SNP6 Copy number analysis (GISTIC2)
Uterine Carcinosarcoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1QR4VKN
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/C1QR4VKN
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 56 tumor samples used in this analysis: 21 significant arm-level results, 25 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 - 25 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
19q12 1.4274e-21 1.4274e-21 chr19:30712323-30831808 0 [ZNF536]
3q26.2 4.8739e-09 4.8739e-09 chr3:168526502-168814908 2
4p16.3 1.4214e-07 1.4214e-07 chr4:1792019-1870419 2
1q22 3.1905e-06 3.1905e-06 chr1:155870519-156017401 8
20q11.21 2.0971e-12 5.9148e-06 chr20:30535307-30921748 10
20q11.21 3.6e-10 0.00027345 chr20:29983442-30369453 14
8p11.21 4.6343e-06 0.00053433 chr8:42725564-47463861 7
8q11.23 4.1938e-06 0.00089729 chr8:48357987-57188018 33
19p13.2 0.0014153 0.0014153 chr19:10492041-10767789 15
8q24.21 2.2187e-08 0.0024551 chr8:129548135-129565078 0 [MIR1208]
6p24.2 0.0026462 0.0026462 chr6:11367262-11448879 1
13q31.3 0.0026462 0.0026462 chr13:90659392-96245151 20
8q24.21 8.9908e-06 0.0029578 chr8:128630217-129102510 9
16p11.2 0.0039776 0.0039776 chr16:30907404-30943981 3
17q25.1 0.00067137 0.0045262 chr17:73581977-73757386 7
10q22.2 0.0058757 0.0058757 chr10:76500842-77828069 11
11q13.1 0.0085652 0.0085652 chr11:63669372-63995301 11
3p25.1 0.010149 0.010149 chr3:13643232-13895816 3
17q12 0.0046324 0.033763 chr17:37822312-37969982 8
5p13.2 0.047229 0.047229 chr5:36321031-36701657 1
Xp11.21 0.04875 0.04875 chrX:55567455-56241386 2
2q13 0.079059 0.079059 chr2:113940840-114236564 4
12q12 0.069456 0.10753 chr12:44445547-46909264 12
12q15 0.049549 0.1956 chr12:69164647-71445992 18
2p14 0.22141 0.22141 chr2:68076781-68330783 1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
MECOM
EGFEM1P
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

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

Genes
FGFR3
LETM1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q22.

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

Genes
RIT1
SSR2
ARHGEF2
KIAA0907
UBQLN4
RXFP4
SCARNA4
SNORA42
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-1825
HCK
PLAGL2
KIF3B
TM9SF4
POFUT1
PDRG1
TSPY26P
C20orf160
XKR7
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-3193
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
LINC00028
DEFB121
DEFB122
DEFB123
DEFB124
PSIMCT-1
MIR3193
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
HOOK3
FNTA
RNF170
SGK196
HGSNAT
POTEA
MIR4469
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.23.

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

Genes
PLAG1
TCEA1
CHCHD7
CEBPD
NPBWR1
LYN
MCM4
MOS
OPRK1
PRKDC
RP1
RPS20
SNAI2
UBE2V2
RGS20
ST18
RB1CC1
LYPLA1
KIAA0146
SNORD54
MRPL15
ATP6V1H
SNTG1
SOX17
EFCAB1
TGS1
XKR4
PCMTD1
TMEM68
PXDNL
FAM150A
C8orf22
SBF1P1
Genes in Wide Peak

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

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

Genes
hsa-mir-1238
hsa-mir-1181
CDKN2D
ILF3
PDE4A
KEAP1
AP1M2
CDC37
S1PR5
SLC44A2
KRI1
ATG4D
LOC147727
MIR1181
MIR1238
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.2.

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

Genes
NEDD9
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q31.3.

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

Genes
hsa-mir-92a-1
hsa-mir-622
DCT
GPC5
CLDN10
GPC6
ABCC4
SOX21
DZIP1
TGDS
LINC00410
GPR180
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
MIR622
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
MYC
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
PVT1
MIR1205
MIR1206
MIR1207
MIR1204
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

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

Genes
CTF1
FBXL19
FBXL19-AS1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
GALK1
ITGB4
RECQL5
SAP30BP
MYO15B
C17orf109
C17orf110
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.2.

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

Genes
hsa-mir-606
VDAC2
KAT6B
DUSP13
C10orf11
ZNF503
COMTD1
SAMD8
ZNF503-AS1
DUPD1
ZNF503-AS2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.1.

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

Genes
COX8A
MARK2
STIP1
FLRT1
MACROD1
OTUB1
NAA40
FERMT3
TRPT1
NUDT22
RCOR2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p25.1.

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

Genes
FBLN2
WNT7A
LOC285375
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
GRB7
PNMT
TCAP
IKZF3
MIEN1
PGAP3
MIR4728
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.2.

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

Genes
SLC1A3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.21.

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

Genes
RRAGB
FOXR2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q13.

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

Genes
PAX8
PSD4
CBWD2
LOC654433
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q12.

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

Genes
NELL2
RNY5
SCAF11
PLEKHA8P1
SLC38A2
SLC38A1
RACGAP1P
TMEM117
ANO6
ARID2
LOC400027
DBX2
Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
LYZ
CNOT2
PTPRB
PTPRR
YEATS4
CCT2
FRS2
CPSF6
KCNMB4
RAB3IP
BEST3
LRRC10
MIR1279
MIR3913-2
MIR3913-1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p14.

