SNP6 Copy number analysis (GISTIC2)
Prostate Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C14M93SG
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 2.0.22 (Firehose task version: 140).

Summary

There were 492 tumor samples used in this analysis: 25 significant arm-level results, 28 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 - 28 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
Xq27.1 2.6886e-07 2.6886e-07 chrX:138564705-138580758 0 [F9]
8q24.21 2.6886e-07 9.927e-07 chr8:127953664-129189823 11
3q26.2 2.6886e-07 6.4879e-06 chr3:169376291-170116437 13
11q13.2 7.8472e-06 7.8472e-06 chr11:66543112-69956664 67
8p11.23 0.00032184 0.00032184 chr8:37058175-39443168 31
Xp22.11 8.9842e-06 0.00037755 chrX:23975644-23983593 0 [CXorf58]
Xq21.1 5.4768e-05 0.00039034 chrX:79251708-79255479 0 [TBX22]
14q21.1 0.00047025 0.00047025 chr14:37963714-38056422 1
1q22 0.0011464 0.0011464 chr1:153559798-155300779 74
Xp22.11 2.2165e-05 0.0026713 chrX:24515774-24522924 1
16q11.2 0.0041215 0.0041215 chr16:46507666-47387972 11
17q23.2 0.0060535 0.0060535 chr17:59788818-60189565 4
Xq25 0.00047025 0.0063545 chrX:126306276-126315813 0 [CXorf64]
4q13.3 0.011376 0.011376 chr4:73389847-74219241 6
12q23.1 0.01384 0.01384 chr12:75332782-123735875 394
Xp21.1 0.0053422 0.01384 chrX:35651236-35660210 0 [MAGEB16]
15q11.2 0.021823 0.021823 chr15:1-26017542 51
7q22.1 0.032693 0.032693 chr7:77428990-108687578 278
3q21.3 6.5212e-05 0.049487 chr3:124584788-158439394 257
Xq21.1 0.037292 0.051638 chrX:80829747-80833679 0 [SH3BGRL]
13q12.11 0.064198 0.064198 chr13:1-24578109 56
7p14.3 0.078261 0.078261 chr7:13797002-38664933 171
9q33.3 0.088693 0.088693 chr9:97960858-141213431 526
20q13.2 0.096109 0.096109 chr20:41749332-63025520 274
4p16.3 0.13657 0.13657 chr4:1-8029694 105
8q22.1 1.407e-05 0.19023 chr8:60962111-123468077 293
5q35.3 0.21663 0.21663 chr5:116910334-180915260 581
19q13.43 0.22867 0.22867 chr19:53895880-58255438 197
Genes in Wide Peak

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

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

Genes
MYC
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
MIR1205
MIR1207
PVT1
MIR1208
Genes in Wide Peak

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

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

Genes
TERC
MECOM
PRKCI
SKIL
SEC62
GPR160
MYNN
LRRC31
PHC3
ACTRT3
LRRC34
LRRIQ4
SAMD7
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
CCND1
FGF3
MIR3164
TPCN2
MIR4691
FAM86C2P
DOC2GP
C11orf72
RN7SL59P
PTPRCAP
RN7SKP239
POLD4
snoU13|ENSG00000238892.1
SYT12
U3|ENSG00000252709.1
ADRBK1
ALDH3B1
ALDH3B2
CHKA
CPT1A
FGF4
GSTP1
IGHMBP2
LRP5
NDUFV1
NDUFS8
PC
PPP1CA
RAD9A
RPS6KB2
AIP
PITPNM1
MTL5
FGF19
RCE1
CDK2AP2
TCIRG1
KDM2A
CLCF1
MYEOV
RHOD
GAL
SUV420H1
CABP2
C11orf24
SSH3
ANO1
PPP6R3
CABP4
CORO1B
CARNS1
LRFN4
C11orf80
TMEM134
UNC93B1
ACY3
MRGPRD
MRGPRF
MRPL21
ORAOV1
C11orf86
NUDT8
ANKRD13D
TBX10
TBC1D10C
GPR152
MIR3163
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
FGFR1
WHSC1L1
ADAM3A
ADAM5
SNORD38|ENSG00000207199.1
PLEKHA2
RPS20P22
STAR
RN7SL709P
BRF2
ZNF703
ADRB3
EIF4EBP1
TACC1
ADAM18
ADAM9
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
RAB11FIP1
TM2D2
PPAPDC1B
GOT1L1
LETM2
HTRA4
ADAM32
C8orf86
Genes in Wide Peak

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

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

Genes
MIPOL1
Genes in Wide Peak

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

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

Genes
MUC1
TPM3
GBAP1
EFNA3
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
ADAR
CHRNB2
CKS1B|ENSG00000173207.8
CLK2
EFNA1
EFNA3
EFNA4
FDPS
GBA
IL6R
ILF2
KCNN3
MTX1
NPR1
PKLR
RAB13
RPS27
S100A1
S100A13
SHC1
THBS3
ADAM15
UBAP2L
DENND4B
SCAMP3
HAX1
PMVK
FAM189B
JTB
SLC27A3
SNAPIN
RUSC1
C1orf43
CHTOP
SLC39A1
ZBTB7B
DPM3
UBE2Q1
LENEP
SLC50A1
ATP8B2
PBXIP1
S100A14
GATAD2B
HCN3
INTS3
TRIM46
FLAD1
AQP10
PYGO2
NUP210L
TDRD10
SHE
DCST2
S100A16
CREB3L4
DCST1
KRTCAP2
CRTC2
MIR92B
MIR190B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.11.

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

Genes
PDK3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q11.2.

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

Genes
ITFG1
snoU13|ENSG00000238834.1
MYLK3
VPS35
ANKRD26P1
DNAJA2
ORC6
SHCBP1
NETO2
GPT2
C16orf87
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.2.

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

Genes
BRIP1
RN7SL800P
MED13
INTS2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
ADAMTS3
ANKRD17
COX18
Genes in Wide Peak

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

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

Genes
BCL7A
BTG1
ALDH2
PTPN11
RN7SL133P
MIR4304
HCAR1
SNORA9|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38|ENSG00000201042.1
RNA5SP374
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56|ENSG00000200112.1
RN7SL865P
SNORA27|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40|ENSG00000264043.2
FICD
RNA5SP371
SNORD74|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13|ENSG00000238914.1
U8|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13|ENSG00000238800.1
SLC5A8
snoU13|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13|ENSG00000239073.1
SNORD74|ENSG00000201502.1
snoU13|ENSG00000238361.1
snoU13|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
HAL
HPD
IGF1
KCNC2
LTA4H
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
PPP1CC
PRKAB1
PSMD9
PXN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SYT1
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UNG
ALX1
BRAP
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
CABP1
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
TRAFD1
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
KERA
KRR1
PRDM4
CIT
PWP1
NUDT4
RPH3A
FBXO21
SETD1B
UHRF1BP1L
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
CORO1C
MGAT4C
FBXW8
HSPB8
UTP20
MRPL42
IFT81
CCDC59
FAM216A
SYCP3
CHST11
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
NTN4
TRPV4
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
NUP37
DDX54
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
NAA25
SLC24A6
CEP290
RNF34
MTERFD3
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
METTL25
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
CCDC64
SDSL
OSBPL8
IQCD
DEPDC4
CCDC38
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
GLIPR1L2
TMEM120B
WDR66
TSPAN19
E2F7
RAD9B
FAM109A
TMTC2
TMTC3
C12orf50
ALDH1L2
CCDC63
CCDC60
PLBD2
FAM71C
CCER1
SLC17A8
LRRC43
TCP11L2
C12orf79
GLIPR1L1
POC1B
OTOGL
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
MMAB
HCAR2
TMEM119
C12orf74
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
CLLU1OS
CLLU1
MIR492
C12orf73
MIR1251
MIR4303
MIR3685
MIR4495
MIR4700
MIR4497
MIR5700
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q11.2.

