Thyroid Adenocarcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16a (cga svn revision 43808).

Summary

There were 268 tumor samples used in this analysis: 18 significant arm-level results, 0 significant focal amplifications, and 13 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.

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 1. Get Full Table Deletions Table - 13 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
--- | --- | --- | --- | ---
Xq22.3 | 0.0057142 | 0.0057142 | chrX:107872289-108781115 | 2
10q23.31 | 0.010342 | 0.010342 | chr10:83636583-94835212 | 82
16q23.3 | 0.036609 | 0.036609 | chr16:78129058-90354753 | 122
8q24.22 | 0.037406 | 0.037406 | chr8:56679786-139512990 | 371
2q37.1 | 0.044371 | 0.044371 | chr2:212238542-243199373 | 288
19q12 | 0.16415 | 0.16851 | chr19:30202912-30414571 | 1
7q22.3 | 0.17667 | 0.17667 | chr7:106673884-116850979 | 43
9q22.32 | 0.18015 | 0.17667 | chr9:97571319-140734188 | 531
17p13.1 | 0.18017 | 0.17667 | chr17:1-9812234 | 267
4p16.1 | 0.27879 | 0.27879 | chr4:1-191154276 | 903
11p15.1 | 0.22354 | 0.27879 | chr11:1-135006516 | 1478
13q32.1 | 0.17376 | 0.27879 | chr13:1-115169878 | 414
22q13.2 | 0.24821 | 0.27879 | chr22:1-51304566 | 560
13q14.2 | 0.16013 | 0.4599 | chr13:1-115169878 | 414

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
GUCY2F
IRS4

Genes in Wide Peak

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

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

Genes
BMPR1A
PTEN
hsa-mir-107
hsa-mir-346
ACTA2
FAS
GLUD1
GRID1
HHEX
HTR7
IDE
IFIT2
IFIT1
IFIT3
KIF11
LIPA
PPP1R3C
RGR
SNCG
LIPF
CH25H
BTAF1
PAPSS2
MINPP1
KIF20B
RPP30
NRG3
C10orf116
LDB3
CPEB3
WAPAL
IFIT5
LRIT1
ANKRD1
GHITM
PANK1
FAM190B
EXOC6
FAM35A
MARCH5
RNLS
STAMBPL1
MMRN2
TNKS2
PCGF5
ATAD1
CDHR1
OPN4
ANKRD22
NUDT9P1
AGAP11
LIPJ
CFL1P1
HECTD2
FGFBP3
LOC170425
FLJ37201
LIPM
CYP26C1
LRIT2
C10orf99
SLC16A12
MIR107
LOC439994
IFIT1B
MIR346
FAM25A
LIPK
LIPN
LOC643529
FAM22A
FAM22D
LOC728190
LOC728218
KLLN
LOC100188947
FAS-AS1
LOC100507470
MARK2P9
MIR4679-1
MIR4679-2
MIR4678

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
MC1R
MVD
CHMP1A
PLCG2
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
C16orf7
KIAA0513
PIEZO1
ATP2C2
MPHOSPH6
COX4NB
TUBB3
PRDM7
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
NECAB2
KLHDC4
DEF8
BANP
ZDHHC7
CENPN
C16orf61
JPH3
KIAA1609
WFDC1
MTHFSD
DBNDD1
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
MGC23284
LINC00311
ZNF778
ACSF3
LINC00304
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q24.22.

