SNP6 Copy number analysis (GISTIC2)
Skin Cutaneous Melanoma (Metastatic)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C15B01DV
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 2.0.21 (Firehose task version: 127).

Summary

There were 366 tumor samples used in this analysis: 23 significant arm-level results, 22 significant focal amplifications, and 33 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 - 22 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
11q13.3 1.4989e-14 1.4989e-14 chr11:69399650-69464717 1
3p13 2.5171e-14 2.5171e-14 chr3:69742923-70094803 2
5p15.33 1.9318e-13 1.9318e-13 chr5:1288616-1300024 1
1p12 5.8018e-12 6.2542e-11 chr1:120229720-120523901 5
6p24.3 9.4427e-09 9.4427e-09 chr6:1977444-14532705 87
1q44 3.5448e-10 1.2897e-08 chr1:245126660-247471120 18
22q13.2 5.0554e-08 5.0554e-08 chr22:41468899-41845216 8
17q25.3 5.4875e-08 5.4875e-08 chr17:67159433-81195210 236
7q34 3.7295e-07 3.7295e-07 chr7:136467935-142508606 72
12q14.1 8.0375e-09 1.6235e-06 chr12:58135797-58215836 10
15q26.2 1.4668e-05 1.4668e-05 chr15:82606423-102531392 169
7p22.1 0.00024256 0.00024256 chr7:1-8532843 93
8q24.21 1.8941e-05 0.00025851 chr8:111566435-146364022 233
12q15 1.0744e-10 0.00043511 chr12:69127775-69670720 5
4q12 0.0027418 0.0027418 chr4:55721956-55767814 0 [KIT]
6q12 0.0073747 0.0073747 chr6:63915276-66019907 5
1q21.3 1.8688e-06 0.0089632 chr1:120523956-156490978 319
19p13.2 0.030897 0.030897 chr19:7300056-7398264 0 [INSR]
20q13.33 0.064606 0.064606 chr20:54375868-63025520 130
13q31.3 0.097638 0.097638 chr13:90269218-91307433 4
8q11.21 0.049717 0.12646 chr8:42932479-52667602 20
5q35.3 0.17365 0.17365 chr5:175337387-180915260 103
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CCND1
Genes in Wide Peak

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

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

Genes
MITF
RN7SL418P
Genes in Wide Peak

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

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

Genes
TERT
Genes in Wide Peak

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

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

Genes
NOTCH2
HMGCS2
ADAM30
PHGDH
REG4
Genes in Wide Peak

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

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

Genes
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
RANBP9
ECI2
FARS2
RPP40
SIRT5
FAM50B
SLC35B3
TBC1D7
NRN1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
WRNIP1
LYRM4
SLC22A23
BLOC1S5
MCUR1
TXNDC5
TMEM14B
RIOK1
ADTRP
SNRNP48
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
PSMG4
C6orf201
PPP1R3G
TMEM170B
MIR4645
MIR5689
MIR5683
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q44.

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

Genes
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
ZNF124
AHCTF1
SCCPDH
KIF26B
ZNF695
TFB2M
SMYD3
ZNF669
EFCAB2
ZNF496
CNST
C1orf229
MIR3916
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q13.2.

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

Genes
EP300
RANGAP1
TEF
TOB2
ZC3H7B
L3MBTL2
CHADL
MIR1281
Genes in Wide Peak

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

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

Genes
ASPSCR1
CANT1
MIR4525
RAB40B
snoU13|ENSG00000238403.1
snoU13|ENSG00000238947.1
DUS1L
PCYT2
SLC25A10
LINC00482
MIR1250
MIR657
MIR4730
CBX8
snoU13|ENSG00000239173.1
ENGASE
DDC8
RN7SL454P
SNORA30|ENSG00000200063.1
RN7SL236P
FLJ45079
LINC00338
LINC00868
MIR636
SNORD1B
SNHG16
PRCD
snoU13|ENSG00000238418.1
MYO15B
RN7SL573P
MIR3615
CD300LD
GPRC5C
RNA5SP448
LINC00469
SSTR2
SCARNA24|ENSG00000252274.1
RN7SKP180
LINC00511
MAP2K6
SNORA40|ENSG00000252352.1
AANAT
ACOX1
ACTG1
BIRC5
ARHGDIA
CD7
CDK3
CSNK1D
SLC25A10
EVPL
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
LGALS3BP
LLGL2
MAFG
NPTX1
P4HB
PDE6G
PRPSAP1
PYCR1
RAC3
RFNG
RPL38
MRPL12
SEC14L1
SECTM1
SRSF2
SGSH
SUMO2
SOX9
SRP68
TBCD
TIMP2
TK1
CBX4
DNAH17
GALR2
SPHK1
SOCS3
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
AATK
KIAA0195
EIF4A3
ALYREF
ABCA10
BAIAP2
ATP5H
ST6GALNAC2
SEPT9
CD300C
CD300A
TMC6
AZI1
GGA3
JMJD6
EXOC7
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NAT9
NARF
SAP30BP
NT5C
CDR2L
MRPS7
HN1
DCXR
ANAPC11
SIRT7
SDK2
TMEM104
C17orf80
CCDC40
NPLOC4
ST6GALNAC1
WDR45B
MIF4GD
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
SLC25A19
UBE2O
FN3K
DNAI2
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
FN3KRP
OGFOD3
ZNF750
NUP85
C17orf70
TSPAN10
QRICH2
CBX2
FAM104A
FBF1
UNK
TRIM47
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
METTL23
SLC38A10
USH1G
CD300LB
KIF19
TBC1D16
AFMID
MGAT5B
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
NOTUM
TMC8
STRA13
LRRC45
SLC39A11
TRIM65
UNC13D
MYADML2
NPB
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
SLC26A11
ENDOV
C17orf89
TMEM105
METRNL
RAB37
ENPP7
OXLD1
CCDC137
ARL16
CD300E
OTOP3
FAM195B
GPR142
ZACN
BTBD17
TEX19
MXRA7
CPSF4L
SMIM5
SMIM6
TEN1
C17orf99
MIR4316
MIR338
MIR3186
MIR3678
MIR3615
MIR4739
MIR4738
MIR4740
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q34.