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

Genes
RNA5SP390
ATP10A
SNORD109B
SNORD115|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64|ENSG00000270704.2
SNHG14
SNURF
snoU13|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13|ENSG00000239083.1
CHEK2P2
RN7SL584P
NDN
SNRPN
UBE3A
MKRN3
CYFIP1
NPAP1
NIPA2
TUBGCP5
NIPA1
GOLGA6L2
HERC2P3
GOLGA6L1
GOLGA8I
GOLGA8EP
OR4M2
POTEB2
MIR4508
POTEB
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
CDK6
AKAP9
FLJ00325
U3|ENSG00000238297.1
snoU109|ENSG00000238832.1
RNA5SP236
SNORD112|ENSG00000251911.1
RN7SL8P
LHFPL3
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
MIR4658
MIR106B
MIR93
MIR25
AZGP1P1
SNORA40|ENSG00000222966.1
CYP3A4
snoU13|ENSG00000239133.1
MYH16
snoU13|ENSG00000238459.1
MIR3609
RN7SL13P
RN7SL478P
RN7SKP104
RN7SL252P
SHFM1
MIR591
PON1
snoU13|ENSG00000238384.1
RN7SKP129
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
snoU13|ENSG00000238739.1
DPY19L2P4
SNORA67|ENSG00000207094.1
snoU13|ENSG00000238587.1
LINC00972
SEMA3A
RNA5SP235
MIR1255B1
RN7SL35P
RN7SL869P
RNA5SP234
ACHE
ASNS
AZGP1
CACNA2D1
CALCR
KRIT1
CD36
AP1S1
COL1A2
CUX1
CYP3A7
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
SLC26A3
EPHB4
EPO
GNAI1
GNB2
GNGT1
GPR22
GRM3
HGF
AGFG2
LAMB1
LRCH4
MCM7
DNAJB9
NPTX2
NRCAM
OCM2
ORC5
SERPINE1
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
POLR2J
PON2
PON3
PRKAR2B
RELN
PSMC2
SRI
SRPK2
SYPL1
TAC1
TAF6
TFR2
TRIP6
VGF
ZAN
ZNF3
ZKSCAN1
ZSCAN21
MTERF
TFPI2
TRRAP
FZD1
BUD31
SGCE
PLOD3
CLDN12
AP4M1
PMPCB
ATP5J2
SEMA3E
MAGI2
DMTF1
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
BET1
COG5
ZNHIT1
SEMA3C
ARPC1A
STAG3
CPSF4
DBF4
COPS6
DUS4L
TP53TG1
PDAP1
LAMB4
LMTK2
PEG10
ZKSCAN5
CLDN15
BRI3
TECPR1
PTCD1
FBXO24
STEAP1
HBP1
DNAJC2
PCLO
PILRA
PNPLA8
FIS1
ACTL6B
SRRT
ASB4
ADAM22
ANKIB1
PUS7
CROT
ALKBH4
SAMD9
ZCWPW1
C7orf43
PPP1R9A
CCDC132
KMT2E
BAIAP2L1
SLC25A40
BCAP29
MEPCE
SLC12A9
ACN9
SMURF1
PHTF2
RINT1
MOSPD3
GIGYF1
CYP3A43
CASD1
ZNF655
PVRIG
TMEM243
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ORAI2
OR2AE1
TSC22D4
TRIM56
ARMC10
RBM48
ZNF394
GTPBP10
TRIM4
MYL10
COL26A1
MUC17
RUNDC3B
C7orf66
THAP5
CCDC71L
BHLHA15
SAMD9L
C7orf62
ZNF804B
ZSCAN25
FAM200A
PPP1R35
GPC2
KIAA1324L
LRWD1
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
MBLAC1
FAM133B
STEAP2
ZNF789
GNAT3
MOGAT3
GJC3
DPY19L2P2
GATS
NAT16
SLC26A5
LAMTOR4
RPL13AP17
LRRD1
C7orf76
KPNA7
C7orf61
UFSP1
SPDYE3
SPDYE2
POLR2J3
EFCAB10
UPK3BL
RASA4B
SPDYE2B
MIR548O
MIR4652
MIR5692C2
MIR5692A1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q21.3.

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

Genes
FOXL2
GATA2
MLF1
RPN1
GMPS
SHOX2
RN7SKP46
RNA5SP146
CCNL1
LINC00881
LINC00880
RN7SKP177
LINC00886
snoU13|ENSG00000271922.1
U8|ENSG00000201398.1
RN7SL300P
RAP2B
SUCNR1
IGSF10
P2RY12
RNA5SP145
FAM188B2
snoU13|ENSG00000243321.2
ANKUB1
TM4SF4
CPHL1P
U3|ENSG00000251800.1
RNA5SP144
PBX2P1
CHST2
RN7SKP25
RNA5SP143
GRK7
RNF7
CLSTN2
RN7SL724P
RN7SKP124
PIK3CB
SOX14
RNA5SP142
RNY4P4
U8|ENSG00000253004.1
RNA5SP141
KY
RPL39P5
RNA5SP140
TFP1
SNORA33|ENSG00000201827.1
snoU13|ENSG00000238701.1
MIR5704
SNORA58|ENSG00000249020.1
RN7SKP212
COL6A4P2
FAM86HP
ALG1L2
RN7SL752P
SNORA7B
RPL32P3
snoU13|ENSG00000238874.1
snoU13|ENSG00000252435.1
RN7SL698P
SNORA24|ENSG00000207130.1
MIR1280
RNA5SP139
NUP210P1
TXNRD3NB
RNA5SP138
U1|ENSG00000272020.1
FAM86JP
snoU13|ENSG00000238992.1
MIR5092
RNA5SP137
AADAC
ACPP
AGTR1
ATP1B3
ATR
CP
CPA3
CPB1
EPHB1
GP9
GYG1
ITGB5
TM4SF1
MBNL1
MCM2
MME
NCK1
P2RY1
PCCB
PFN2
PLOD2
PLS1
PLSCR1
PLXNA1
PPP2R3A
PTX3
RARRES1
RASA2
RBP1
RBP2
RHO
RYK
SIAH2
SLCO2A1
HLTF
SSR3
TF
TFDP2
TRH
TRPC1
CLRN1
ZIC1
CNBP
ZNF148
RAB7A
KCNAB1
BFSP2
RUVBL1
SNX4
MBD4
H1FX
SLC33A1
COPB2
TSC22D2
P2RY14
STAG1
ALDH1L1
TOPBP1
MRPL3
RNF13
MGLL
MRAS
COPG1
PLCH1
TMCC1
PLXND1
DNAJC13
U2SURP
C3orf27
ANAPC13
ARMC8
WWTR1
TIPARP
ARHGEF26
PCOLCE2
NPHP3
ATP2C1
SERP1
ACAD9
ASTE1
KLF15
GPR171
SEC61A1
PIK3R4
PODXL2
COMMD2
A4GNT
DBR1
CLDN18
RSRC1
AMOTL2
ACKR4
RAB6B
SELT
P2RY13
IL20RB
GPR87
XRN1
SLC41A3
MSL2
FAIM
SLC25A36
CDV3
IFT122
MUC13
LXN
C3orf37
MRPS22
PLSCR2
PLSCR4
HEG1
KIAA1257
SRPRB
BPESC1
EEFSEC
TMEM108
ZXDC
VEPH1
EFCC1
NEK11
UBA5
C3orf36
CEP63
CEP70
ABTB1
SLC35G2
ESYT3
EIF2A
ZIC4
ACAD11
CHCHD6
HPS3
SLC12A8
GFM1
EFCAB12
SPSB4
ACPL2
TXNRD3
OSBPL11
TM4SF18
MED12L
CPNE4
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
H1FOO
ROPN1B
C3orf22
C3orf55
C3orf79
NUDT16P
DNAJB8
CHST13
KBTBD12
DHX36
DZIP1L
ALG1L
C3orf58
ZBTB38
COL6A5
GK5
SLC9A9
C3orf56
C3orf33
TRIM42
RAB43
AADACL2
GPR149
PAQR9
NME9
CCDC37
NMNAT3
PRR23B
PRR23C
PLSCR5
LEKR1
C3orf72
TMEM14E
PRR23A
MIR548I1
ISY1
MIR4788
MIR5186
Genes in Wide Peak