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

Genes
C1D

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
19p13.3 2.1663e-13 2.1663e-13 chr19:1-1107034 46
15q15.1 6.0948e-10 6.0948e-10 chr15:28096454-40886552 95
5q11.2 6.2454e-07 6.2454e-07 chr5:58260298-59787985 3
Xp21.2 1.2556e-05 1.2556e-05 chrX:30870233-32665140 3
2q22.1 2.6035e-05 2.6035e-05 chr2:139655617-143637838 1
12q23.1 6.5476e-05 0.00010382 chr12:99124001-100107912 2
16q23.1 0.00022218 0.00022619 chr16:78016120-79627770 2
4q22.1 0.00015704 0.00027725 chr4:90844993-93240505 1
13q14.2 5.6442e-05 0.00035561 chr13:48833767-49281290 3
3q13.31 0.00045292 0.00045292 chr3:116161663-118620828 1
22q13.31 0.0014783 0.0014783 chr22:41958863-51304566 141
3p21.1 1.4236e-05 0.001687 chr3:52572448-61547330 56
20p12.1 0.0045484 0.0045606 chr20:14302876-16252980 3
1p36.21 0.0056859 0.0056859 chr1:1-19401404 297
8p21.3 0.0081246 0.0084296 chr8:1-37561346 271
9p24.1 0.0088283 0.0086566 chr9:7799607-12693402 1
4q34.3 0.00023214 0.023306 chr4:171973965-191154276 88
3p14.1 6.6464e-05 0.027613 chr3:55108056-93777876 108
17p13.1 0.045924 0.043462 chr17:8371221-25626166 154
13q12.11 0.017521 0.051566 chr13:20795889-23755126 15
11p15.5 0.05228 0.052466 chr11:1-22216204 354
6q26 0.060912 0.06248 chr6:161693099-163153207 1
17q21.32 0.06581 0.065115 chr17:40069743-46187564 158
11q14.1 0.041519 0.069636 chr11:82995735-85348444 2
9q33.3 0.07374 0.11028 chr9:80943738-141213431 643
14q21.1 0.12005 0.12131 chr14:39652220-44977111 6
Xq25 0.1227 0.1227 chrX:120183502-155270560 309
7q11.22 0.131 0.131 chr7:66780207-70601215 1
11q24.2 0.098729 0.131 chr11:85330201-135006516 399
18q22.2 0.13587 0.131 chr18:47089955-78077248 123
19q13.33 0.13418 0.131 chr19:37145637-59128983 852
16p13.3 0.14458 0.14433 chr16:1-1834723 85
10q23.31 0.131 0.15299 chr10:77119066-135534747 490
12q24.31 0.033266 0.15299 chr12:120875791-133851895 134
9q21.13 0.093685 0.19376 chr9:35113248-128199872 515
7q36.1 0.19992 0.20048 chr7:73817072-159138663 681
10q21.1 0.16961 0.22933 chr10:54521118-57378256 4
Genes in Wide Peak

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

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

Genes
FSTL3
hsa-mir-3187
hsa-mir-1302-11
AZU1
HCN2
BSG
CDC34
CNN2
CFD
ARID3A
ELANE
GPX4
GZMM
PALM
POLR2E
POLRMT
PRTN3
PTBP1
MADCAM1
PPAP2C
MED16
ABCA7
HMHA1
SHC2
FGF22
THEG
MIER2
RNF126
WDR18
LPPR3
OR4F17
KISS1R
R3HDM4
C19orf6
TPGS1
GRIN3B
C19orf21
C2CD4C
ODF3L2
WASH5P
FLJ45445
PRSS57
FAM138F
FAM138A
MIR3187
MIR4745
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
BUB1B
C15orf55
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
ACTC1
APBA2
CHRM5
CHRNA7
IVD
MEIS2
TRPM1
PLCB2
RYR3
SCG5
SRP14
THBS1
TJP1
HERC2
AQR
ARHGAP11A
SLC12A6
RASGRP1
GPR176
BAHD1
FAN1
GOLGA8A
FAM189A1
DKFZP434L187
GREM1
RPUSD2
TMEM85
KLF13
MTMR10
ZNF770
NOP10
NDNL2
C15orf24
PAK6
AVEN
GJD2
C15orf29
C15orf41
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
CHST14
LOC145845
TMCO5A
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
FSIP1
LPCAT4
LOC283710
FAM98B
GOLGA8G
FMN1
MRPL42P5
C15orf52
C15orf53
C15orf54
MIR211
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
C15orf56
PHGR1
LOC646278
LOC653075
ANP32AP1
LOC100131089
ANKRD63
GOLGA8F
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1233-2
MIR3942
LOC100507466
MIR4509-1
MIR4509-2
MIR4510
MIR4509-3
TMCO5B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
hsa-mir-582
PDE4D
PART1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.2.

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

Genes
hsa-mir-548f-5
DMD
FTHL17
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

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

Genes
LRP1B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

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

Genes
ANKS1B
FAM71C
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
CLEC3A
WWOX
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
FAM190A
Genes in Wide Peak

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

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

Genes
RB1
RCBTB2
LPAR6
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
LSAMP-AS3
Genes in Wide Peak

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

Table S34.  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
hsa-mir-33a
ACR
ARSA
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
NAGA
NDUFA6
NHP2L1
PMM1
PPARA
MAPK11
MAPK12
SBF1
SREBF2
TCF20
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
RRP7A
MCAT
PPPDE2
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
SEPT3
PANX2
PARVG
CERK
EFCAB6
CENPM
ALG12
CRELD2
C22orf46
CCDC134
ADM2
SCUBE1
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
POLDIP3
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
TNFRSF13C
MEI1
FAM109B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
WBP2NL
SERHL2
RNU12
ATP5L2
LOC284933
RPL23AP82
BK250D10.8
LOC339685
C22orf34
CHKB-CPT1B
LOC388906
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
MIR33A
LINC00229
FAM116B
PIM3
SHISA8
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100132273
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 3p21.1.

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

Genes
FHIT
PBRM1
ARF4
C3orf51
CACNA1D
DNASE1L3
FLNB
ITIH1
ITIH3
ITIH4
PDHB
PRKCD
NEK4
TKT
WNT5A
SLMAP
ACOX2
HESX1
RPP14
FAM107A
FAM208A
ERC2
APPL1
GNL3
SPCS1
ARHGEF3
SFMBT1
IL17RD
PXK
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
ABHD6
LRTM1
SELK
RFT1
ACTR8
FAM3D
ASB14
C3orf67
KCTD6
DNAH12
PDE12
FAM116A
CCDC66
SPATA12
TMEM110
MUSTN1
SNORD19
SNORD69
ESRG
SNORD19B
MIR3938
TMEM110-MUSTN1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
FLRT3
MACROD2
MACROD2-AS1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.21.