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

Genes
BRAF
KIAA1549
CREB3L2
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
CHRM2
NDUFB2
PRSS1
TAS2R38
PTN
AKR1D1
SSBP1
TBXAS1
TRIM24
MGAM
DGKI
CLEC5A
MKRN1
DENND2A
HIPK2
ATP6V0A4
TAS2R3
TAS2R4
MRPS33
TAS2R5
ZC3HAV1
KIAA1147
PARP12
TTC26
JHDM1D
SLC37A3
ADCK2
ZC3HAV1L
OR9A4
PRSS37
SVOPL
PRSS58
CLEC2L
C7orf55
TMEM213
UBN2
RAB19
WEE2
MIR490
MTRNR2L6
TMEM178B
MIR4468
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
METTL21B
MARCH9
AGAP2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.2.

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

Genes
BLM
IDH2
NTRK3
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109|ENSG00000239197.1
snoU13|ENSG00000238981.1
RN7SL363P
SNORD18|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
SNORD74|ENSG00000200206.1
RNA5SP400
RN7SL428P
CSPG4P12
SNORA25|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
HDGFRP3
SCARNA15|ENSG00000252690.2
GOLGA6L10|ENSG00000254374.2
RN7SL410P
GOLGA6L9|ENSG00000196648.6
UBE2Q2P3
RN7SL256P
RN7SL61P
CSPG4P8
UBE2Q2P2
ACAN
ALDH1A3
ANPEP
BNC1
CHD2
FES
IGF1R
MAN2A2
MEF2A
MFGE8
NMB
FURIN
PCSK6
PDE8A
PLIN1
POLG
RLBP1
RPS17
SH3GL3
SNRPA1
NR2F2
AP3B2
ST8SIA2
PEX11A
IQGAP1
PRC1
SLC28A1
HOMER2
ZNF592
SV2B
AP3S2
SEMA4B
ABHD2
AKAP13
CHSY1
SYNM
SEC11A
VPS33B
MRPL46
OR4F4
SLCO3A1
NGRN
RHCG
BTBD1
TM6SF1
SCAND2P
ZSCAN2
DET1
FANCI
MCTP2
VIMP
UNC45A
RGMA
WDR93
ADAMTSL3
ALPK3
KLHL25
CPEB1
AEN
TTC23
MRPS11
LRRK1
TM2D3
FAM103A1
WDR73
TICRR
RCCD1
ARRDC4
LINC00923
C15orf40
TARSL2
LRRC28
AGBL1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
ADAMTS17
DNM1P46
CERS3
FAM169B
KIF7
ZNF710
HDDC3
UBE2Q2P1
SPATA41
GDPGP1
OR4F6
OR4F15
FAM174B
GOLGA6L9|ENSG00000197978.8
TTLL13
GOLGA6L10|ENSG00000205281.6
MIR1276
MIR1179
MIR3174
RPS17L
MIR4515
MIR548AP
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.1.

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

Genes
PMS2
CARD11
RPA3
PMS2CL
GRID2IP
FLJ20306
RN7SL851P
SNORA42|ENSG00000207217.1
RN7SL556P
ZNF815P
MIR589
snoU13|ENSG00000238394.1
ZNF890P
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
ACTB
GNA12
GPER
ICA1
LFNG
NUDT1
PDGFA
PRKAR1B
RAC1
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KDELR2
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
C1GALT1
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM220A
ZFAND2A
GLCCI1
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
SLC29A4
RSPH10B
COL28A1
OCM
RSPH10B2
ANKRD61
MIR3683
MIR4656
Genes in Wide Peak

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

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

Genes
EXT1
MYC
RECQL4
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25|ENSG00000251744.1
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
ADCY8
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
PTK2
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
GPAA1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
KHDRBS3
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
MTBP
AGO2
COMMD5
MRPL13
ATAD2
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
THEM6
FAM49B
CHRAC1
EXOSC4
TRMT12
WDYHV1
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
DSCC1
DERL1
SLC52A2
GSDMD
ARHGAP39
ZNF34
SHARPIN
SCRT1
TRAPPC9
TATDN1
MAF1
UTP23
PARP10
C8orf76
TIGD5
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
NAPRT1
TBC1D31
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
FAM84B
FAM91A1
SLC30A8
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
SPATC1
MROH5
MAFA
SAMD12
MIR30B
MIR30D
LRRC24
MROH6
FER1L6
MROH1
FAM203B
OC90
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3610
MIR4662B
MIR4663
MIR4664
MIR5194
Genes in Wide Peak

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

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

Genes
MDM2
SLC35E3
CPM
CPSF6
NUP107
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
FKBP1C
PTP4A1
PHF3
LGSN
EYS
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
ARNT
BCL9
MUC1
NOTCH2
TPM3
PDE4DIP
BGLAP
SNORA26|ENSG00000252236.1
SCARNA4|ENSG00000252808.1
SNORA42|ENSG00000207475.1
snoU13|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
CHRNB2
CKS1B|ENSG00000173207.8
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FCGR1A
FDPS
FLG
FMO5
GBA
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LMNA
LOR
MCL1
SMCP
MEF2D
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SSR2
VPS72
THBS3
TCHH
CCT3
TUFT1
DAP3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
PRPF3
ARHGEF2
CHD1L
SLC25A44
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
SLC27A3
TDRKH
CD160
PMF1
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SMG5
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
LAMTOR2
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
C1orf56
MSTO1
GOLPH3L
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
UBQLN4
RAB25
PGLYRP4
RHBG
ATP8B2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
SEMA4A
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
PAQR6
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
POLR3GL
TMEM79
LCE3D
AQP10
PYGO2
NUP210L
MEX3A
C1orf85
PGLYRP3
GABPB2
TCHHL1
RPTN
TDRD10
SHE
DCST2
LIX1L
TSACC
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
NBPF12
LELP1
DCST1
BNIPL
SPRR4
PPIAL4A
LCE4A
NBPF11
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF16
ANKRD34A
HIST2H2AB
S100A7A
RXFP4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
NOTCH2NL
LYSMD1
HRNR
FLG2
VHLL
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
C2CD4D
NBPF20
MIR4257
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