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

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

Genes
ANKRD20A19P
LINC00352
LINC00327
LINC00362
RNY3P4
LINC00621
SNORD36|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27|ENSG00000252128.1
snoU13|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
FGF9
GJA3
GJB2
MIPEP
SGCG
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
TNFRSF19
XPO4
MRP63
TPTE2
N6AMT2
SKA3
MICU2
SPATA13
C1QTNF9B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p14.3.

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

Genes
HOXA13
ETV1
HNRNPA2B1
HOXA9
HOXA11
JAZF1
RN7SL83P
TRGV1
TRGV2
TRGV3
TRGV4
TRGV5
TRGV8
TRGV9
TRGV10
TRGV11
TRGJP1
TRGJP
TRGJ1
TRGC1
TRGJP2
TRGJ2
TRGC2
SNORA51|ENSG00000200113.1
snoU13|ENSG00000238772.1
MIR1200
PP13004
SEPT7
DPY19L2P1
MIR548N
SNORA31|ENSG00000251802.1
RN7SL132P
RNA5SP229
snoU13|ENSG00000252706.1
RN7SL505P
RP9P
SNORA31|ENSG00000251999.1
AQP1
CRHR2
MIR550A1
snoU13|ENSG00000238906.1
TRIL
RN7SL365P
EVX1
HOTTIP
HOTAIRM1
U3|ENSG00000202233.1
CYCS
snoU13|ENSG00000239098.1
RNA5SP228
snoU13|ENSG00000238849.1
SNORD65|ENSG00000212264.1
MALSU1
SNORD93
RNA5SP227
MIR1183
RN7SL542P
SP8
SNORD56|ENSG00000200753.1
MIR3146
RN7SKP266
SNORA63|ENSG00000199473.1
ISPD
ADCYAP1R1
AHR
AMPH
AOAH
AQP1
CHN2
DGKB
DFNA5
GARS
GHRHR
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
IL6
ITGB8
MEOX2
NPY
PDE1C
RP9
SFRP4
SP4
TWIST1
DNAH11
TAX1BP1
SKAP2
CREB5
NFE2L3
HDAC9
RAPGEF5
SCRN1
KIAA0087
ELMO1
NOD1
GPNMB
AGR2
IGF2BP3
PPP1R17
NUPL2
HIBADH
INMT
FKBP9
CBX3
AVL9
SNX13
DPY19L1
KIAA0895
LSM5
SOSTDC1
KBTBD2
OSBPL3
TSPAN13
BBS9
BZW2
SNX10
TRA2A
NT5C3A
NME8
MPP6
ANLN
CPVL
TOMM7
EPDR1
FKBP14
CDCA7L
KLHL7
STK31
ANKMY2
TBX20
NEUROD6
NPVF
HERPUD2
GGCT
EEPD1
STARD3NL
FAM188B
FAM126A
PLEKHA8
CCDC126
C7orf31
AGR3
BMPER
PRPS1L1
TWISTNB
C7orf41
PRR15
FERD3L
CCDC129
ZNRF2
TMEM196
STEAP1B
C7orf71
ABCB5
FAM221A
MACC1
GPR141
NPSR1
AGMO
MIR148A
MIR196B
WIPF3
MIR550A2
LRRC72
MIR550A3
Genes in Wide Peak

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

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

Genes
ABL1
FANCC
NOTCH1
RALGDS
SET
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13|ENSG00000238530.1
MIR455
COL27A1
FKBP15
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
ABCA1
ABCA2
AK1
ALAD
ALDOB
AMBP
ASS1
BAAT
C5
C8G
CACNA1B
CCBL1
ENTPD2
CDK9
CEL
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CYLC2
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
NR6A1
GLE1
GNG10
GOLGA1
GOLGA2
RAPGEF1
GRIN1
GSN
HSD17B3
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
PRPF4
KLF4
GTF3C5
LHX2
MED27
PTGES
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
ANP32B
AGPAT2
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7A
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
PMPCA
ASTN2
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
RABGAP1
TMEM245
CIZ1
DFNB31
NELFB
NIPSNAP3A
NSMF
GPSM1
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
BSPRY
TOR4A
TEX10
EXD3
FAM206A
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
RABL6
CDK5RAP2
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
SLC46A2
ZNF462
PRDM12
SUSD1
DDX31
FAM129B
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
HIATL2
NTNG2
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
TMEM141
C9orf37
MVB12B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
MRRF
ARRDC1
DPH7
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
PTRH1
PIP5KL1
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
SLC34A3
DAB2IP
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
C9orf96
OLFML2A
QSOX2
ZNF367
C9orf91
NAIF1
ANKS6
CDC26
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
FAM78A
OR13C9
OR13D1
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
ERCC6L2
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR147A
MIR181A2
MIR181B2
MIR199B
NUTM2G
C9orf173
NRARP
DNAJC25
MIR600HG
MIR602
RNF208
CARD9
MIR3154
CCDC180
MIR3689A
MIR3911
MIR3927
MIR3689B
MIR3689D1
MIR3689F
MIR3960
MIR4674
MIR4478
MIR3689C
MIR3689D2
MIR3689E
MIR548AW
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
GNAS
SS18L1
NPBWR2
MIR647
MIR1914
C20ORF135
SLC2A4RG
MIR4326
MIR3196
HAR1A
HAR1B
LINC00029
GID8
LINC00659
LINC00686
MIR133A2
MIR4758
ATP5E
MGC4294
ANKRD60
RAE1
RN7SL170P
U3|ENSG00000252536.1
FAM209A
GCNT7
snoU13|ENSG00000238294.1
RNA5SP487
RNU4ATAC7P
RN7SKP184
RN7SL603P
MIR3194
RN7SL672P
RN7SL636P
LINC00651
snoU13|ENSG00000239157.1
RN7SL197P
KCNB1
SNORD12
SNORD12B
SNORD12C
ZFAS1
LINC00494
SNORD36|ENSG00000252227.1
RNA5SP486
RN7SL243P
MIR3616
RN7SKP33
SNX21
RNU6ATAC38P
SPINT4
WFDC10A
RNA5SP485
RBPJL
RN7SL31P
KCNK15
MIR3646
R3HDML
FITM2
RN7SL443P
SCARNA15|ENSG00000252193.1
RN7SL666P
ADA
BMP7
CD40
CDH4
CEBPB
CHRNA4
COL9A3
CSE1L
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
EYA2
HNF4A
KCNG1
KCNQ2
KCNS1
LAMA5
MC3R
MMP9
MYBL2
MYT1
NFATC2
NTSR1
OPRL1
PCK1
PFDN4
PI3
PLTP
CTSA
PPP1R3D
PSMA7
PTGIS
PTK6
PTPN1
RPS21
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SRMS
STAU1
STK4
AURKA
TAF4
TCEA2
TFAP2C
TNNC2
TPD52L2
UBE2V1
YWHAB
ZNF217
NCOA3
BCAS1
STX16
TNFRSF6B
MATN4
DPM1
WISP2
VAPB
B4GALT5
SPATA2
OSBPL2
ACOT8
ATP9A
SGK2
ARFRP1
RGS19
SYCP2
WFDC2
ARFGEF2
TCFL5
SPINT3
TOMM34
SERINC3
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
HRH3
SLC9A8
ADNP
ZMYND8
SPO11
PRPF6
L3MBTL1
MTG2
GMEB2
TP53TG5
MOCS3
SLCO4A1
STMN3
SLC35C2
SLMO2
IFT52
NELFCD
RTFDC1
OSER1
PIGT
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
PCMTD2
MRGBP
PPP4R1L
RBM38
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
DOK5
DBNDD2
RNF114
SULF2
PMEPA1
CASS4
EPPIN
JPH2
SALL4
ZNFX1
RAB22A
SLC12A5
ZNF512B
PREX1
COL20A1
NCOA5
CDH26
SLC17A9
ELMO2
ZNF335
PCIF1
FAM217B
CDH22
SLC13A3
GDAP1L1
C20orf195
PPDPF
TTPAL
BIRC7
NPEPL1
DNAJC5
PABPC1L
TUBB1
ZBP1
SLC2A10
CABLES2
PARD6B
ZGPAT
TOX2
HELZ2
SYS1
WFDC8
ZSWIM1
TP53RK
DNTTIP1
FAM210B
PHACTR3
BHLHE23
NKAIN4
WFDC12
SPATA25
OCSTAMP
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
WFDC3
CBLN4
CTCFL
SAMD10
ABHD16B
RIMS4
NEURL2
ZSWIM3
C20orf62
WFDC6
FAM65C
RBBP8NL
GTSF1L
WFDC5
LSM14B
WFDC13
APCDD1L
C20orf201
WFDC11
WFDC9
WFDC10B
LINC00176
C20orf197
TMEM189
FAM209B
MIR296
MIR645
MIR646
MIR298
MIR1257
MIR4325
MTRNR2L3
MIR3617
MIR4756
MIR4532
MIR4533
MIR548AG2
Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
EVC
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
SH3BP2
WFS1
NELFA
SLBP
NOP14
FAM193A
KIAA0232
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
NSG1
STX18
FGFRL1
CYTL1
PIGG
BLOC1S4
STK32B
LYAR
TBC1D14
SORCS2
UVSSA
ZFYVE28
AFAP1
TNIP2
HAUS3
MFSD7
TMEM175
ABLIM2
TMEM128
TMEM129
MRFAP1
TADA2B
MRFAP1L1
EVC2
OTOP1
JAKMIP1
FAM53A
ZBTB49
CCDC96
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
PSAPL1
MIR378D1
MIR4800
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q22.1.

