-A1KZ-01A-11D-A24M-01
TCGA-DX-A1L0-01A-11D-A24M-01
TCGA-DX-A1L1-01A-11D-A24M-01
TCGA-DX-A1L2-01A-22D-A24M-01
TCGA-DX-A1L3-01A-11D-A24M-01
TCGA-DX-A1L4-01A-12D-A26F-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file 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.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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