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
RERE
CA6
CASP9
TNFRSF8
CDK11B
CLCN6
CLCNKA
CLCNKB
CORT
DFFA
DFFB
DVL1
MEGF6
EPHA2
ENO1
MTOR
GABRD
GNB1
ZBTB48
TNFRSF9
MFAP2
MTHFR
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLOD1
EXOSC10
PRKCZ
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TNFRSF1B
TP73
TNFRSF4
ZBTB17
PRDM2
MMP23B
MMP23A
KCNAB2
ALDH4A1
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
MFN2
ANGPTL7
UBE4B
MAD2L2
PDPN
MASP2
UTS2
RER1
MST1P2
MST1P9
PADI2
PARK7
CTRC
ACOT7
CLSTN1
SPEN
KIF1B
PLEKHM2
KAZN
CAMTA1
DNAJC16
ATP13A2
TARDBP
ICMT
PADI4
CHD5
C1orf144
NOC2L
FBXO2
FBXO6
OR4F3
HSPB7
ARHGEF16
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
CELA2B
SDF4
PADI3
ERRFI1
FBXO42
MXRA8
HES2
FBLIM1
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
ARHGEF10L
VPS13D
ATAD3A
PANK4
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
AGTRAP
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
HES4
MIIP
CELA2A
NMNAT1
VWA1
PRAMEF1
PRAMEF2
NADK
EFHD2
MMEL1
RSG1
OR4F5
NOL9
AGMAT
LINC00115
MORN1
GPR157
SPSB1
GLTPD1
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
SLC25A33
DDI2
LZIC
C1orf170
CROCCP2
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf158
FBXO44
CROCCP3
FHAD1
LOC115110
RBP7
ACAP3
UBE2J2
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
KLHDC7A
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf64
SLC2A7
CALML6
TMEM201
C1orf86
C1orf126
ATAD3C
LOC254099
TTLL10
NPHP4
FAM41C
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PRAMEF4
PRAMEF13
RNF223
PRAMEF3
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC649330
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
NPPA-AS1
MIR4251
MIR4252
MIR3675
ENO1-AS1
APITD1-CORT
MIR4695
MIR4689
MIR4632
MIR4417
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

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

Genes
PCM1
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
hsa-mir-548v
hsa-mir-383
hsa-mir-598
hsa-mir-1322
hsa-mir-4286
hsa-mir-124-1
hsa-mir-597
hsa-mir-548i-3
hsa-mir-596
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
GSR
GTF2E2
NRG1
LOXL2
LPL
MSR1
MSRA
NEFM
NEFL
NKX3-1
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
UBXN8
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
MTMR7
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
FBXO25
FGF20
ADAMDEC1
CNOT7
PURG
ZDHHC2
SLC25A37
SCARA3
TMEM66
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
AGPAT5
INTS9
CSGALNACT1
HR
PBK
ZNF395
DEFB103B
BIN3
TEX15
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
DUSP26
HMBOX1
MCPH1
PPP1R3B
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
TTI2
REEP4
STMN4
SOX7
FAM167A
SLC35G5
LINC00208
C8orf12
MAK16
FUT10
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
NKX2-6
SGCZ
UNC5D
DEFB104A
LOC157273
SGK223
PEBP4
CDCA2
ESCO2
FBXO16
LOC157627
C8orf42
ERICH1
TDH
C8orf48
KCNU1
ZNF596
DEFT1P
R3HCC1
PRSS55
C8orf74
LGI3
DEFB105A
DEFB106A
DEFB107A
DEFB109P1
DEFB130
NEIL2
LOC254896
FLJ10661
XKR6
LOC286059
LOC286083
EFHA2
LOC286114
SCARA5
LOC286135
LOC340357
LOC349196
USP17L2
XKR5
FAM90A25P
LOC389641
C8orf80
LOC392196
MIR124-1
MIR320A
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
MIR383
DEFB107B
DEFB104B
DEFB106B
DEFB105B
C8orf58
DEFB135
DEFB136
DEFB134
C8orf75
MBOAT4
DEFB109P1B
RPL23AP53
FAM90A14
FAM86B2
SPAG11A
MIR596
MIR597
MIR598
DEFA1B
FAM90A20
FAM90A19
ZNF705D
LOC100128750
FAM66B
LOC100128993
ZNF705G
FAM66E
LOC100132396
FAM66D
FAM66A
LOC100133267
LOC100287015
DEFT1P2
DEFB4B
MIR1322
MIR548I3
MIR4287
MIR3148
MIR4288
MIR3926-2
MIR3622A
MIR3926-1
MIR3622B
LOC100506990
LOC100507156
LOC100507341
MIR548O2
MIR4659A
MIR4660
MIR4659B
LOC100652791
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.1.

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

Genes
PTPRD
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
ADAM29
SCRG1
FAM149A
FBXO8
DUX2
PDLIM3
GALNT7
CLDN22
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
LOC100506229
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
FHIT
MITF
FOXP1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
ARF4
C3orf51
DNASE1L3
EPHA3
FLNB
GBE1
GPR27
HTR1F
CNTN3
PDHB
POU1F1
PROS1
PTPRG
ROBO1
ROBO2
ATXN7
TMF1
WNT5A
SLMAP
ACOX2
CGGBP1
CADPS
SUCLG2
HESX1
UBA3
MAGI1
PSMD6
ARL6IP5
RPP14
FAM107A
PDZRN3
FRMD4B
FAM208A
RYBP
CHMP2B
LRIG1
ERC2
APPL1
ARHGEF3
IL17RD
PXK
FEZF2
EBLN2
SHQ1
ZNF654
LMOD3
ADAMTS9
ABHD6
C3orf14
PROK2
THOC7
ID2B
KBTBD8
SLC25A26
FAM3D
C3orf49
SNTN
SYNPR
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
ARL13B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
C3orf64
C3orf38
CCDC66
LOC285401
EIF4E3
SPATA12
VGLL3
LOC401074
FAM19A1
STX19
LOC440970
FLJ20518
FAM86DP
MIR548A2
GXYLT2
ZNF717
LOC100287879
FRG2C
MIR1284
MIR1324
MIR3136
MIR4272
MIR4273
MIR3938
LOC100506994
LOC100507062
ADAMTS9-AS2
MIR4795
MIR4444-1
LOC100652759
Genes in Wide Peak