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

Genes
COX6C
EXT1
MYC
PLAG1
NCOA2
CHCHD7
hsa-mir-30d
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
hsa-mir-1204
hsa-mir-548d-1
hsa-mir-2053
hsa-mir-548a-3
hsa-mir-3151
hsa-mir-1273
hsa-mir-875
hsa-mir-3150
hsa-mir-3149
hsa-mir-2052
hsa-mir-124-2
ADCY8
ANGPT1
ANXA13
ASPH
ATP6V1C1
OSGIN2
CA1
CA2
CA3
CA8
CALB1
RUNX1T1
CDH17
CRH
CYP7A1
DECR1
DPYS
E2F5
EYA1
FABP4
FABP5
GEM
HAS2
HNF4G
IL7
IMPA1
EIF3E
KCNQ3
KCNS2
LYN
MATN2
MMP16
MOS
MYBL1
NBN
NDUFB9
NOV
ODF1
TNFRSF11B
PDE7A
ENPP2
PENK
PMP2
POLR2K
POU5F1B
PKIA
PVT1
PEX2
RAB2A
RAD21
RPL7
RPL30
RPS20
SDC2
SDCBP
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TTPA
COL14A1
UQCRB
YWHAZ
FZD6
NSMAF
EIF3H
RIPK2
GGH
WISP1
CPNE3
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
TTC35
RIMS2
TOX
MTSS1
PTDSS1
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
ARFGEF1
COLEC10
KHDRBS3
POP1
COPS5
WWP1
STMN2
RNF139
ZHX1
ZHX2
EFR3A
RRS1
SULF1
ZFPM2
HEY1
TRAM1
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
C8orf71
RGS22
PTTG3P
SNORA72
SNORD54
PABPC1
KCNV1
STAU2
MTBP
BHLHE22
MRPS28
MRPL13
ATAD2
ASAP1-IT1
LRP12
RRM2B
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
FAM82B
ZNF706
UBR5
FAM49B
AZIN1
OTUD6B
GDAP1
PDP1
CNGB3
ESRP1
IMPAD1
TMEM70
TRMT12
OXR1
WDYHV1
ARMC1
UBE2W
LAPTM4B
C8orf39
TMEM55A
CHD7
SYBU
INTS8
PAG1
GSDMC
C8orf44
JPH1
ENY2
CPA6
ZFAT
PRDM14
SNX16
NECAB1
DEPTOR
ZBTB10
DSCC1
DERL1
PLEKHF2
ZFAND1
ZFHX4
NIPAL2
CSPP1
BAALC
GRHL2
VCPIP1
PREX2
SLC25A32
TM7SF4
SLCO5A1
CRISPLD1
TATDN1
NACAP1
NCALD
UTP23
TRIM55
C8orf76
NUDCD1
FAM83A
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
TMEM67
MTDH
CHMP4C
PKHD1L1
WDR67
HPYR1
TP53INP1
TGS1
MAL2
CSMD3
FBXO32
SLC26A7
CTHRC1
OSR2
C8orf34
ZNF572
FAM92A1
C8orf38
ABRA
TMEM71
ADHFE1
UBXN2B
DCAF4L2
RALYL
TMEM65
LOC157381
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
TMEM74
FAM91A1
C8orf45
CLVS1
C8orf84
CNBD1
SLC30A8
SNX31
TMEM64
SDR16C5
C8orf47
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NSMCE2
LOC286094
C8orf83
DPY19L4
FBXO43
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
LOC286190
KLHL38
RSPO2
SLC10A5
CA13
XKR9
LOC389676
RBM12B
LOC392232
GDF6
LOC401463
C8orf59
SAMD12
MIR124-2
MIR30B
MIR30D
FER1L6-AS1
FLJ39080
FLJ46284
FLJ42969
C8orf85
LINC00251
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
ZNF704
C8orf69
SNHG6
SNORD87
LINC00535
UG0898H09
RAD21-AS1
FABP9
FABP12
FER1L6
MIR599
LOC727677
LOC728724
OC90
MIR875
LOC100127983
LOC100128126
TCF24
LOC100130155
LOC100130231
LOC100130298
LOC100130301
LRRC69
LOC100131726
LOC100132891
LOC100192378
REXO1L2P
LOC100288748
MIR1205
MIR1206
MIR1207
MIR1204
MIR2053
MIR2052
MIR1208
MIR3150A
MIR3151
LOC100499183
LOC100500773
MIR3150B
MIR3610
LOC100505659
LOC100505676
LOC100505718
LOC100507117
LOC100507632
LOC100507651
C8orf44-SGK3
ZHX1-C8ORF76
MIR378D2
MIR4661
MIR4663
MIR4471
MIR4470
LOC100616530
PCAT1
LINC00536
FSBP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.1.