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

Genes
EXT1
COX6C
NCOA2
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
SNORD112|ENSG00000252559.1
TMEM74
RNA5SP275
snoU13|ENSG00000238687.1
RIMS2
MIR3151
RNU6ATAC8P
snoU13|ENSG00000238533.1
snoU13|ENSG00000238372.1
RN7SL563P
NACAP1
RN7SKP249
RN7SL685P
RNU6ATAC41P
MIR1273A
SNORD77|ENSG00000212414.1
RN7SL350P
RN7SKP85
KCNS2
NIPAL2
SNORA72|ENSG00000207067.1
LAPTM4B
U3|ENSG00000207215.1
PTDSS1
snoU13|ENSG00000238791.1
FSBP
RNA5SP274
LINC00535
RN7SKP231
snoU13|ENSG00000239134.1
MIR4661
RN7SL777P
RNA5SP273
LINC00534
RNA5SP272
MMP16
REXO1L10P|ENSG00000255940.1
REXO1L11P
REXO1L10P|ENSG00000270416.1
snoU13|ENSG00000238566.1
SLC10A5
IMPA1P
RN7SL308P
RN7SL107P
SNORA20|ENSG00000206649.1
RN7SL41P
snoU13|ENSG00000238595.1
CASC9
RNA5SP271
U8|ENSG00000200191.1
RN7SL19P
snoU13|ENSG00000238450.1
RNA5SP270
RN7SL675P
RN7SKP29
RNA5SP269
PREX2
RNA5SP268
SNORD87
LINC00967
PDE7A
LINC00966
RN7SKP135
RN7SL135P
NKAIN3
RN7SKP97
CA8
ANGPT1
ASPH
ATP6V1C1
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CRH
DECR1
DPYS
E2F5
EYA1
FABP4
FABP5
GEM
HNF4G
IL7
IMPA1
EIF3E
MATN2
MYBL1
NBN
NOV
ODF1
TNFRSF11B
ENPP2
PMP2
POLR2K
PKIA
PEX2
RAB2A
RAD21
RPL7
RPL30
SDC2
SNTB1
SPAG1
STK3
TAF2
TCEB1
TERF1
KLF10
TPD52
TRHR
TRPS1
TTPA
COL14A1
UQCRB
YWHAZ
FZD6
RIPK2
GGH
CPNE3
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
EMC2
HRSP12
CPQ
ARFGEF1
POP1
COPS5
WWP1
STMN2
RRS1
SULF1
ZFPM2
HEY1
TRAM1
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
PABPC1
KCNV1
STAU2
MTBP
BHLHE22
MRPS28
MRPL13
LRP12
RRM2B
MTERFD1
PI15
ZC2HC1A
LACTB2
RMDN1
ZNF706
UBR5
AZIN1
OTUD6B
GDAP1
PDP1
CNGB3
ESRP1
TMEM70
OXR1
ARMC1
UBE2W
TMEM55A
CHD7
SYBU
INTS8
PAG1
C8orf44
JPH1
ENY2
CPA6
PRDM14
SNX16
NECAB1
DEPTOR
ZBTB10
DSCC1
PLEKHF2
ZFAND1
ZFHX4
CSPP1
BAALC
GRHL2
VCPIP1
SLC25A32
DCSTAMP
SLCO5A1
CRISPLD1
NCALD
UTP23
TRIM55
NUDCD1
LRRCC1
TSPYL5
DNAJC5B
PSKH2
MED30
TMEM67
MTDH
CHMP4C
PKHD1L1
TP53INP1
MAL2
CSMD3
SLC26A7
CTHRC1
OSR2
C8orf34
FAM92A1
NDUFAF6
ABRA
ADHFE1
DCAF4L2
RALYL
RDH10
C8orf56
ANKRD46
C8orf37
VPS13B
SLC7A13
MCMDC2
CLVS1
SBSPON
CNBD1
SLC30A8
SNX31
TMEM64
C8orf47
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
TRIQK
DPY19L4
FBXO43
PPP1R42
RSPO2
CA13
XKR9
C8orf87
RBM12B
GDF6
C8orf59
SAMD12
ZNF704
SNHG6
FABP9
FABP12
MIR548A3
MIR599
MIR875
TCF24
LRRC69
MIR2053
MIR3150B
MIR3610
MIR378D2
MIR4471
MIR4470
MIR5680
MIR5708
MIR5681A
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
TRIM52
SNORD95|ENSG00000264549.1
SNORD96A
LINC00847
MIR340
RN7SKP150
MIR1229
HMGB3P22
RN7SL71P
ZNF879
ZNF354B
AACSP1
RN7SKP70
RN7SL646P
RN7SL562P
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
RN7SKP148
snoU13|ENSG00000239026.1
NSG2
RNA5SP200
SNORA74B
ATP6V0E1
MIR5003
SNORA57|ENSG00000212529.1
C5orf50
SNORA70|ENSG00000206909.1
RN7SL339P
snoU13|ENSG00000252387.1
RN7SL623P
MIR4454
KCNMB1
LCP2
C5orf58
MIR378E
MIR585
MIR103A1
PANK3
FBLL1
SNORA40|ENSG00000253065.1
RN7SKP60
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68|ENSG00000252458.1
LSM11
THG1L
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
RNA5SP198
RN7SKP232
RNA5SP197
ZNF300P1
snoU13|ENSG00000239191.1
snoU13|ENSG00000238369.1
MIR378A
RN7SL868P
U3|ENSG00000221043.1
MIR143HG
RN7SKP145
MIR584
SH3TC2
SPINK13
RN7SL791P
RNA5SP196
GPR151
RN7SKP246
KCTD16
RN7SL87P
RN7SL68P
PCDHGB8P
PCDHB18
PCDHB17
PCDHA14
WDR55
MIR3655
SNORA27|ENSG00000200235.1
SNORD45|ENSG00000200051.1
CYSTM1
PURA
TMEM173
ECSCR
RN7SKP64
RNA5SP195
SNORA74A
SNORA74|ENSG00000252213.1
RNA5SP194
RN7SL867P
snoU13|ENSG00000238745.1
SNORD63|ENSG00000206989.1
SNORD63|ENSG00000222937.1
RN7SL682P
snoU13|ENSG00000238605.1
NPY6R
MIR874
RNA5SP193
FBXL21
TIFAB
MIR4461
MIR4461
PCBD2
RN7SL541P
PPP2CA
SKP1
snoU13|ENSG00000238796.1
HSPA4
LEAP2
UQCRQ
RNA5SP192
snoZ6|ENSG00000253067.1
HINT1
RNA5SP191
RNU6ATAC10P
KIAA1024L
MIR4633
C5orf63
RN7SKP117
RN7SL711P
RN7SL689P
snoU13|ENSG00000239103.1
snoU13|ENSG00000252295.1
snoU13|ENSG00000239067.1
snoU13|ENSG00000239084.1
RNA5SP190
RN7SL174P
TNFAIP8
MIR5706
snoU13|ENSG00000239011.1
DTWD2
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDX1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
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
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
LECT2
LMNB1
LOX
LTC4S
SMAD5
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPIC
PPP2R2B
MAPK9
PROP1
RARS
RPS14
SGCD
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
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
FAXDC2
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
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
TSPAN17
OR4F3
OR2V1
HAVCR1
CYFIP2
PKD2L2
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
DDX41
NOP16
LARS
CXXC5
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
TMED9
ZCCHC10
CDHR2
SPDL1
TMCO6
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
NMUR2
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
ZNF608
PCDHB16
HMHB1
C5orf54
SIL1
ARAP3
RMND5B
GRAMD3
PCYOX1L
CCNJL
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PSD2
THOC3
MEGF10
SPINK7
HAVCR2
PHYKPL
SMIM3
FCHSD1
UNC5A
LYRM7
TRIM41
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
SCGB3A2
C5orf47
PPARGC1B
PRRC1
ZNF474
OR2Y1
AFAP1L1
GRPEL2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
CREBRF
CEP120
SLC25A48
SRFBP1
ZMAT2
BTNL9
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
STK32A
SLC36A1
RASGEF1C
EFCAB9
SH3PXD2B
FAM153A
RELL2
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
FAM170A
ARSI
PFN3
IRGM
CATSPER3
NIPAL4
DND1
SIMC1
C5orf48
PROB1
C5orf46
ARHGEF37
SPINK6
ANKHD1
MIR143
MIR145
MIR146A
SPINK14
FNDC9
C5orf56
IGIP
CTXN3
GRXCR2
SPINK9
ZFP62
CCNI2
CBY3
FAM153C
FAM196B
C5orf52
MIR1303
MIR3141
MIR3912
MIR3936
MIR3661
MIR4634
MIR378H
MIR4460
MIR4638
MIR5197
MIR5692C1
Genes in Wide Peak