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

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

Genes
MAP2K4
GAS7
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FOXO3B
FLII
KCNJ12
LLGL1
MEIS3P1
MFAP4
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
PMP22
MAPK7
MAP2K3
PRPSAP2
RCVRN
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
MYH13
TMEM11
GLP2R
NTN1
STX8
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
GRAP
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
PIK3R5
DHRS7B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
C17orf48
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
FAM106A
LRRC48
MGC12916
ATPAF2
SPECC1
MYOCD
CDRT7
CDRT15P1
USP43
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
CDRT15
WDR16
CCDC42
PIK3R6
TRIM16L
MFSD6L
USP32P1
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
USP32P2
TBC1D28
CDRT15L2
C17orf103
FLJ34690
CDRT4
CCDC144B
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
CCDC144C
TBC1D26
CDRT1
SPDYE4
TMEM220
SHISA6
FAM211A
KRT16P2
GRAPL
PIRT
CDRT15P2
FAM83G
KRT16P3
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
MIR744
FAM106CP
KCNJ18
LOC100289255
MIR1288
MIR1180
MTRNR2L1
FAM18B2-CDRT4
MIR4731
MIR4522
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

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

Genes
FGF9
IFT88
SAP18
GJB6
LATS2
CRYL1
IL17D
XPO4
MRP63
N6AMT2
SKA3
EFHA1
ZDHHC20
BASP1P1
MIR4499
Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
SERGEF
OR5E1P
OR10A3
FXC1
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
PIDD
KCNQ1DN
SOX6
PARVA
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
NAV2
SYT8
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
LDHAL6A
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
MRGPRX1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
B7H6
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
NAV2-AS4
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
LOC494141
MIR483
SNORA3
SNORA52
LOC644656
RASSF10
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
LOC729013
MIR675
LOC100126784
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
MIR210HG
LOC100506305
LOC100506540
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR4694
MIR4687
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
PARK2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.32.

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

Genes
BRCA1
ETV4
hsa-mir-152
hsa-mir-4315-1
hsa-mir-2117
AOC2
ARL4D
ATP6V0A1
FMNL1
CDC27
CNP
CRHR1
DHX8
DUSP3
EZH1
FZD2
G6PC
KAT2A
GFAP
CCR10
GRN
HCRT
HSD17B1
IFI35
ITGA2B
ITGB3
KPNB1
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
NAGLU
NFE2L1
NMT1
NSF
PPY
PYY
RAB5C
RPL27
SLC4A1
SP2
STAT3
STAT5A
STAT5B
MLX
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
RND2
CNTNAP1
AOC3
BECN1
MAP3K14
EFTUD2
NPEPPS
GOSR2
TBKBP1
PLEKHM1
LRRC37A
HDAC5
GJC1
PSME3
NBR2
RAMP2
VAT1
HEXIM1
C1QL1
RUNDC3A
CBX1
GPATCH8
KCNH4
FAM215A
TUBG2
NKIRAS2
CCDC56
PSMC3IP
TBX21
SOST
COPZ2
ARL17A
SLC25A39
HIGD1B
LRRC37A4
PNPO
ATXN7L3
WNK4
C17orf53
TMUB2
DHX58
PRR15L
ACBD4
DCAKD
PLEKHH3
DBF4B
CDK5RAP3
SP6
COASY
AARSD1
TTC25
VPS25
TMEM101
GHDC
LRRC46
SCRN2
AOC4
G6PC3
ASB16
HSPB9
PLCD3
TMEM106A
OSBPL7
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
C17orf57
MRPL10
CD300LG
KIF18B
RUNDC1
C17orf69
NAGS
FAM134C
IMP5
ARHGAP27
ZNF385C
STH
KIAA1267
C17orf105
FAM171A2
C17orf104
PTRF
C17orf65
LOC388387
CCDC103
RPRML
MGC57346
MIR152
LRRC37A2
LOC644172
LOC644246
MRPL45P2
NSFP1
LOC100128977
LOC100130148
LOC100130581
LOC100133991
LOC100190938
MIR2117
MIR4315-2
MIR4315-1
ARL17B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.1.

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

Genes
DLG2
TMEM126B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q33.3.

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

Genes
ABL1
FANCC
NOTCH1
OMD
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
AUH
BAAT
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
CKS2
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
GAS1
NR6A1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
HSPA5
TNC
IARS
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PHF2
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLE1
TLE4
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
FAM120A
PMPCA
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
GOLM1
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
FAM22F
DIRAS2
ASPN
BSPRY
C9orf167
TEX10
LPPR1
EXD3
FAM206A
STX17
NOL8
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
C9orf86
CDK5RAP2
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
BDAG1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
NAA35
SLC28A3
CARD9
SUSD1
IPPK
DDX31
FAM129B
MRPL41
WNK2
SECISBP2
C9orf16
MAPKAP1
ZCCHC6
GALNT12
EHMT1
SVEP1
RMI1
PTGES2
GKAP1
AKNA
MIR600HG
URM1
ISCA1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC16
LOC158257
FAM120AOS
LINC00475
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
C9orf96
OLFML2A
QSOX2
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
FRMD3
C9orf43
LINC00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
TPRN
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
LOC340508
LOC340515
GPR144
FAM75D5
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf170
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC440173
FAM75C1
LOC441454
LOC441455
FAM22G
LOC441461
C9orf173
NRARP
C9orf129
PALM2-AKAP2
LOC494127
DNAJC25
DNAJC25-GNG10
MIR455
NRON
FAM163B
FLJ40292
TUBBP5
RNF224
FAM75C2
C9orf29
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA84
SNORA70C
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
UNQ6494
LOC100129316
LOC100129722
LOC100130954
LOC100131193
LOC100132077
FAM157B
LOC100132781
RNU6ATAC
LINC00092
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3154
MIR2861
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3621
MIR3910-1
MIR3689A
MIR3911
MIR3910-2
MIR3689B
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506599
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4670
MIR4672
MIR3689E
MIR4479
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.1.

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

Genes
CTAGE5
FSCB
MIA2
LRFN5
FBXO33
LOC100288846
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq25.