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.3.

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

Genes
MET
CAPZA2
CAV1
CAV2
DLD
SLC26A3
GPR22
IFRD1
LAMB1
DNAJB9
NRCAM
SLC26A4
PPP1R3A
PRKAR2B
DOCK4
COG5
DUS4L
ZNF277
TFEC
LAMB4
TES
HBP1
MDFIC
PNPLA8
GPR85
LRRN3
BCAP29
TMEM168
CBLL1
IMMP2L
ST7-AS1
ST7-AS2
ST7-OT3
FOXP2
C7orf60
C7orf66
THAP5
LOC286002
C7orf53
ST7-OT4
LOC401397
EIF3IP1
MIR3666

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.32.

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

Genes
ABL1
FANCC
NOTCH1
RALGDS
SET
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
BAAT
C5
C8G
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL2
CYLC2
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
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
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
ANP32B
AGPAT2
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
PMPCA
ASTN2
FKBP15
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
BSPRY
C9orf167
TEX10
LPPR1
EXD3
FAM206A
STX17
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
C9orf86
CDK5RAP2
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
BDAG1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
MIR600HG
URM1
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
HIATL2
C9orf125
NTNG2
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
C9orf96
OLFML2A
QSOX2
ZNF883
C9orf21
ZNF367
C9orf91
NAIF1
ANKS6
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC340508
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR32
C9orf106
LCN10
LOC441454
LOC441455
FAM22G
LOC441461
C9orf173
NRARP
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
NRON
FAM163B
FLJ40292
RNF224
C9orf29
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
LOC100129722
LOC100130954
LOC100131193
LOC100132781
RNU6ATAC
LINC00092
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3154
MIR2861
MIR3134
C9orf174
LOC100499484
MIR3621
MIR3689A
MIR3911
MIR3689B
LOC100505478
LOC100506100
LOC100506190
LOC100506599
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4672
MIR3689E
MIR4479

Genes in Wide Peak

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

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

Genes
PER1
TP53
USP6
hsa-mir-4314
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ACADVL
ALOX12
ALOX12B
ALOX12P2
ALOX15
ALOX15B
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHD3
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
GUCY2D
HIC1
ITGAE
MNT
MYH10
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFAS
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RCVRN
RPA1
RPL26
SHBG
SLC2A4
SOX15
VAMP2
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
TNFSF13
TNFSF12
TM4SF5
RABEP1
KCNAB3
AURKB
GLP2R
NTN1
STX8
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
GABARAP
NLRP1
ARHGEF15
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
KIAA0664
SMG6
WSCD1
CTDNEP1
PIK3R5
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
RANGRF
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
C17orf59
GPR172B
WRAP53
RNMTL1
VPS53
C17orf85
TSR1
DHX33
PLSCR3
NLGN2
ZBTB4
CXCL16
TRAPPC1
ALOXE3
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
CTC1
NDEL1
PITPNM3
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
TMEM107
LSMD1
NEURL4
ZNF594
HES7
SPATA22
TXNDC17
MIR22HG
TMEM88
SAT2
SMYD4
CNTROB
RPL29P2
CYB5D1
OVCA2
USP43
KRBA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
DNAH2
RTN4RL1
WDR16
CCDC42
PIK3R6
ODF4
KCTD11
MFSD6L
TRPV3
SLC16A11
FBXO39
DHRS7C
SLC16A13
C17orf74
SPNS3
C17orf61
BCL6B
LOC284009
VMO1
LOC284023
LINC00324
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
SPDYE4
OR3A4P
SLC25A35
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
RNF222
SNORA48
SNORD10
OR1D4
SCARNA21
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
LOC100128288
C17orf107
LOC100130950
DBIL5P
MIR1253
LOC100306951
MIR3183
MIR4314
MIR3676
LOC100506388
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4520A
MIR4521
MIR4520B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.1.