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

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

Genes
TFPT
ZNF331
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13|ENSG00000239137.1
KIR3DX1
LILRA6
LENG1
NDUFA3
MIR935
MIR371B
RN7SL317P
ZNF813
ZNF761
FCAR
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR1
LAIR2
CNOT3
PEG3
PRKCG
PTPRH
RPL28
RPS9
AURKC
TNNI3
TNNT1
ZNF17
ZNF154
NCR1
LILRB2
ZNF211
TRAPPC2P1
ZNF460
LILRB1
LILRB5
LILRB4
LILRA1
LILRB3
LILRA3
LILRA2
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
PRPF31
UBE2S
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
EPS8L1
ZNF444
NLRP2
ZNF416
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
CACNG8
CACNG7
CACNG6
ZNF667
TSEN34
MBOAT7
ZSCAN5A
ZNF419
ISOC2
ZNF671
BRSK1
SUV420H2
FIZ1
GALP
ZNF628
ZNF551
ZNF835
ZNF765
NLRP12
MYADM
LENG9
RDH13
ZIM3
LENG8
KIR3DL3
ZNF543
COX6B2
OSCAR
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
TMEM190
TMC4
TPM3P9
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF550
ZNF579
NLRP7
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
VSTM1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZNF530
DNAAF3
LILRA5
ZNF773
ZNF470
ZNF749
ZNF772
TARM1
MIR371A
MIR372
MIR373
DPRX
MIR498
MIR520E
MIR519E
MIR520F
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
SHISA7
SGK110
MIR1323
ZNF865
MIR4752

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
10q23.31 2.8262e-97 2.8262e-97 chr10:89617158-90034038 3
6q14.3 2.8449e-74 2.8449e-74 chr6:87800060-88001063 1
13q14.13 3.3037e-73 3.6241e-56 chr13:44451821-48879660 43
21q22.3 3.9641e-75 4.056e-49 chr21:42827479-42911705 2
17p13.1 4.2109e-35 4.2172e-35 chr17:7505228-7591760 5
5q21.1 1.0118e-36 1.1155e-28 chr5:98134187-99875640 1
8p21.3 1.1086e-30 2.172e-23 chr8:20153951-25048845 48
12p13.1 2.1153e-22 2.1153e-22 chr12:12844234-12921132 2
3p13 7.7481e-21 7.7481e-21 chr3:71874461-72622531 5
16q24.1 6.7117e-39 1.1027e-19 chr16:83853134-87119808 38
17q21.31 3.7517e-15 3.8405e-15 chr17:42102307-42651945 20
2q22.1 2.3691e-21 1.1267e-12 chr2:132506741-141000702 37
16q22.3 2.1561e-32 3.251e-10 chr16:72142073-74472459 7
21q22.2 1.0757e-41 3.1227e-07 chr21:39665722-40155078 2
13q22.1 6.5823e-36 1.9169e-05 chr13:60735713-81800340 68
1q42.3 0.00014003 0.00021258 chr1:224927969-237207188 144
9p23 0.00024273 0.00024273 chr9:7887952-12687261 3
5q11.2 1.5287e-28 0.0004632 chr5:54597198-57789060 21
19q13.2 0.0014573 0.0014011 chr19:42731571-42891571 7
2q22.3 3.8447e-14 0.0014833 chr2:146092408-150190650 10
4q28.2 0.0030644 0.0031653 chr4:115720296-134070791 57
11p11.2 0.0044993 0.0043835 chr11:37721288-49054288 80
18q23 1.0107e-06 0.0063883 chr18:68317374-78077248 38
1p31.3 0.00069136 0.0077161 chr1:63901623-66226788 18
5q13.2 2.7472e-26 0.010012 chr5:66492413-72750050 46
11q23.2 1.1706e-07 0.017991 chr11:113343413-114999314 17
12q24.32 0.023518 0.022887 chr12:123752264-133851895 81
8p23.2 2.7346e-08 0.027216 chr8:2112968-4985851 3
1p22.1 0.0056609 0.034399 chr1:82457075-107602611 141
15q21.3 0.043588 0.043268 chr15:56756286-58245985 8
6p25.1 0.054986 0.054986 chr6:4071224-9597208 31
2p21 0.10084 0.099345 chr2:31042414-47146045 95
3q29 0.16842 0.16849 chr3:194988874-198022430 47
1q23.1 0.14088 0.17582 chr1:156902282-157964746 11
11q22.3 0.00024479 0.2189 chr11:102955092-122320965 188
18q21.31 0.0010715 0.2189 chr18:51910315-71741815 75
7q31.33 0.24875 0.25335 chr7:124404074-129472001 42
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.3.