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

Genes
ELF4
GPC3
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
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
ABCD1
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CD40LG
CDR1
CETN2
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
GPC4
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
OPN1MW
GDI1
GRIA3
HCFC1
HMGB3
HPRT1
IDH3G
IDS
IGSF1
IL9R
IRAK1
L1CAM
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA5
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
OCRL
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SMARCA1
SOX3
SRD5A1P1
SSR4
VAMP7
TAZ
VBP1
XPNPEP2
ZIC3
ZNF75D
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
CXorf1
GPR50
RAB33A
ARHGEF6
MAGEC1
MAMLD1
BCAP31
ODZ1
SPRY3
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
TREX2
LDOC1
FAM127B
SRPK3
SNORA70
SNORD61
RBMX
HTATSF1
PNMA3
SPANXA1
CTAG2
NSDHL
ZDHHC9
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
CXorf48
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
FAM45B
GABRQ
MOSPD1
THOC2
PDZD4
RAP2C
FAM3A
BCORL1
SPANXD
SPANXC
FUNDC2
PRRG3
BRCC3
MAP7D3
GPR101
CD99L2
H2AFB3
USP26
PHF6
TMEM185A
SLITRK2
MGC16121
PNMA6A
FATE1
HS6ST2
FRMD7
CXorf40A
FAM58A
MMGT1
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
CSAG1
FMR1NB
LOC158696
ARHGAP36
FAM122B
FAM122C
SPANXE
SPANXF1
DDX26B
ZNF449
VMA21
CTAG1A
MAGEA2B
ATP11C
RP1-177G6.2
LOC286467
LINC00204B
DCAF12L2
OR13H1
CCDC160
CXorf66
UBE2NL
CSAG3
LINC00086
MIR105-1
MIR105-2
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
F8A2
F8A3
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
CXorf69
LINC00087
MIR542
SNORA36A
SNORA56
MAGEA9B
OPN1MW2
CSAG2
SPANXB1
SPANXA2
CT45A2
MIR767
FMR1-AS1
MIR509-2
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR934
MIR509-3
MIR891A
MIR892A
LOC100128420
CXorf51A
LOC100129515
LOC100129520
LOC100129662
HSFX2
CXorf64
LOC100131434
CXorf68
LINC00204A
CXorf51B
SPANXB2
MTCP1NB
LOC100272228
PNMA6C
PNMA6D
MIR1184-1
MIR320D2
MIR718
MIR2114
MIR514B
MIR3202-2
MIR4330
MIR1184-3
MIR1184-2
MIR3202-1
HSFX1
LOC100506757
LOC100507404
MAGEA10-MAGEA5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.22.

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

Genes
AUTS2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.2.

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PICALM
PCSK7
ARHGEF12
MAML2
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CTSC
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
GRIA4
GRIK4
GRM5
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
TRPC6
TYR
UPK2
ZBTB16
ZNF202
CUL5
FZD4
BARX2
OR7E2P
JRKL
EED
ZNF259
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
C2CD2L
NAALAD2
RBM7
MPZL2
YAP1
HYOU1
ATP5L
ME3
GPR83
SRSF8
ADAMTS8
PRSS23
TREH
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
RAB38
CADM1
PANX1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
CHORDC1
ACAD8
B3GAT1
DCPS
C11orf54
ZBTB44
THYN1
DDX25
NOX4
NTM
CDON
SIDT2
TRAPPC4
C11orf73
CWC15
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
SYTL2
ANKRD49
TTC12
C11orf57
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TMEM126B
TEX12
CRTAM
TMPRSS4
IFT46
C11orf75
PRDM10
TRIM49
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CREBZF
CARD18
CCDC81
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TMEM135
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
TMEM126A
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
KIAA1731
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
SLC36A4
FAT3
TRIM64
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
CCDC67
PATE1
C11orf65
ADAMTS15
MPZL3
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
CCDC83
HEPACAM
OAF
CCDC89
ANGPTL5
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
HEPHL1
C11orf34
VSTM5
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
SCARNA9
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49L1
LOC100128239
LOC100132078
PATE3
LOC100288077
LOC100288346
MIR1304
BACE1-AS
MIR4301
MIR3167
MIR1260B
LOC100499227
MIR3920
MIR3656
LOC100506368
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.2.

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

Genes
BCL2
MALT1
hsa-mir-122
hsa-mir-4320
CDH7
CYB5A
DCC
FECH
KDSR
GALR1
GRP
LMAN1
SMAD4
MBD1
MBP
MC4R
ME2
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
CXXC1
ST8SIA3
MEX3C
TMX3
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
MRO
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
SKA1
CCDC11
DOK6
RNF152
LINC00305
C18orf26
BOD1P
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
SCARNA17
SNORA37
LOC100130522
LOC100131655
LOC100287225
MIR4320
LOC100505474
LOC100505549
LOC100505776
LOC100505817
MIR4529
MIR3591
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
AKT2
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
hsa-mir-641
A1BG
ACTN4
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
PPP6R1
CARD8
SIRT2
CYP2G1P
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
ZNF345
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
PRX
SPTBN4
MARK4
CATSPERG
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
WDR87
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
SNORD35B
ZNF347
ZNF577
ZNF607
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
ZNF585B
TIMM50
SHKBP1
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
ZNF540
ZNF525
SPACA4
ZNF585A
NLRP7
GGN
CADM4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
LOC284408
LOC284412
VSTM1
TMEM150B
FAM71E2
HKR1
VN1R2
VN1R4
NLRP9
ZNF546
MYPOP
NANOS2
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
C19orf51
ZNF233
LILRA5
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
LOC386758
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF793
PAPL
LOC390940
ZNF805
SPRED3
ZNF321P
LGALS17A
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
TMEM91
LOC643669
LOC644554
LOC646508
SBK2
LOC646862
PSG10P
LGALS7B
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
LOC100129935
SGK110
BSPH1
LOC100131691
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
ERVV-2
LOC100287177
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
LOC100507433
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
LOC100631378
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