Table S17.  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
BMP7
CDH4
CHRNA4
COL9A3
CSTF1
CTSZ
EDN3
EEF1A2
KCNQ2
LAMA5
MC3R
MYT1
NTSR1
OPRL1
PCK1
PPP1R3D
PSMA7
PTK6
RPS21
SRMS
AURKA
TAF4
TCEA2
TFAP2C
TPD52L2
STX16
TNFRSF6B
VAPB
OSBPL2
ARFRP1
RGS19
SYCP2
TCFL5
ADRM1
OGFR
DIDO1
HRH3
SPO11
PRPF6
MTG2
GMEB2
SLCO4A1
STMN3
SLMO2
NELFCD
RTFDC1
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
PCMTD2
MRGBP
PPP4R1L
RBM38
ARFGAP1
PMEPA1
CASS4
RAB22A
ZNF512B
COL20A1
CDH26
SLC17A9
FAM217B
C20orf195
PPDPF
BIRC7
NPEPL1
DNAJC5
TUBB1
ZBP1
CABLES2
ZGPAT
HELZ2
FAM210B
PHACTR3
BHLHE23
NKAIN4
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
CBLN4
CTCFL
SAMD10
ABHD16B
RBBP8NL
LSM14B
APCDD1L
C20orf201
LINC00176
C20orf197
FAM209B
MIR296
MIR646
MIR298
MIR1257
MIR4325
MTRNR2L3
MIR4532
MIR4533
MIR548AG2
Genes in Wide Peak

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

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

Genes
RNA5SP34
LINC00559
SNORD38|ENSG00000200733.1
MIR622
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.21.

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

Genes
SNORA7|ENSG00000201316.1
RN7SKP294
UBE2V2
CEBPD
RN7SKP32
LINC00293
RN7SKP41
U3|ENSG00000201329.1
POTEA
FNTA
MCM4
PRKDC
SNAI2
SPIDR
SNTG1
EFCAB1
SGK196
PXDNL
HGSNAT
C8orf22
Genes in Wide Peak

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

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

Genes
NSD1
TRIM52
SNORD95|ENSG00000264549.1
SNORD96A
LINC00847
MIR340
RN7SKP150
MIR1229
HMGB3P22
RN7SL71P
ZNF879
ZNF354B
AACSP1
RN7SKP70
RN7SL646P
RN7SL562P
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
CANX
CLTB
DBN1
F12
FGFR4
FLT4
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
LTC4S
MGAT1
MAPK9
PROP1
SLC34A1
SNCB
ZNF354A
SQSTM1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
ZNF346
TSPAN17
OR4F3
OR2V1
PRELID1
ZNF354C
C5orf45
DDX41
NOP16
UIMC1
RAB24
FAM193B
TMED9
CDHR2
NHP2
RNF130
KIAA1191
CLK4
CNOT6
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
PRR7
TRIM7
MXD3
THOC3
PHYKPL
UNC5A
TRIM41
COL23A1
SCGB3A1
GPRIN1
OR2Y1
BTNL9
HIGD2A
FAM153B
RASGEF1C
FAM153A
OR2V2
ZNF454
C5orf60
PFN3
SIMC1
ZFP62
CBY3
FAM153C
MIR4638

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 - 33 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
9p21.3 4.1507e-217 1.2977e-211 chr9:21959052-22003135 2
11q23.3 3.4268e-29 3.4268e-29 chr11:119176500-120198092 12
10q23.31 3.64e-26 5.3901e-24 chr10:89617158-89755074 3
4q34.3 1.2734e-15 1.2734e-15 chr4:179280062-182757119 4
2q37.3 3.2268e-12 3.2268e-12 chr2:239359581-242296448 32
15q21.1 1.0184e-13 6.0312e-10 chr15:44702831-45026122 6
6q26 5.6612e-11 2.0614e-08 chr6:161693099-163153207 1
1p36.31 7.2372e-09 2.9439e-07 chr1:1-6847369 116
3q13.31 3.9313e-07 3.9313e-07 chr3:116297365-118620828 4
5q31.3 1.422e-07 6.8353e-07 chr5:132435573-166712758 337
1p22.1 1.4903e-06 7.6439e-06 chr1:82457075-119426205 286
10p15.3 3.0627e-05 3.202e-05 chr10:1-688423 6
16p13.3 9.2613e-05 8.9518e-05 chr16:5144019-7780235 2
12q23.3 0.00053958 0.00054748 chr12:79845629-133851895 456
16q24.3 0.00028794 0.00074909 chr16:81745039-90354753 111
10q26.3 2.1153e-06 0.0013585 chr10:134944852-135093385 5
8p23.3 0.0045748 0.0046166 chr8:1-2793575 12
5q12.1 0.00087465 0.0053393 chr5:58151172-59818245 3
19p13.3 0.0060031 0.0057823 chr19:1-2166394 83
6q22.31 2.9439e-07 0.013064 chr6:90060552-151980729 336
9p23 1.2594e-14 0.021774 chr9:7887952-12687261 3
5p15.31 0.022732 0.023301 chr5:1-29949316 98
15q13.3 1.5835e-08 0.027745 chr15:27776739-43001452 163
13q34 0.042833 0.043698 chr13:95861243-115169878 135
14q23.3 0.045691 0.062815 chr14:66963153-67658112 1
Xp21.1 0.063832 0.062815 chrX:30870233-32665140 4
4p16.3 0.090664 0.08901 chr4:1-6275649 84
16q12.1 0.035815 0.11976 chr16:31804435-64977852 158
10q21.1 0.065526 0.14221 chr10:48433736-61548801 70
3p25.1 0.14721 0.14827 chr3:1-62306281 562
14q32.31 0.099665 0.16061 chr14:71578164-107349540 389
17p13.3 0.23044 0.23044 chr17:1-1826620 34
11p15.5 0.23937 0.24091 chr11:2320967-2406244 2
Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.3.