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

Genes
FGFR3
IL2
KDR
KIT
PDGFRA
RAP1GDS1
WHSC1
PHOX2B
DUX4
CHIC2
TET2
FBXW7
FIP1L1
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
hsa-mir-1269
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
ADRA2C
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA2P1
ANXA3
ANXA5
APBB2
AREG
RHOH
ART3
ATOH1
ATP5I
NKX3-2
BMP3
BMPR1B
BST1
BTC
CAMK2D
CASP3
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
CD38
LRBA
CDS1
CLGN
CENPC1
CENPE
CLCN3
CNGA1
CPE
CRMP1
CSN1S1
CSN2
CSN3
CTBP1
CTSO
DGKQ
DCK
DCTD
DHX15
DMP1
DRD5
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
EPHA5
EREG
ETFDH
EVC
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGF5
FGG
FRG1
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GC
GK2
GK3P
GLRB
GNRHR
GPM6A
GRK4
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HTT
HGFAC
UBE2K
HMGB2
HMX1
HNRNPD
HPGD
HSP90AA4P
HSP90AB3P
HTN1
HTN3
IBSP
IDUA
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
LETM1
LRPAP1
MAD2L1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MSX1
MTNR1A
MTTP
MUC7
MYL5
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PCDH7
PDE6B
PDHA2
PET112
PF4
PF4V1
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPBP
PPID
PPP2R2C
PPP3CA
PRKG2
MAPK10
PTPN13
QDPR
REST
RFC1
RGS12
RNF4
ABCE1
RPL9
RPL34
RPS3A
S100P
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SH3BP2
SNCA
SOD3
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
TDO2
TEC
TLL1
TLR1
TLR2
TLR3
TRPC3
TXK
UBE2D3
UCHL1
UCP1
UGDH
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
VEGFC
WFS1
WHSC2
ZNF141
SLBP
GLRA3
ACOX3
SPARCL1
SMARCA5
SORBS2
PRSS12
CPZ
NOP14
FAM193A
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
PROM1
HERC3
SNORD73A
STBD1
CDKL2
PAPSS1
LDB2
LRAT
AIMP1
NDST3
SLIT2
RAB28
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
KIAA0232
MFAP3L
SEC24D
G3BP2
WDR1
HS3ST1
FGFBP1
HNRPDL
TSPAN5
ENAM
C4orf6
FAM13A
MFSD10
SPRY1
MAEA
TLR6
PCGF3
ANAPC10
ATP8A1
SPON2
PGRMC2
SEC24B
TACC3
SLC30A9
CXCL13
SLC34A2
MAB21L2
PAICS
MXD4
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
CPLX1
HPSE
SLC26A1
NMU
SMR3B
NPFFR2
PPARGC1A
PPBPL2
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
MAN2B2
ANP32C
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXL5
FBXO8
DUX2
SMR3A
D4S234E
PPA2
DAPP1
DKK2
FAM184B
INTU
NAAA
GPR78
COQ2
ARFIP1
SULT1B1
PDLIM3
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
MRPS18C
LAP3
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
NUDT9
NUP54
STX18
FGFRL1
CLDN22
CYTL1
GAR1
SH3TC1
UGT2B28
RBM47
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
PIGG
DCAF16
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
CCDC109B
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
UBA6
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
C4orf43
UFSP2
CNO
C4orf21
STK32B
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
CDKN2AIP
LYAR
ODZ3
N4BP2
TMEM184C
SEPT11
EXOC1
LRP2BP
TMEM165
PDGFC
SLC2A9
FSTL5
BDH2
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
DANCR
KIAA1211
RNF150
KIAA1239
TBC1D14
SORCS2
CC2D2A
KLHL8
PCDH10
KIAA1430
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
KIAA1530
METTL14
WDR19
ZFYVE28
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
AFAP1