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

Genes
ZNF292
Genes in Wide Peak

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

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

Genes
LCP1
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31|ENSG00000199477.1
SNORA31|ENSG00000253051.1
7SK|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13|ENSG00000238932.1
TSC22D1
LINC00284
CPB2
ESD
GTF2F2
HTR2A
TPT1
SUCLA2
ITM2B
ZC3H13
LRCH1
NUFIP1
MED4
NUDT15
KIAA1704
SMIM2
KIAA0226L
COG3
LACC1
FAM194B
SPERT
LRRC63
SLC25A30
SIAH3
KCTD4
SERP2
Genes in Wide Peak

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

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

Genes
TMPRSS2
SNORA32|ENSG00000207503.1
Genes in Wide Peak

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

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

Genes
TP53
snoU13|ENSG00000251860.1
ATP1B2
SHBG
SAT2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.1.

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

Genes
CHD1
Genes in Wide Peak

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

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

Genes
RN7SL651P
NEFL
SNORA67|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13|ENSG00000238466.1
U3|ENSG00000251944.1
BMP1
POLR3D
EGR3
DMTN
GFRA2
LOXL2
NEFM
PPP3CC
SFTPC
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
ADAM28
XPO7
RHOBTB2
SLC39A14
ADAMDEC1
PIWIL2
HR
BIN3
KIAA1967
PDLIM2
FAM160B2
REEP4
CHMP7
PEBP4
R3HCC1
LGI3
MIR320A
C8orf58
Genes in Wide Peak

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

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

Genes
MIR613
CDKN1B
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238568.1
RYBP
LINC00870
LINC00877
RN7SL271P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.1.

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

Genes
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
COX4I1
FOXF1
FOXL1
FOXC2
IRF8
MBTPS1
TAF1C
USP10
KIAA0513
ATP2C2
EMC8
GSE1
COTL1
MLYCD
OSGIN1
NECAB2
ZDHHC7
WFDC1
MTHFSD
KLHL36
HSDL1
CRISPLD2
DNAAF1
SLC38A8
ADAD2
FAM92B
C16orf74
MIR1910
MIR5093
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

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

Genes
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
GRN
ITGA2B
SLC4A1
UBTF
HDAC5
RUNDC3A
SLC25A39
ATXN7L3
C17orf53
TMUB2
G6PC3
ASB16
LSM12
FAM171A2
Genes in Wide Peak

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

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

Genes
RN7SL283P
SNORA72|ENSG00000206901.1
RN7SKP286
NXPH2
RNA5SP105
RN7SKP141
SNORA40|ENSG00000208308.1
snoU13|ENSG00000238337.1
MIR5590
RNA5SP104
RN7SKP93
RN7SKP154
RN7SKP103
RN7SL701P
CCNT2
DARS
GPR39
HNMT
LCT
MCM6
MGAT5
CXCR4
RAB3GAP1
UBXN4
R3HDM1
MAP3K19
THSD7B
TMEM163
ZRANB3
LYPD1
ACMSD
SPOPL
NCKAP5
C2orf27B
ANKRD30BL
MIR663B
MIR3679
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.3.

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

Genes
NPIPB15
HCCAT5
ZFHX3
PSMD7
PMFBP1
C16orf47
CLEC18B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.2.

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

Genes
ERG
LINC00114
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q22.1.

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

Genes
RNA5SP33
LINC00331
RNY3P3
LINC00446
RN7SL810P
RNY3P7
CLN5
RN7SL571P
LINC00561
C13orf45
LINC00347
LINC00381
RNY1P5
LINC00402
LINC00392
LINC00393
RNY1P8
SNORA9|ENSG00000199282.1
SNORA68|ENSG00000251715.1
SNORD37|ENSG00000212377.1
RNA5SP32
LINC00348
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
KLF5
DACH1
EDNRB
LMO7
PCDH9
POU4F1
UCHL3
SCEL
TBC1D4
SPRY2
PIBF1
KLF12
DIS3
MYCBP2
FBXL3
NDFIP2
KLHL1
RBM26
PCDH20
RNF219
BORA
TDRD3
KCTD12
SLAIN1
COMMD6
MZT1
IRG1
MIR3169
MIR3665
MIR4704
MIR548X2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.3.

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

Genes
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13|ENSG00000239094.1
snoU13|ENSG00000238545.1
ACTA1
ACTN2
PARP1
AGT
ARF1
LYST
EPHX1
GALNT2
GNG4
GUK1
H3F3A
ITPKB
KCNK1
LBR
LGALS8
MTR
NID1
PSEN2
RAB4A
SRP9
TARBP1
TBCE
LEFTY2
GPR137B
TSNAX
HIST3H3
GNPAT
CDC42BPA
GGPS1
TMEM63A
TOMM20
URB2
LEFTY1
SPHAR
CAPN9
COG2
RBM34
ABCB10
TAF5L
DISC1
PYCR2
TRIM17
ARID4B
EGLN1
MAP10
HEATR1
ENAH
NUP133
ERO1LB
ADCK3
GJC2
SIPA1L2
RHOU
ACBD3
ARV1
JMJD4
C1orf35
TTC13
PGBD5
PCNXL2
TRIM11
MIXL1
SPRTN
OBSCN
MLK4
C1orf198
WNT3A
HIST3H2A
SNAP47
CCSAP
DNAH14
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
EXOC8
SDE2
IBA57
LIN9
PRSS38
IRF2BP2
C1orf95
FAM89A
COA6
TRIM67
C1orf145
C1orf148
MT1HL1
MIR1537
MIR4666A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
RN7SL5P
SNORD27|ENSG00000251699.1
PTPRD
Genes in Wide Peak

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

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

Genes
IL6ST
snoU13|ENSG00000238899.1
snoU13|ENSG00000238717.1
RNU6ATAC2P
RNA5SP185
RNA5SP184
snoU13|ENSG00000238326.1
RNA5SP183
MIR5687
MAP3K1
PPAP2A
PLK2
SKIV2L2
DDX4
GPBP1
ANKRD55
SETD9
IL31RA
SLC38A9
MIER3
ACTBL2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.2.

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

Genes
CIC
MEGF8
ERF
GSK3A
PAFAH1B3
PRR19
TMEM145
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.3.

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

Genes
SNORA48|ENSG00000212181.1
RNA5SP106
snoU13|ENSG00000238860.1
snR65|ENSG00000253036.1
ACVR2A
KIF5C
ORC4
EPC2
MBD5
LYPD6B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q28.2.