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

Genes
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
MCAM
PVRL1
USP2
TRIM29
POU2F3
RNF26
MFRP
C1QTNF5
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 4q34.3.

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

Genes
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
Genes in Wide Peak

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

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

Genes
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
AGXT
KIF1A
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PPP1R7
HDAC4
CAPN10
PASK
SNED1
ANO7
ANKMY1
C2orf54
TWIST2
MTERFD2
OTOS
MYEOV2
OR6B3
DUSP28
AQP12A
OR6B2
PRR21
AQP12B
MIR4269
MIR4786
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

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

Genes
B2M
RN7SL347P
EIF3J
CTDSPL2
SPG11
PATL2
Genes in Wide Peak

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

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

Genes
PARK2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
RPL22
TNFRSF14
PRDM16
snoU13|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
CDK11B
DFFB
DVL1
GABRD
GNB1
ZBTB48
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
KCNAB2
TNFRSF25
TNFRSF18
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
RER1
ACOT7
ICMT
CHD5
NOC2L
ARHGEF16
SSU72
WRAP73
SDF4
MXRA8
HES2
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
DNAJC11
AJAP1
PLEKHG5
LRRC47
HES4
VWA1
NADK
MMEL1
NOL9
LINC00115
MORN1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
ATAD3B
PLEKHN1
C1orf170
THAP3
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
PHF13
CCDC27
CALML6
C1orf86
ATAD3C
TTLL10
NPHP4
C1orf174
KLHL17
TMEM52
AGRN
GPR153
FAM132A
HES5
SMIM1
RNF207
HES3
MIR200A
MIR200B
ANKRD65
MIR429
TMEM88B
C1orf233
CDK11A
SLC35E2B
OR4F29
MIR4252
MIR4689
MIR4417
Genes in Wide Peak

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

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

Genes
LINC00901
TUSC7
RN7SL582P
MIR4447
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q31.3.

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

Genes
CD74
EBF1
ITK
PDGFRB
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
ADRB2
ANXA6
ATOX1
CAMK2A
CAMLG
CCNG1
CD14
CDC25C
CDX1
CSF1R
CSNK1A1
CTNNA1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EGR1
ETF1
FABP6
FAT2
FGF1
GABRA1
GABRA6
GABRB2
GABRG2
GFRA3
GLRA1
GM2A
GPX3
GRIA1
NR3C1
HARS
HMMR
HSPA9
NDST1
HTR4
IK
IL9
IL12B
LECT2
SMAD5
MFAP3
NDUFA2
NEUROG1
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPP2R2B
RPS14
SGCD
SLC6A7
SPARC
SPINK1
SPOCK1
TAF7
TCF7
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
PTTG1
CNOT8
HAND1
MED7
MYOT
NRG2
CXCL14
H2AFY
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
SLU7
SEC24A
FAXDC2
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
SYNPO
ABLIM3
HMGXB3
ARHGAP26
FSTL4
ATP10B
PHF15
LARP1
HARS2
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
KLHL3
HAVCR1
CYFIP2
PKD2L2
IL17B
MAT2B
MRPL22
PCDHB1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
LARS
CXXC5
KDM3B
RBM27
TMCO6
GALNT10
RBM22
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
TRPC7
PCDHB16
HMHB1
C5orf54
SIL1
ARAP3
PCYOX1L
CCNJL
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PSD2
SPINK7
HAVCR2
SMIM3
FCHSD1
CDKN2AIPNL
TIMD4
ZNF300
MYOZ3
SLC35A4
PWWP2A
C1QTNF2
SCGB3A2
PPARGC1B
AFAP1L1
GRPEL2
UBLCP1
C5orf24
C5orf20
SLC36A2
SLC25A48
ZMAT2
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
SPATA24
DNAJC18
STK32A
SLC36A1
RELL2
SLC36A3
KIF4B
ARSI
IRGM
CATSPER3
NIPAL4
DND1
PROB1
C5orf46
ARHGEF37
SPINK6
ANKHD1
MIR143
MIR145
MIR146A
SPINK14
FNDC9
IGIP
GRXCR2
SPINK9
C5orf52
MIR1303
MIR3141
MIR3661
MIR378H
MIR5197
MIR5692C1
Genes in Wide Peak

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

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

Genes
NRAS
BCL10
TRIM33
RBM15
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
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
ADORA3
AGL
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFRN
ABCD3
RAP1A
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TGFBR3
TSHB
VCAM1
CSDE1
EVI5
CDC7
BCAR3
LMO4
CDC14A
RTCA
SLC16A4
CD101
CLCA3P
CLCA2
HS2ST1
LPPR4
TSPAN2
BCAS2
CEPT1
VAV3
LAMTOR5
AP4B1
PHTF1
AHCYL1
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
PTPN22
CHIA
GPSM2
SLC25A24
TMED5
SH3GLB1
SNX7
GPR88
TRMT13
RSBN1
ZNHIT6
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
OLFML3
AMIGO1
ODF2L
PTBP2
DNASE2B
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
STRIP1
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
PIFO
C1orf162
SYT6
SAMD13
TMEM56
NBPF4
SLC30A7
CHIAP2
FNDC7
SASS6
HFM1
UBL4B
SPAG17
HIPK1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
CCDC18
MYBPHL
GBP7
C1orf146
FAM69A
SLC6A17
C1orf137
FRRS1
MIR197
C1orf180
RBMXL1
NBPF6
MIR760
MIR320B1
MIR378G
MIR137HG
MIR4423
Genes in Wide Peak

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

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

Genes
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ZMYND11
Genes in Wide Peak

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

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

Genes
SNORA40|ENSG00000252138.1
RBFOX1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.3.