Table S55.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3177
hsa-mir-662
hsa-mir-3176
ARHGDIG
CLCN7
HBA1
HBA2
HBM
HBQ1
HBZ
MPG
NME3
NME4
SOLH
SSTR5
TPSAB1
UBE2I
NPRL3
AXIN1
RGS11
CACNA1H
BAIAP3
RHBDL1
PIGQ
RAB11FIP3
IFT140
TELO2
MSLN
STUB1
MRPL28
MAPK8IP3
TPSD1
TPSG1
DECR2
SOX8
POLR3K
GNG13
LUC7L
CRAMP1L
RAB40C
TMEM8A
CHTF18
RHBDF1
NARFL
LINC00235
TPSB2
PDIA2
UNKL
LMF1
FAM173A
MRPS34
METRN
SNRNP25
TMEM204
ITFG3
WDR24
HAGHL
C16orf13
FAM195A
GNPTG
RHOT2
HN1L
SPSB3
RPUSD1
C16orf42
WFIKKN1
CCDC78
C16orf11
FBXL16
LOC146336
WDR90
EME2
NHLRC4
C16orf91
JMJD8
PRR25
C1QTNF8
PTX4
MSLNL
CCDC154
MIR662
LOC100134368
DDX11L10
MIR3177
MIR3176
Genes in Wide Peak

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

Table S56.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BMPR1A
FGFR2
TLX1
NFKB2
PTEN
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
hsa-mir-606
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
ANXA11
FAS
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GLUD1
GOT1
PRLHR
GPR26
GRK5
GRID1
HABP2
HELLS
HHEX
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KCNMA1
KIF11
ABLIM1
LIPA
MAT1A
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGR
RGS10
RPS24
SCD
SFRP5
SFTPD
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
MBL1P
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
DLG5
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
PPIF
ACTR1A
SMNDC1
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
TUBGCP2
PRDX3
C10orf116
VAX1
ATE1
POLR3A
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
LRIT1
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
ANKRD1
GHITM
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
PANK1
FAM190B
EXOC6
FAM35A
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
ZMIZ1
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
FAM213A
WDR96
LRRC27
TNKS2
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
C10orf11
PCGF6
LOXL4
ZDHHC16
C10orf58
DYDC2
PCGF5
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ZNF503
ATAD1
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
OPN4
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
ANKRD22
SFXN2
PDZD8
C10orf32
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
LIPJ
CFL1P1
TRUB1
VTI1A
LOC143188
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
LOC170425
EMX2OS
PPAPDC1A
PAOX
FAM24B
LOC219347
PLAC9
ZCCHC24
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
FLJ37201
LOC283038
LOC283050
LOC283089
O3FAR1
KCNK18
LIPM
CYP26C1
VWA2
NANOS1
LRIT2
HMX3
NHLRC2
C10orf96
FLJ46361
SH2D4B
C10orf99
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
C10orf62
LOC439990
LOC439994
IFIT1B
FRG2B
MIR346
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
LOC642361
FAM196A
FAM25A
LIPK
LIPN
LOC643529
RPL13AP6
LOC650623
SFTPA1
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
FAM22A
FAM22D
LOC728190
LOC728218
DUX4L2
LOC728558
LOC729020
SFTPA2
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100128292
ZNF503-AS2
LOC100132987
KLLN
LOC100169752
LOC100188947
DNMBP-AS1
LOC100288974
LOC100289509
MIR1287
MIR1307
MIR2110
FAS-AS1
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
LOC100507470
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4678
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.31.

Table S57.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BCL7A
hsa-mir-4304
ACADS
SCARB1
COX6A1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
P2RX4
P2RX7
POLE
PSMD9
PXMP2
RAN
CLIP1
SFSWAP
HNF1A
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
ULK1
DENR
OASL
DYNLL1
SRSF9
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RNF10
MPHOSPH9
CAMKK2
ZNF268
TMED2
SNRNP35
FZD10
MLXIP
P2RX2
SETD1B
ANKLE2
ABCB9
RIMBP2
ATP6V0A2
HCAR1
GALNT9
ARL6IP4
POP5
ANAPC5
TRIAP1
RHOF
SBNO1
ZCCHC8
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
C12orf43
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
RNF34
CCDC92
PUS1
COQ5
CCDC62
KDM2B
UNC119B
ORAI1
C12orf65
TMEM132C
TMEM132B
LOC116437
TMEM132D
SLC15A4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
MORN3
GATC
HNF1A-AS1
DDX51
HCAR2
LOC338799
EP400NL
RILPL1
IL31
SETD8
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
LOC647589
SNORA49
LOC100128554
LOC100130238
LOC100190940
ZNF605
MIR4304
MIR3612
MIR3908
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4700
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.13.