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

Genes
IL2
SNORA70|ENSG00000252014.1
RN7SL205P
RNY5P4
snoU13|ENSG00000238802.1
HSPA4L
INTU
RN7SL335P
QRFPR
RN7SKP137
MAD2L1
SNORA11|ENSG00000221245.1
C4orf3
CEP170P1
SNHG8
NT5C3AP1
MTRNR2L13
RN7SL808P
ANXA5
CCNA2
FABP2
FGF2
EXOSC9
TRPC3
PRSS12
PDE5A
NDST3
SEC24D
SPRY1
PGRMC2
PLK4
PRDM5
NUDT6
MYOZ2
USP53
LARP1B
BBS7
ANKRD50
METTL14
IL21
NDST4
NDNF
FAT4
TNIP3
PHF17
C4orf29
SLC25A31
KIAA1109
SCLT1
C4orf33
TMEM155
ADAD1
TRAM1L1
SPATA5
BBS12
SYNPO2
MFSD8
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p11.2.

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

Genes
DDB2
EXT2
CREB3L1
OR4C5
MIR3161
RNA5SP340
snoU13|ENSG00000252447.1
KBTBD4
PTPMT1
RN7SL652P
RN7SL772P
SNORD67|ENSG00000212135.1
SNORD67|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
PHF21A
CHST1
CD82
C11orf96
RN7SKP287
HNRNPKP3
SNORA31|ENSG00000251838.1
ACP2
ARHGAP1
CHRM4
CRY2
F2
LRP4
MDK
MYBPC3
NDUFS3
PSMC3
PTPRJ
RAPSN
SPI1
DGKZ
API5
MADD
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
NR1H3
CELF1
NUP160
FNBP4
MTCH2
PACSIN3
HSD17B12
SLC35C1
AMBRA1
KBTBD4
TTC17
PRDM11
SYT13
LRRC4C
ALX4
C11orf49
ZNF408
AGBL2
ARFGAP2
ACCS
TSPAN18
SLC39A13
C1QTNF4
OR4X2
OR4B1
GYLTL1B
C11orf94
ALKBH3
OR4C3
OR4S1
ACCSL
OR4X1
FAM180B
OR4A47
MIR670
MIR4487
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
CYB5A
MBP
NFATC1
ZNF236
CTDP1
TSHZ1
TXNL4A
ADNP2
KCNG2
TIMM21
ZNF407
CNDP2
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
LINC00908
ATP9B
LINC00909
HSBP1L1
C18orf63
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.3.

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

Genes
JAK1
snoU13|ENSG00000238931.1
LEPROT
MIR4794
RN7SL130P
DLEU2L
RN7SL488P
AK4
ROR1
PGM1
DNAJC6
ITGB3BP
LEPR
RAVER2
CACHD1
EFCAB7
UBE2U
MIR3671
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.2.

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

Genes
PIK3R1
MIR4804
RN7SL153P
MIR4803
snoU13|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13|ENSG00000238334.1
SNORA50|ENSG00000220986.1
RN7SL103P
7SK|ENSG00000249352.3
U8|ENSG00000212249.2
CCNB1
CDK7
FOXD1
GTF2H2
TNPO1
MAP1B
NAIP
PMCHL2
RAD17
SMN1
SMN2
TAF9
SERF1A
CARTPT
MRPS27
BDP1
MCCC2
SLC30A5
CENPH
PTCD2
MRPS36
FCHO2
TMEM171
TMEM174
MARVELD2
ZNF366
CCDC125
GTF2H2C
SERF1B
OCLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

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

Genes
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
HTR3A
NNMT
ZBTB16
HTR3B
ZW10
RBM7
REXO2
C11orf71
NXPE4
USP28
TMPRSS5
NXPE1
NXPE2
CLDN25
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.32.

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

Genes
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13|ENSG00000238822.1
RN7SL534P
snoU13|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9|ENSG00000206897.1
SNRNP35
RNA5SP375
SCARB1
STX2
GOLGA3
GTF2H3
MMP17
POLE
PXMP2
SFSWAP
UBC
ZNF10
ZNF26
ZNF84
ULK1
PIWIL1
NCOR2
ZNF268
TMED2
FZD10
P2RX2
ANKLE2
RIMBP2
ATP6V0A2
GALNT9
SBNO1
CHFR
EP400
DHX37
FBRSL1
DDX55
AACS
NOC4L
TCTN2
CCDC92
PUS1
TMEM132D
SLC15A4
FAM101A
ZNF664
GLT1D1
PGAM5
RILPL2
DNAH10
GPR133
DDX51
EP400NL
RILPL1
SETD8
ZNF605
MIR3908
MIR4419B
MIR5188
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

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

Genes
RN7SL872P
RNA5SP251
CSMD1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p22.1.

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

Genes
BCL10
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
ACTBP12
RN7SL235P
RN7SL653P
BARHL2
U3|ENSG00000199666.1
RN7SKP272
snoU13|ENSG00000239176.1
GBP1P1
GBP6
RN7SL583P
RNA5SP52
RNA5SP51
SNORD81|ENSG00000199934.1
C1orf52
CTBS
SPATA1
RPF1
UOX
SNORA2|ENSG00000199959.1
TTLL7
ABCA4
AGL
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
BRDT
CLCA1
CNN3
COL11A1
DBT
DPYD
S1PR1
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GNG5
GTF2B
CYR61
PRKACB
PKN2
ABCD3
RPL5
TGFBR3
VCAM1
EVI5
CDC7
BCAR3
LMO4
CDC14A
RTCA
CLCA3P
CLCA2
HS2ST1
LPPR4
GLMN
CLCA4
MTF2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
TMED5
SH3GLB1
SNX7
GPR88
TRMT13
ZNHIT6
PALMD
FNBP1L
LRRC8D
PRMT6
MCOLN3
RNPC3
CCBL2
ODF2L
PTBP2
DNASE2B
HIAT1
SYDE2
ZNF644
LRRC8C
GBP4
GBP5
SSX2IP
OLFM3
WDR63
SLC44A3
LRRC39
SAMD13
TMEM56
SLC30A7
SASS6
HFM1
EPHX4
MCOLN2
COL24A1
ZNF326
BTBD8
CCDC18
GBP7
C1orf146
FAM69A
FRRS1
C1orf180
RBMXL1
MIR760
MIR378G
MIR137HG
MIR4423
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.3.

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

Genes
TCF12
MYZAP
LINC00926
snoU13|ENSG00000239035.1
ZNF280D
POLR2M
CGNL1
GCOM1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.1.

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

Genes
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
BMP6
DSP
F13A1
RREB1
SSR1
CDYL
EEF1E1
ECI2
FARS2
RPP40
SLC35B3
NRN1
LYRM4
BLOC1S5
TXNDC5
RIOK1
SNRNP48
CAGE1
C6orf201
PPP1R3G
MIR5683
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p21.