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

Genes
BCL7A
BTG1
ALDH2
PTPN11
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
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
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DCN
EPYC
DTX1
DUSP6
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
LTA4H
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
KERA
PRDM4
CIT
PWP1
NUDT4
FZD10
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
UTP20
MRPL42
IFT81
CCDC59
FAM216A
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
METTL25
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
CCDC64
SDSL
IQCD
DEPDC4
CCDC38
TMEM132D
SLC15A4
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
RAD9B
FAM109A
TMTC2
TMTC3
C12orf50
ALDH1L2
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
CCER1
SLC17A8
LRRC43
TCP11L2
C12orf79
POC1B
OTOGL
GPR133
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
DDX51
MMAB
HCAR2
TMEM119
C12orf74
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
CLLU1OS
CLLU1
MIR492
C12orf73
ZNF605
MIR1251
MIR4303
MIR3685
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR5188
MIR5700
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

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

Genes
CBFA2T3
FANCA
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13|ENSG00000239186.1
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
MIR3182
RN7SL134P
snoU13|ENSG00000238321.1
RN7SKP190
7SK|ENSG00000260682.2
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
VPS9D1
KIAA0513
PIEZO1
ATP2C2
MPHOSPH6
EMC8
TUBB3
PRDM7
TCF25
ZCCHC14
GSE1
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
JPH3
WFDC1
MTHFSD
DBNDD1
KLHL36
CDT1
MAP1LC3B
HSDL1
CRISPLD2
SPIRE2
CENPBD1
ZNF276
SDR42E1
RNF166
DNAAF1
SPATA2L
SPATA33
ZC3H18
SLC38A8
ADAD2
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
C16orf74
MIR1910
C16orf95
MIR5093
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
ADAM8
UTF1
VENTX
KNDC1
MIR202
Genes in Wide Peak

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

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

Genes
RPL23AP53
OR4F21
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
TDRP
ERICH1
ZNF596
MIR596
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

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

Genes
FKSG52
MIR582
PDE4D
Genes in Wide Peak

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

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

Genes
STK11
TCF3
FSTL3
RN7SL226P
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
EFNA2
ELANE
GAMT
MKNK2
GPX4
GZMM
PALM
POLRMT
PRTN3
PTBP1
RPS15
MADCAM1
PPAP2C
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
DAZAP1
FGF22
THEG
MBD3
MIER2
PCSK4
BTBD2
RNF126
WDR18
REXO1
LPPR3
ABHD17A
KLF16
KISS1R
MUM1
MIDN
R3HDM4
TMEM259
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
GRIN3B
MOB3A
MISP
PLK5
C2CD4C
C19orf25
ATP8B3
C19orf26
ODF3L2
ADAMTSL5
MEX3D
PRSS57
MIR3187
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
GOPC
snoU13|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13|ENSG00000238594.1
RAET1K
SNORA2|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
STXBP5
RNA5SP222
FBXO30
STX11
PEX3
RNA5SP221
ADAT2
VTA1
GJE1
RN7SKP106
RNA5SP220
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
snoU13|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18|ENSG00000252249.1
U3|ENSG00000221455.1
U3|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13|ENSG00000238747.1
RN7SL11P
AIM1
AMD1
ARG1
CCNC
COL10A1
CTGF
EPB41L2
EPHA7
EYA4
FABP7
FOXO3
FUCA2
FYN
GJA1
GPR6
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
MAP3K5
NMBR
PCMT1
ENPP1
ENPP3
PEX7
PLAGL1
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
SGK1
SIM1
SMPD2
MAP3K7
TCF21
NR2E1
TPD52L1
UTRN
EPM2A
DDO
SNX3
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
MED23
FHL5
AKAP7
ATG5
AKAP12
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
FUT9
TRAF3IP2
HBS1L
SMPDL3A
ASCC3
RAB32
KATNA1
BVES
SEC63
ANKRD6
CDK19
TAB2
MDN1
TSPYL4
SASH1
UFL1
HEY2
ASF1A
CCDC28A
MTHFD1L
PNISR
MOXD1
FBXL4
PDE7B
SESN1
OSTM1
NDUFAF4
DSE
HDDC2
TUBE1
C6orf203
CDC40
RWDD1
AIG1
HECA
COQ3
IL20RA
AHI1
RMND1
SOBP
QRSL1
VNN3
ECHDC1
PDSS2
GPR126
KIAA1244
NHSL1
LYRM2
PLEKHG1
SERINC1
HACE1
ZBTB2
BEND3
ABRACL
RRAGD
PBOV1
BACH2
TRMT11
PERP
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
MANEA
ADGB
CCDC170
ULBP2
ULBP1
GPR63
PPP1R14C
RNF146
SF3B5
TAAR8
ARMC2
L3MBTL3
MCHR2
FAXC
GJA10
LRP11
LTV1
USP45
REPS1
PPIL4
SLC22A16
ARHGAP18
GTF3C6
MTFR2
KLHL32
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAAR9
TAAR1
NCOA7
HINT3
RAET1E
ZC2HC1B
RAET1L
SAMD3
RNF217
NKAIN2
OLIG3
TXLNB
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
MMS22L
MCM9
SHPRH
CEP57L1
PPIL6
DCBLD1
TAAR6
SLC35D3
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
SUMO4
CENPW
SOGA3
CEP85L
THEMIS
LIN28B
SAMD5
IYD
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR587
MIR588
METTL24
TRAPPC3L
MIR2113
MIR3144
MIR3668
SMLR1
MIR4464
MIR4643
MIR4465
MIR548AJ1
MIR548AI
MIR548H5
Genes in Wide Peak

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

Table S41.  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 5p15.31.