GUF1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
NCAPG
HHIP
NDST4
AGXT2L1
USP46
MRPL1
RASL11B
ELOVL6
TNIP2
HAUS3
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
FLJ13197
MLF1IP
THAP9
NSUN7
UGT2A3
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
ABCA11P
SCD5
DNAJB14
TMEM156
WWC2
FRAS1
NAA15
CWH43
C4orf29
ALPK1
GRPEL1
MED28
CXXC4
KCNIP4
CEP44
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
FGFBP2
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
MFSD7
NOA1
TMEM175
ABLIM2
HOPX
COL25A1
USP38
LNX1
C4orf49
AFAP1-AS1
NAA11
AGPAT9
CBR4
PIGY
TMEM128
CABS1
ZNF518B
FHDC1
FLJ20021
MGC45800
PRMT10
CCDC149
DDX60L
YTHDC1
C4orf42
TMEM129
NAF1
MOB1B
TIFA
FAM114A1
RG9MTD2
MRFAP1
LOC93622
TADA2B
TBCK
HTRA3
HELQ
CYP2U1
C1QTNF7
MRFAP1L1
DDIT4L
CLNK
WDR17
ARAP2
GDEP
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
SPATA18
C4orf32
TMPRSS11B
GNPDA2
SPATA4
CPEB2
EVC2
ARL9
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
OTOP1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
NFXL1
NIPAL1
PAQR3
SHISA3
LOC152578
SCFD2
C4orf38
ZNF595
LOC152742
C4orf39
JAKMIP1
THAP6
C4orf26
KLB
FAM53A
PPM1K
C4orf45
METTL19
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
FREM3
MMAA
ZBTB49
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
GSX2
ZNF721
SYNPO2
C4orf46
SLC10A4
TIGD4
TMEM154
C4orf34
TMEM192
RWDD4
CCDC111
TAPT1
FLJ39653
TRIML2
CNOT6L
TECRL
LCORL
C4orf22
LOC255130
EPGN
ZNF718
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
CCDC96
BOD1L
FDCSP
NAP1L5
LOC285419
DCAF4L1
CYP4V2
LOC285441
LOC285456
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285501
FAM13A-AS1
GPRIN3
COX18
YIPF7
FRYL
RNF175
LOC285540
LOC285547
LOC285548
FAM200B
C4orf37
CSN1S2AP
C4orf10
ZAR1
CCDC158
TMPRSS11A
LOC339975
TRIML1
LRRC66
NAT8L
LOC340017
LOC344967
PRSS48
SOWAHB
LRIT3
C4orf44
SLC10A6
HSD17B13
FAM86EP
ANKRD37
POLN
PCNAP1
KCNIP4-IT1
KCTD8
C4orf52
BEND4
GRXCR1
TMPRSS11F
LOC389247
USP17L6P
USP17
HSP90AB2P
TRIM61
HELT
C4orf48
DTHD1
LOC401127
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
FLJ14186
C4orf3
LOC401164
LOC402160
RPL21P44
FAM92A3
WDFY3-AS2
MIR218-1
MIR302A
C4orf11
LOC441009
MTHFD2L
LOC441025
TMEM150C
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC550112
LOC550113
UGT2A2
LOC641364
LOC641365
LOC641518
ZNF876P
SLED1
LOC644145
LOC644248
DEFB131
TMPRSS11GP
CLRN2
CEP170P1
LOC645513
LOC646576
C4orf51
LOC650293
FLJ38576
DUX4L6
DUX4L5
DUX4L3
ZNF732
SCARNA22
SNORA24
SNORA26
MIR572
MIR573
MIR574
MIR575
MIR577
MIR578
LINC00290
LOC728175
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
DUX4L2
CETN4P
FAM160A1
FLJ36777
LOC731424
RELL1
PSAPL1
SNHG8
MIR943
FAM47E
LOC100129858
LOC100129917
LOC100129931
FTLP10
LOC100130872
CLDN24
LOC100133461
LOC100144602
PP12613
LOC100288255
ERVMER34-1
MIR1243
MIR2054
MIR1305
MIR548I2
MIR1973
CSN1S2BP
TMED11P
MIR4274
MIR3140
MIR4275
MIR3138
MIR4276
LOC100499177
MIR3945
MIR3684
MIR3688-1
LOC100505545
LOC100505702
LOC100505875
SLIT2-IT1
LOC100505912
LOC100505989
LOC100506013
LOC100506035
LOC100506085
LOC100506122
LOC100506229
LOC100506462
LOC100506564
LOC100506746
LOC100507053
LOC100507096
LOC100507266
1/2-SBSRNA4
MIR4453
MIR378D1
MIR4799
MIR548AJ2
MIR4802
MIR4450
MIR3688-2
MIR4451
MIR4800
MIR4801
MIR4449
MIR4798
FAM47E-STBD1
HTT-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.1.