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

Genes
EML4
RHOQ
RN7SL817P
RN7SL414P
SLC3A1
snoU13|ENSG00000239052.1
RN7SKP66
SNORD75|ENSG00000221300.1
snoZ247
HNRNPA1P57
SNORA67|ENSG00000252473.1
RN7SL96P
GEMIN6
LINC00211
RN7SL602P
RNA5SP92
RNA5SP91
SNORD112|ENSG00000252502.1
LINC00486
MIR4765
MIR558
YIPF4
DPY30
SRD5A2
EHD3
RNA5SP90
ZFP36L2
CYP1B1
EPAS1
LTBP1
VIT
PIGF
PPM1B
PRKCE
EIF2AK2
SRSF7
SIX3
SLC8A1
SOS1
SPAST
STRN
XDH
MAP4K3
COX7A2L
CRIPT
PREPL
FEZ2
SOCS5
LRPPRC
CEBPZ
CDC42EP3
SIX2
HAAO
PRKD3
RASGRP3
QPCT
FAM98A
MEMO1
CRIM1
DYNC2LI1
HEATR5B
SRBD1
NDUFAF7
TTC27
SLC30A6
BIRC6
MTA3
NLRC4
THADA
ATL2
ABCG5
ABCG8
GALNT14
CAMKMT
THUMPD2
ATP6V1E2
DHX57
PKDCC
HNRNPLL
PLEKHH2
GALM
TMEM178A
MYADML
RMDN2
OXER1
KCNG3
GPATCH11
CDKL4
TMEM247
SULT6B1
C2orf91
CAPN14
MORN2
ARHGEF33
MIR548AD
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

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

Genes
TFRC
FAM157A
FYTTD1
snoU13|ENSG00000238491.1
MIR4797
U4|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
APOD
BDH1
DLG1
MFI2
MUC4
PAK2
PCYT1A
PPP1R2
RPL35A
KIAA0226
TNK2
NCBP2
ACAP2
PIGX
PIGZ
IQCG
LRCH3
CEP19
LMLN
TM4SF19
ZDHHC19
RNF168
SLC51A
FBXO45
MUC20
SENP5
TCTEX1D2
SMCO1
WDR53
ANKRD18DP
NRROS
LINC00885
MIR570
MIR922
Genes in Wide Peak

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

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

Genes
RN7SL612P
MIR765
CD5L
ETV3
ARHGEF11
FCRL2
FCRL5
FCRL4
FCRL1
FCRL3
ETV3L
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
RNA5SP348
ACAT1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HTR3A
IL10RA
IL18
MCAM
KMT2A
NCAM1
NNMT
NPAT
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
SLN
SORL1
TAGLN
TECTA
UPK2
ZBTB16
CUL5
USP2
HTR3B
ZW10
UBE4A
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK3
BACE1
TRIM29
CADM1
POU2F3
REXO2
TIMM8B
SIDT2
TRAPPC4
FXYD6
C11orf71
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
VPS11
TEX12
IFT46
DSCAML1
ARHGAP20
USP28
CARD18
AASDHPPT
ABCG4
C11orf1
RNF26
DYNC2H1
NLRX1
PDZD3
PDGFD
TMPRSS5
MFRP
BCO2
TMPRSS13
MSANTD4
BUD13
TMEM25
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
APOA5
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
TMEM136
ANKK1
RNF214
FOXR1
CCDC153
CCDC84
C11orf53
C11orf87
C11orf92
C11orf88
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
CLDN25
MIR4301
CASP12
MIR4491
MIR4492
MIR4693
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.31.

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

Genes
BCL2
MALT1
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
snoU13|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8|ENSG00000199713.1
RN7SL112P
SNORD28|ENSG00000252284.1
FECH
U3|ENSG00000212539.1
TXNL1
SNORA73|ENSG00000201816.1
RNA5SP459
CDH7
KDSR
GRP
LMAN1
MC4R
NARS
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
RAB27B
SERPINB3
SERPINB4
TCF4
SERPINB7
TNFRSF11A
SOCS6
ONECUT2
VPS4B
CD226
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
CDH20
CDH19
RAX
ST8SIA3
TMX3
ZCCHC2
ZNF532
KIAA1468
CCDC102B
CCDC68
NETO1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
CCBE1
CBLN2
GTSCR1
DOK6
LINC00305
DYNAP
BOD1L2
HMSD
CPLX4
MIR122
MIR4529
MIR5011
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.33.

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

Genes
SMO
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
ARF5
OPN1SW
FLNC
GRM8
IMPDH1
IRF5
LEP
NRF1
PAX4
ATP6V1F
AHCYL2
TNPO3
POT1
SND1
HILPDA
FSCN3
RBM28
METTL2B
STRIP2
LRRC4
CCDC136
GCC1
FAM71F1
ZNF800
FAM71F2
PRRT4
MIR182
MIR183
MIR96
SMKR1
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 25 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 1300 0.03 -0.265 1 0.05 3.52 0.000804
1q 1195 0.05 2.3 0.0551 0.02 -1.77 1
2p 624 0.02 -2.97 1 0.03 -1.77 1
2q 967 0.01 -2.74 1 0.04 -0.236 1
3p 644 0.08 3.27 0.00311 0.02 -2.95 1
3q 733 0.11 6.62 1.79e-10 0.01 -3.53 1
4p 289 0.02 -4.05 1 0.05 -0.981 1
4q 670 0.02 -2.85 1 0.04 -1.43 1
5p 183 0.04 -2.47 1 0.04 -2.65 1
5q 905 0.03 -1.72 1 0.05 0.497 0.604
6p 710 0.02 -2.9 1 0.05 0.599 0.592
6q 556 0.01 -3.99 1 0.08 3.04 0.00378
7p 389 0.21 14 0 0.00 -4.73 1
7q 783 0.19 15.8 0 0.01 -3.87 1
8p 338 0.14 5.43 1.95e-07 0.44 33.8 0
8q 551 0.25 18.9 0 0.09 2.73 0.00932
9p 301 0.07 0.377 1 0.05 -0.888 1
9q 700 0.10 5.67 5.88e-08 0.02 -2.52 1
10p 253 0.03 -2.65 1 0.09 1.99 0.0594
10q 738 0.03 -2.02 1 0.09 4.83 3.94e-06
11p 509 0.05 -0.303 1 0.02 -3.38 1
11q 975 0.06 2.13 0.0753 0.01 -2.89 1
12p 339 0.03 -2.77 1 0.10 3.81 0.000318
12q 904 0.04 -0.582 1 0.04 0.0827 0.87
13q 560 0.02 -3.08 1 0.16 10.4 0
14q 938 0.02 -2.29 1 0.05 1.53 0.144
15q 810 0.01 -3.25 1 0.07 3.15 0.00278
16p 559 0.07 1.16 0.502 0.07 1.75 0.0971
16q 455 0.02 -3.26 1 0.22 15.8 0
17p 415 0.02 -3.59 1 0.16 9.47 0
17q 972 0.02 -1.99 1 0.04 0.516 0.604
18p 104 0.04 -2.32 1 0.15 6.59 1.55e-10
18q 275 0.02 -3.25 1 0.21 13.2 0
19p 681 0.02 -2.6 1 0.04 -1.18 1
19q 935 0.02 -1.89 1 0.04 -0.319 1
20p 234 0.05 -1.36 1 0.05 -1.54 1
20q 448 0.06 0.093 1 0.02 -3.49 1
21q 258 0.04 -1.65 1 0.05 -1.12 1
22q 564 0.01 -4.14 1 0.10 4.27 5.03e-05
Xp 418 0.02 -3.88 1 0.08 2.11 0.0477
Xq 668 0.01 -3.76 1 0.08 3.54 0.000804
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/PRAD-TP/19079296/GDAC_MergeDataFiles_12186442/PRAD-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_GENCODE_v18_20140127.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 492 Input Tumor Samples.

Tumor Sample Names
TCGA-2A-A8VL-01A-21D-A376-01
TCGA-2A-A8VO-01A-11D-A376-01
TCGA-2A-A8VT-01A-11D-A376-01
TCGA-2A-A8VV-01A-11D-A376-01
TCGA-2A-A8VX-01A-11D-A376-01
TCGA-2A-A8W1-01A-11D-A376-01
TCGA-2A-A8W3-01A-11D-A376-01
TCGA-2A-AAYF-01A-11D-A41J-01
TCGA-2A-AAYO-01A-11D-A41J-01
TCGA-2A-AAYU-01A-11D-A41J-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)