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

Genes
RN7SKP207
SNORA18|ENSG00000252601.1
SNORD29
SNORA40|ENSG00000252083.1
C5orf17
RN7SL572P
GUSBP1
snoU13|ENSG00000238674.1
RN7SL58P
SNORD81|ENSG00000212278.1
FTH1P10
RN7SKP133
RNA5SP180
RNA5SP179
RNA5SP178
MIR887
U8|ENSG00000202269.1
MIR4637
FAM105A
CT49
ANKRD33B
CMBL
FAM173B
RNA5SP177
SNORD123
MIR4636
RNA5SP176
RN7SKP79
UBE2QL1
RN7SKP73
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
ADCY2
CDH9
CDH10
CDH12
CDH18
CTNND2
DAP
DNAH5
MTRR
MYO10
PMCHL1
SDHA
SLC6A3
SLC9A3
SRD5A1
TERT
TRIO
SEMA5A
TRIP13
PDCD6
MARCH6
BASP1
SLC12A7
PAPD7
TPPP
EXOC3
CCT5
FBXL7
KIAA0947
IRX4
TAS2R1
FAM134B
NSUN2
CEP72
ANKH
PRDM9
AHRR
MRPL36
BRD9
FASTKD3
IRX1
ZDHHC11
LPCAT1
CLPTM1L
ROPN1L
MED10
NKD2
FAM105B
ZNF622
C5orf55
C5orf49
C5orf38
IRX2
ADAMTS16
SLC6A19
SLC6A18
MARCH11
MIR4277
MIR4458
MIR4457
MIR4456
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.3.

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

Genes
BUB1B
snoU13|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13|ENSG00000238564.1
THBS1
FAM98B
U3|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77|ENSG00000212415.1
snoU13|ENSG00000238342.1
RN7SL286P
RN7SL539P
GOLGA8O
U8|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18|ENSG00000206849.1
MIR211
RN7SL82P
U8|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
ACTC1
APBA2
CAPN3
CHRM5
GANC
GCHFR
ITPKA
IVD
LTK
MEIS2
TRPM1
OCA2
PLCB2
RAD51
RYR3
SCG5
SPINT1
SRP14
TJP1
TYRO3
SNAP23
HERC2
AQR
ARHGAP11A
RASGRP1
GPR176
CHP1
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
FAM189A1
TMEM87A
RPAP1
GREM1
RPUSD2
EHD4
NDUFAF1
NUSAP1
EMC4
SPTBN5
KLF13
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
RMDN3
DNAJC17
NOP10
NDNL2
EMC7
PAK6
CASC5
AVEN
VPS18
ZNF106
CHAC1
KATNBL1
C15orf41
ZFYVE19
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
CHST14
PLA2G4E
TMCO5A
OTUD7A
SPRED1
PGBD4
EXD1
FSIP1
RHOV
LPCAT4
PLA2G4F
LRRC57
NUTM1
PLA2G4D
GOLGA8G
FMN1
C15orf52
C15orf53
C15orf54
HERC2P9
GOLGA8B
EIF2AK4
C15orf62
GOLGA8N
C15orf56
PHGR1
ANKRD63
JMJD7
PLA2G4B
MIR4510
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q34.

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

Genes
ERCC5
MIR548AR
LINC00565
LINC00452
LINC00453
LINC00454
GRK1
DCUN1D2
LINC00403
LINC00404
SNORD44
LINC00354
LINC00346
LINC00567
snoU13|ENSG00000238629.1
RN7SL783P
RN7SKP10
LINC00676
RNA5SP39
MIR1267
SNORD31
LINC00443
LINC00551
ARGLU1
LINC00460
RNA5SP38
SNORA25|ENSG00000252550.1
LINC00344
LINC00343
METTL21EP
RNY5P8
LINC00283
CCDC168
snoU13|ENSG00000238869.1
LINC00555
MIR4705
RNY1P2
MIR2681
FGF14
LINC00411
GGACT
LINC00554
snoU13|ENSG00000238305.1
SNORA25|ENSG00000201245.1
MIR4306
RNY3P6
LINC00449
MIR623
RN7SKP9
RN7SL60P
RN7SKP8
snoU13|ENSG00000238407.1
RAP2A
RNA5SP37
snoU13|ENSG00000238522.1
SNORD112|ENSG00000252154.1
RN7SKP7
LINC00359
RN7SL164P
HS6ST3
snR65|ENSG00000251901.1
RNY4P27
RNY3P8
snoU13|ENSG00000238463.1
ATP4B
COL4A1
COL4A2
GPR183
EFNB2
F7
F10
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
MBNL2
FARP1
TUBGCP3
TNFSF13B
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
OXGR1
BIVM
TMCO3
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
TEX30
ADPRHL1
TEX29
SPACA7
RNF113B
CLYBL
METTL21C
NALCN
DAOA
CHAMP1
UBAC2
TMEM255B
C13orf35
FAM155A
MIR3170
MIR4502
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
GPHN
Genes in Wide Peak

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

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

Genes
MIR548F5
MIR3915
RNA5SP501
FTHL17
Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
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
RGS12
RNF4
SH3BP2
NELFA
SLBP
NOP14
FAM193A
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
NSG1
STX18
FGFRL1
CYTL1
PIGG
STK32B
LYAR
UVSSA
ZFYVE28
TNIP2
HAUS3
MFSD7
TMEM175
TMEM128
TMEM129
EVC2
OTOP1
JAKMIP1
FAM53A
ZBTB49
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
MIR378D1
MIR4800
Genes in Wide Peak

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

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

Genes
CYLD
HERPUD1
snoU13|ENSG00000238507.1
RN7SKP76
RN7SL143P
SLC38A7
snoU13|ENSG00000239121.1
SNORA50|ENSG00000206952.2
SNORA46|ENSG00000207493.1
RN7SL645P
TEPP
MT1DP
MT1M
MT1E
MT1L
MT2A
OGFOD1
MIR3935
IRX6
RN7SL841P
CRNDE
FTO
RNA5SP427
snoU13|ENSG00000238645.1
CASC16
LINC00919
RN7SKP142
HNRNPA1P48
RNA5SP426
NKD1
SNORD112|ENSG00000252077.1
snoU13|ENSG00000238544.1
SNORA70|ENSG00000252526.1
RNY4P3
snoU13|ENSG00000239038.1
snoU13|ENSG00000239013.1
RN7SL54P
LONP2
RNA5SP425
RNA5SP424
ITFG1
snoU13|ENSG00000238834.1
MYLK3
VPS35
ANKRD26P1
RNA5SP423
RNA5SP422
RNA5SP421
RNA5SP420
RNA5SP419
RNA5SP418
RNA5SP417
RNA5SP416
RNA5SP415
RNA5SP413
RNA5SP410
RNA5SP409
RNA5SP408
RNA5SP407
RNA5SP406
LINC00273
ARHGAP23P1
HERC2P8
HERC2P5
TP53TG3
TP53TG3D
HERC2P4
ADCY7
AMFR
BBS2
CBLN1
CDH8
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1F
MT1G
MT1H
MT1JP
MT1X
MT3
PHKB
POLR2C
RBL2
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC12A3
GPR56
N4BP1
NUP93
IRX5
DNAJA2
KATNB1
ZNF267
NUDT21
CNOT1
ZNF423
RPGRIP1L
ARL2BP
ORC6
TOX3
CCDC113
C16orf80
BRD7
PLLP
CES1P1
LPCAT2
HEATR3
DOK4
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
IRX3
USB1
SHCBP1
SETD6
FAM192A
CHD9
NETO2
NLRC5
CCDC135
CAPNS2
MT4
GPT2
ABCC11
RSPRY1
CCDC102A
ABCC12
C16orf78
SNX20
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
SLC6A10P
C16orf87
C16orf97
TP53TG3C
TP53TG3B
Genes in Wide Peak