Table S58.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FANCC
GNAQ
OMD
PAX5
SYK
TAL2
XPA
NR4A3
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
ABCA1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
APBA1
AUH
BAAT
KLF9
C5
CA9
CCIN
TNFSF8
CD72
CKS2
CLTA
COL15A1
SLC31A1
SLC31A2
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
DBC1
ECM2
LPAR1
S1PR3
MEGF9
STOM
FBP1
FKTN
FOXE1
FXN
NR5A1
GAS1
NR6A1
GCNT1
GGTA1P
GNG10
GOLGA1
GPR21
GSN
HNRNPK
HSD17B3
HSPA5
TNC
IARS
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
NPR2
NTRK2
ROR2
OGN
ORM1
ORM2
PAPPA
PDCL
PCSK5
PGM5
PHF2
PPP3R2
PPP6C
PRKACG
PSMB7
PSMD5
PTCH1
PTGS1
PTPN3
RAD23B
RGS3
RMRP
RORB
SHB
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TXN
UGCG
CORO2A
ZFP37
ZNF189
ZFAND5
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
CTNNAL1
FBP2
PRPF4
KLF4
LHX2
GRHPR
FAM189A2
TJP2
ATP6V1G1
GABBR2
GDA
GNA14
RGP1
TRIM14
MELK
RUSC2
ZBTB5
TNFSF15
PTBP3
GNE
RABEPK
CREB3
UNC13B
SEMA4D
ANP32B
SPTLC1
SMC2
ZBTB6
NEK6
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC35D2
CNTRL
AKAP2
RPL35
FRMPD1
ZNF510
HABP4
PTGR1
TRIM32
ERP44
SMC5
FAM120A
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA0368
TDRD7
SLC44A1
CDK20
RABGAP1
TMEM2
C9orf5
C9orf4
DFNB31
NIPSNAP3A
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
INVS
SIT1
PSAT1
UBQLN1
DEC1
PCA3
EXOSC3
FAM108B1
GOLM1
C9orf156
RAB14
TMEM8B
SHC3
POLE3
NANS
MRPL50
RC3H2
EPB41L4B
FAM22F
DIRAS2
ASPN
BSPRY
TEX10
LPPR1
FAM206A
C9orf95
STX17
NOL8
C9orf40
TMEM38B
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDK5RAP2
BARX1
RNF20
OR2S2
BDAG1
ZBTB26
GBA2
DENND1A
SLC46A2
LINC00474
C9orf80
ZNF462
NAA35
SLC28A3
SUSD1
POLR1E
IPPK
WNK2
SECISBP2
DCAF10
ZCCHC6
GALNT12
CNTNAP3
SVEP1
RMI1
TRPM3
GKAP1
AKNA
MIR600HG
ISCA1
ARPC5L
HDHD3
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
HIATL1
HINT2
C9orf100
C9orf3
COL27A1
ALG2
FGD3
C9orf30
MCART1
MRRF
RBM18
FP588
KIF12
PALM2
WDR31
ZNF618
FAM122A
GRIN3A
TMC1
RNF183
C9orf41
C9orf57
C9orf85
C9orf135
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
TRPM6
RNF38
GLIPR2
DAB2IP
NXNL2
OR1Q1
TTLL11
RASEF
FAM201A
RG9MTD3
LOC158257
FAM120AOS
LINC00475
LOC158376
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
OLFML2A
C9orf71
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
ANKRD18A
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
CRB2
SCAI
C9orf47
C9orf79
LOC286238
LOC286297
LINC00256A
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
LOC340508
LOC340515
GPR144
FAM75D5
OR1J1
OR1B1
IGFBPL1
MURC
FOXD4L4
AQP7P1
PTAR1
C9orf102
KGFLP1
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
C9orf128
OR13J1
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR204
MIR23B
MIR24-1
MIR27B
MIR32
MIR7-1
C9orf103
LOC440173
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
LOC441461
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
LOC572558
PGM5P2
MIR455
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75C2
HRCT1
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
MSMP
SNORD90
MIR600
MIR601
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
SNORA84
SNORA70C
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LINC00476
LOC100129034
UNQ6494
LOC100129316
LOC100132077
LOC100132352
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
LINC00092
LOC100286938
LOC100288842
MIR548H3
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3910-1
MIR3910-2
MIR3651
LOC100505478
LOC100506710
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR4667
MIR4540
MIR4475
MIR4478
MIR4670
MIR4476
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.1.

Table S59.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BRAF
CDK6
EZH2
HIP1
MET
SMO
AKAP9
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
ABP1
ACHE
AKR1B1
ARF5
ASNS
AZGP1
OPN1SW
BPGM
CACNA2D1
CALCR
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
KRIT1
CD36
CDK5
CFTR
CHRM2
AP1S1
CLCN1
COL1A2
CPA1
CPA2
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNAI1
GNB2
GNG11
GNGT1
GPR22
GPR37
GRM3
GRM8
GTF2I
GTF2IP1
HGF
MNX1
AGFG2
HSPB1
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MDH2
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PIP
PMS2P1
PMS2L2
PMS2P5
PMS2P3
PODXL
POLR2J
PON1
PON2
PON3
POR
PPP1R3A
PRKAR2B
PRSS1
PRSS2
RELN
PSMC2
TAS2R38
PTN
PTPN12
PTPRN2
PTPRZ1
RARRES2
RHEB
CCL24
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
SRI
AKR1D1
SRPK2
SSBP1
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
YWHAG
ZNF3
ZKSCAN1
ZSCAN21
ZP3
ZYX
MTERF
SHFM1
TFPI2
ST7
ARHGEF5
ZNF212
TRRAP
FZD1
ZNF282
CUL1
TRIM24
BUD31
SGCE
MGAM
WASL
PLOD3
CLDN12
DGKI
AP4M1
ATP6V1F
ACCN3
PMPCB
ATP5J2
GTF2IRD1
PDIA4
UBE3C
FAM131B
SEMA3E
DOCK4
FAM115A
MAGI2
DMTF1
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
AASS
SLC25A13
LRRC17
POP7
BET1
CCL26
SEMA3A
FAM3C
COG5
ZNHIT1
SEMA3C
ARPC1A
SH2B2
STAG3
FGL2
CPSF4
FASTK
DBF4
COPS6
DUS4L
ZNF277
ABCB8
TP53TG1
PDAP1
TFEC
LAMB4
LMTK2
POMZP3
PAXIP1
KLHDC10
PEG10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
STEAP1
COPG2
HBP1
DNAJC2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
PCLO
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRB
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
LUC7L2
MRPS33
STYXL1
ASB4
NUB1
NAA38
ADAM22
PION
GPR85
TAS2R5
STAG3L1
ANKIB1
CHPF2
PUS7
ING3
LRRN3
CROT
ALKBH4
SAMD9
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
PPP1R9A
CCDC132
AGK
METTL2B
MLL5
BAIAP2L1
SLC25A40
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
PHTF2
ACTR3B
KIAA1147
RHBDD2
FAM40B
ESYT2
ZNF398
CCDC146
GATAD1
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
RABL5
CYP3A43
CASD1
LRRC61
C7orf49
ZNF655
PVRIG
C7orf23
GCC1
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ZNF767
C7orf58
TTC26
ORAI2
UPK3B
JHDM1D
OR2AE1
WBSCR16
TSC22D4
TRIM56
TMUB1
ARMC10
TMEM120A
IMMP2L
CTTNBP2
RBM48
ZNF394
GTF2IRD2
MYH16
SLC37A3
KRBA1
FAM71F1
MGC16142
SLC35B4
TMEM209
TMEM60
GTPBP10
TRIM4
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
MYL10
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
DTX2
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
EMID2
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
SRCRB4D
ASZ1
MUC17
RNF32
ASB15
RUNDC3B
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
NSUN5P1
RBM33
MGC27345
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
BHLHA15
ZNF800
GIMAP1
LOC202781
C7orf33
SAMD9L
C7orf62
ZNF804B
FABP5P3
ZNF498
FAM200A
PPP1R35
GPC2
SRRM3
RSBN1L
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
UBN2
MBLAC1
FAM133B
TAS2R39
TAS2R40
TAS2R41
STEAP2
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
DLX6-AS1
ZNF789
LOC286002
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
GNAT3
MOGAT3
FAM71F2
STRA8
KLRG2
WDR86
GJC3
DPY19L2P2
LOC349160
GATS
GSTK1
TRIM73
NAT16
SLC26A5
LHFPL3
KCP
TRIM74
FLJ43663
RNF148
SPDYE8P
GATSL1
GTF2IRD2B
MGC72080
C7orf59
FEZF1
FAM180A
OR2A25
OR2A5
RPL13AP17
LRRD1
FLJ42280
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
KPNA7
C7orf61
UFSP1
MIR106B
MIR129-1
MIR153-2
MIR182
MIR183
MIR25
MIR29A
MIR29B1
MIR93
MIR96
LOC407835
DTX2P1-UPK3BP1-PMS2P11
SPDYE3
SPDYE2
AKR1B15
CTAGE15P
OR2A9P
OR2A2
DPY19L2P4
STAG3L2
SPDYE5
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR489
MIR490
FDPSL2A
ZNF862
LOC645249
LOC645591
AZGP1P1
LOC646329
C7orf73
NCF1
ACTR3C
NCF1C
SNORA14A
MIR591
MIR592
MIR593
MIR595
LOC723809
MIR653
LOC728066
LOC728377
LOC728743
GATSL2
SPDYE6
TMEM229A
LOC730441
LUZP6
MIR671
LOC100093631
POM121C
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
RPL19P12
LOC100129845
LOC100130705
EFCAB10
LOC100130880
LOC100131176
LOC100132707
LOC100132832
LOC100133091
LOC100134229
LOC100134713
UPK3BL
LOC100216545
LOC100216546
LOC100287482
MOXD2P
LOC100289187
LOC100289561
ZNF783
MIR548F3
MIR548I4
SPDYE2L
MIR548M
MIR548F4
SAP25
MIR548T
MIR4285
MTRNR2L6
MIR3609
MIR3907
MIR3666
LOC100505483
LOC100505854
MAGI2-AS3
LOC100506136
LOC100506585
LOC100507421
ATP5J2-PTCD1
GIMAP1-GIMAP5
MIR4653
MIR4652
MIR4468
MIR4651
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.1.