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

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

Genes
NCOA4
LINC00948
LINC00844
RN7SKP196
snoU13|ENSG00000238970.1
SNORD2|ENSG00000238707.1
snoU13|ENSG00000238355.1
MIR548F1
RNA5SP318
MIR605
RMRPP4
RNA5SP317
LINC00843
SNORA74|ENSG00000223111.1
SNORA74|ENSG00000223182.1
RNA5SP316
FAM25D
FAM21D
PARG
C10orf53
DRGX
C10orf128
WDFY4
RNA5SP315
RN7SL527P
GLUD1P2
RNA5SP314
CHAT
ERCC6
MBL2
MSMB
PRKG1
MAPK8
SLC18A3
TFAM
UBE2D1
ZWINT
DKK1
CSTF2T
PTPN20B
A1CF
OGDHL
CISD1
ASAH2
ARHGAP22
PCDH15
BICC1
PHYHIPL
C10orf71
FRMPD2
FAM170B
VSTM4
SLC16A9
FAM13C
IPMK
SGMS1
FAM21A
BMS1P5
AGAP6
LRRC18
FAM25C
TIMM23B
AGAP7
ASAH2B
AGAP8
TIMM23
MIR4294
MTRNR2L5
MIR3924
PGBD3
Genes in Wide Peak

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

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

Genes
VHL
CTNNB1
FANCD2
FHIT
MLH1
MYD88
PPARG
RAF1
XPC
BAP1
SRGAP3
SETD2
PBRM1
PTPRG
U3|ENSG00000212211.1
NPCDR1
RPP14
RNU6ATAC26P
PDE12
snoU13|ENSG00000238905.1
HESX1
RNA5SP133
RN7SKP45
MIR3938
ESRG
CHDH
SNORD63|ENSG00000251987.1
SNORA26|ENSG00000212608.1
SNORD38|ENSG00000207109.1
RN7SL821P
snoU13|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19|ENSG00000222345.1
SNORD19B|ENSG00000238862.1
SNORD19|ENSG00000212493.1
SNORD19B|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13|ENSG00000238350.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000251938.1
PRSS44
PRSS45
SNORD77|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
U8|ENSG00000212145.2
RN7SKP58
SCARNA21|ENSG00000252409.1
ZNF621
SNORA64|ENSG00000202517.1
RN7SL411P
SNORA62|ENSG00000202363.1
SNORA6
MIR26A1
ITGA9
RNA5SP129
snoU13|ENSG00000238929.1
RNU6ATAC4P
TRANK1
HSPD1P6
RN7SKP227
RNA5SP128
RN7SL296P
TMPPE
CCR4
TRIM71
snoU13|ENSG00000238646.1
SNORA25|ENSG00000201701.1
OSBPL10
STT3B
RNA5SP127
U3|ENSG00000199927.1
LINC00693
CMC1
RN7SL859P
SNORD5|ENSG00000272166.1
RNA5SP126
RNA5SP125
RN7SL216P
LINC00691
UBE2E2
HMGB1P5
RNY4P22
MIR3135A
U7|ENSG00000271841.1
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13|ENSG00000238345.1
snoU13|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13|ENSG00000239126.1
EGOT
SNORA43|ENSG00000253049.1
RN7SKP144
RN7SL120P
ACAA1
ACVR2B
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR5
CCR8
ACKR2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FBLN2
FLNB
GNAI2
GOLGA4
XCR1
GPX1
GRM2
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RAB5A
RARB
RPL15
RPL29
RPL32
SATB1
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
CLEC3B
TNNC1
TOP2B
UBA7
UBE2E1
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
BHLHE40
HYAL2
KAT2B
BSN
ACKR5
RPL14
SEC22C
RRP9
LRRFIP2
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
TBC1D5
TATDN2
IP6K1
EPM2AIP1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
NPRL2
CXCR6
CHL1
ARPP21
CCR9
USP19
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
EXOSC7
CAND2
CLASP2
RAD54L2
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
THUMPD3
MYRIP
PTPN23
DNAH1
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LMCD1
ARHGEF3
VILL
SSUH2
TRNT1
DYNC1LI1
C3orf18
CRBN
SS18L2
CCDC174
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
ELP6
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
ANO10
DALRD3
ARL8B
SETD5
TMEM40
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
BRK1
ZKSCAN7
RAD18
SEMA3G
KIF15
PCBP4
ABHD6
LRTM1
KIAA1143
HHATL
WDR48
LRRN1
SELK
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
WDR82
TSEN2
C3orf20
ATRIP
NICN1
MON1A
JAGN1
IL17RC
ABHD14B
GTDC2
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ACTR8
CMTM7
ZNF501
FANCD2OS
LRRC3B
GALNT15
GPR62
KCNH8
FAM3D
LYZL4
KLHL40
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
LSMEM2
ASB14
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
ZCWPW2
NEK10
CMTM8
CCDC13
FGD5
CNTN4
XIRP1
TTC21A
C3orf67
KCTD6
KLHDC8B
DNAH12
DENND6A
ZNF620
ALS2CL
TMIE
FBXW12
ZNF619
LINC00692
CCDC66
TCAIM
SUMF1
RPUSD3
PRRT3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
TPRXL
ZNF445
SPATA12
TOPAZ1
TMEM110
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
MIR425
GLB1
SPINK8
ARIH2OS
C3orf84
MIR563
FAM198A
CCR2
PRSS46
MIR378B
MIR4271
MIR3714
KRBOX1
MIR4787
MIR4791
MIR4790
MIR4443
MIR4792
MIR4442
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.31.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
SERPINA3
ACYP1
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF5
EML1
ESRRB
FOS
GALC
GSTZ1
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
ATXN3
ALDH6A1
SERPINA5
PGF
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSEN1
PSMC1
ABCD4
MOK
SEL1L
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
DLK1
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
AREL1
TECPR2
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
SNW1
TTLL5
RCOR1
PACS2
ANGEL1
PPP1R13B
FLRT2
SIPA1L1
DCAF4
KIF26A
TMEM251
MLH3
GPR132
POMT2
COQ6
FCF1
SERPINA10
EVL
GSKIP
CINP
ASB2
ZFYVE1
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
VRTN
FLVCR2
GPATCH2L
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
MOAP1
IRF2BPL
INF2
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
AMN
SLIRP
DNAL1
RPS6KL1
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
ELMSAN1
NEK9
EXOC3L4
WDR20
IFT43
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
GSC
SERPINA12
PRIMA1
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
SYNE3
EML5
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
SERPINA9
VSX2
COX8C
ASPG
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
C14orf180
MIR127
MIR136
MIR154
MIR203
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
MIR4505
MIR151B
MIR4710
MIR2392
Genes in Wide Peak

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

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

Genes
TLCD2
snoU13|ENSG00000238946.1
RN7SL105P
BHLHA9
MIR3183
TIMM22
DBIL5P
DOC2B
ABR
CRK
MYO1C
SERPINF1
PITPNA
SERPINF2
RPA1
YWHAE
SCARF1
RPH3AL
PRPF8
GEMIN4
GLOD4
INPP5K
RNMTL1
VPS53
NXN
FAM57A
RILP
SMYD4
SLC43A2
WDR81
TUSC5
FAM101B
C17orf97
MIR22HG
Genes in Wide Peak

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

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

Genes
RPL26P30
TSPAN32
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 23 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 0.26 0.751 0.823 0.22 -0.914 1
1q 1195 0.49 10.4 0 0.19 -1.78 1
2p 624 0.21 -2.38 1 0.18 -3.38 1
2q 967 0.20 -1.91 1 0.18 -3.04 1
3p 644 0.20 -2.37 1 0.20 -2.37 1
3q 733 0.22 -1.52 1 0.19 -2.82 1
4p 289 0.19 -3.2 1 0.26 -0.682 1
4q 670 0.16 -3.85 1 0.27 0.332 0.81
5p 183 0.25 -1.32 1 0.29 0.293 0.81
5q 905 0.18 -2.65 1 0.32 2.88 0.00727
6p 710 0.43 6.48 3.13e-10 0.38 4.22 5.43e-05
6q 556 0.17 -3.04 1 0.57 12.4 0
7p 389 0.58 12.7 0 0.13 -4.26 1
7q 783 0.57 13.1 0 0.13 -3.88 1
8p 338 0.38 4.07 0.000104 0.31 1.17 0.284
8q 551 0.48 8.92 0 0.17 -3.01 1
9p 301 0.12 -4.09 1 0.68 16.7 0
9q 700 0.12 -4.46 1 0.54 11.6 0
10p 253 0.06 -6.11 1 0.58 12.6 0
10q 738 0.02 -6.49 1 0.62 15.5 0
11p 509 0.14 -4.42 1 0.38 4.66 8e-06
11q 975 0.13 -4.14 1 0.44 8.05 2.96e-15
12p 339 0.20 -3 1 0.21 -2.61 1
12q 904 0.13 -5.01 1 0.21 -1.93 1
13q 560 0.32 2.16 0.0612 0.30 1.2 0.284
14q 938 0.16 -3.34 1 0.34 3.83 0.000259
15q 810 0.27 0.54 0.983 0.19 -2.77 1
16p 559 0.18 -3.54 1 0.24 -1.17 1
16q 455 0.16 -3.92 1 0.33 2.51 0.02
17p 415 0.14 -4.44 1 0.39 4.86 3.41e-06
17q 972 0.19 -2.26 1 0.23 -0.732 1
18p 104 0.19 -3.21 1 0.34 2.36 0.0281
18q 275 0.16 -4.32 1 0.31 1.47 0.204
19p 681 0.18 -3.04 1 0.26 -0.0518 1
19q 935 0.19 -2.63 1 0.24 -0.493 1
20p 234 0.43 6.1 2.94e-09 0.13 -5.07 1
20q 448 0.50 9.47 0 0.07 -6.32 1
21q 258 0.23 -2.02 1 0.23 -1.73 1
22q 564 0.39 4.84 3.31e-06 0.16 -3.66 1
Xq 668 0.15 -4.18 1 0.29 1.2 0.284
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/SKCM-TM/11449218/GDAC_MergeDataFiles_11451695/SKCM-TM.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 366 Input Tumor Samples.

Tumor Sample Names
TCGA-3N-A9WB-06A-11D-A38F-01
TCGA-3N-A9WC-06A-11D-A38F-01
TCGA-3N-A9WD-06A-11D-A38F-01
TCGA-BF-AAP0-06A-11D-A396-01
TCGA-D3-A1Q1-06A-21D-A194-01
TCGA-D3-A1Q3-06A-11D-A194-01
TCGA-D3-A1Q4-06A-11D-A194-01
TCGA-D3-A1Q5-06A-11D-A194-01
TCGA-D3-A1Q6-06A-11D-A194-01
TCGA-D3-A1Q7-06A-11D-A192-01

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)