Table S60.  Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-548f-1
MBL2
PCDH15
MTRNR2L5
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 21 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 0.51 2.14 0.118 0.28 -0.938 1
1q 1955 0.65 3.91 0.000928 0.38 0.118 0.821
2p 924 0.43 -0.377 1 0.06 -4.51 1
2q 1556 0.39 -0.221 1 0.06 -4.18 1
3p 1062 0.29 -1.72 1 0.48 0.509 0.582
3q 1139 0.54 1.31 0.381 0.44 0.0706 0.821
4p 489 0.33 -1.48 1 0.67 2.53 0.0255
4q 1049 0.09 -3.32 1 0.63 2.78 0.0137
5p 270 0.44 -0.775 1 0.35 -1.82 1
5q 1427 0.19 -2.77 1 0.39 -0.364 0.917
6p 1173 0.58 2.1 0.118 0.22 -2.21 1
6q 839 0.55 1.31 0.381 0.24 -2.34 1
7p 641 0.45 -0.29 1 0.42 -0.64 0.985
7q 1277 0.40 -0.39 1 0.33 -1.15 1
8p 580 0.53 0.612 0.798 0.65 2.18 0.0526
8q 859 0.60 1.81 0.202 0.45 -0.0531 0.834
9p 422 0.20 -2.59 1 0.69 2.93 0.0114
9q 1113 0.06 -3.02 1 0.73 4.34 0.000288
10p 409 0.60 1.2 0.418 0.68 2.39 0.0337
10q 1268 0.49 0.722 0.784 0.54 1.43 0.209
11p 862 0.14 -3.44 1 0.52 0.913 0.401
11q 1515 0.22 -2.16 1 0.49 1.18 0.278
12p 575 0.49 0.128 1 0.42 -0.735 0.992
12q 1447 0.26 -1.97 1 0.31 -1.37 1
13q 654 0.50 0.309 1 0.63 2.08 0.0623
14q 1341 0.24 -1.95 1 0.55 1.86 0.0968
15q 1355 0.17 -2.5 1 0.62 2.87 0.0116
16p 872 0.39 -0.617 1 0.70 3.4 0.00341
16q 702 0.32 -1.33 1 0.74 3.85 0.000784
17p 683 0.24 -1.94 1 0.75 4.05 0.000512
17q 1592 0.45 0.585 0.798 0.46 0.773 0.463
18p 143 0.46 -0.622 1 0.49 -0.292 0.911
18q 446 0.39 -1.19 1 0.48 -0.148 0.86
19p 995 0.56 1.48 0.345 0.50 0.633 0.527
19q 1709 0.62 3.02 0.0127 0.52 1.42 0.209
20p 355 0.76 3.65 0.00176 0.37 -1.1 1
20q 753 0.84 5.23 3.46e-06 0.47 0.0177 0.822
21q 509 0.46 -0.266 1 0.45 -0.438 0.923
22q 921 0.35 -1 1 0.69 3.28 0.00411
Xq 1312 0.28 -1.61 1 0.51 1.23 0.274
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/UCS-TP/5949701/GDAC_MergeDataFiles_4313924/UCS-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 56 Input Tumor Samples.

Tumor Sample Names
TCGA-N5-A4RA-01A-11D-A28Q-01
TCGA-N5-A4RD-01A-11D-A28Q-01
TCGA-N5-A4RF-01A-11D-A28Q-01
TCGA-N5-A4RJ-01A-11D-A28Q-01
TCGA-N5-A4RM-01A-11D-A28Q-01
TCGA-N5-A4RN-01A-12D-A28Q-01
TCGA-N5-A4RO-01A-11D-A28Q-01
TCGA-N5-A4RS-01A-11D-A28Q-01
TCGA-N5-A4RT-01A-11D-A28Q-01
TCGA-N5-A4RU-01A-31D-A28Q-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.

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)
[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)
[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)
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