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

Genes
BIRC3
ATM
CCND1
CARS
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
HRAS
LMO1
LMO2
MEN1
MLL
NUMA1
NUP98
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
hsa-mir-3163
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-3162
hsa-mir-130a
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ACAT1
ACP2
ACRV1
ACTN3
ADM
ADRBK1
AP2A2
APLNR
ALDH3B1
ALDH3B2
AMPD3
APBB1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
RHOG
ARHGAP1
PHOX2A
ARL2
ARNTL
ARRB1
ART1
ASCL2
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CCKBR
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
TPP1
CLNS1A
CNGA4
CNTF
COPB1
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSD
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
MARK2
CTTN
ESRRA
ETS1
F2
FAU
MS4A2
FDX1
FEN1
FGF3
FGF4
FKBP2
FOLH1
FOLR1
FOLR2
FOLR3
FSHB
FTH1
FUT4
SLC37A4
LRRC32
GAS2
GIF
GNG3
GRIA4
GRIK4
GRM5
GSTP1
GTF2H1
GUCY1A2
H2AFX
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HMBS
SLC29A2
HPX
HSPA8
HSPB2
DNAJC4
HTR3A
IGF2
IGHMBP2
IL10RA
IL18
ILK
INCENP
INS
INPPL1
IRF7
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KCNQ1
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LSP1
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MUC2
MUC6
MYBPC3
MYO7A
MYOD1
NAP1L4
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
NUCB2
OMP
OPCML
SLC22A18
SLC22A18AS
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PDE3B
PGA5
PGR
PIK3C2A
PLCB3
POLR2G
POLR2L
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
PRKRIR
PSMA1
PSMC3
PSMD13
PTH
PTPRCAP
PTPRJ
PTS
PVRL1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
RNH1
SNORD15A
ROM1
MRPL23
RPL27A
RPLP2
RPS3
RPS6KB2
RPS13
RPS25
RRM1
SAA1
SAA2
SAA3P
SAA4
SC5DL
SCN2B
SCN4B
SCT
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SMPD1
SORL1
SPI1
SPTBN2
SRPR
TRIM21
SSRP1
ST5
ST14
STIM1
STX3
STX5
ABCC8
TAGLN
TAF10
TALDO1
TCN1
TEAD1
TECTA
TH
THRSP
THY1
TSPAN4
TM7SF2
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TRPC6
TSG101
PHLDA2
TUB
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WEE1
WNT11
SF1
ZFPL1
ZNF143
ZBTB16
ZNF195
ZNF202
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIBP2
PPFIA1
SLC43A1
IFITM1
DGKZ
CHST1
BARX2
API5
MADD
OR7E2P
OR6A2
DCHS1
EIF3F
JRKL
CTSF
EED
FADD
BANF1
ZNF259
MTMR2
RPS6KA4
BRSK2
AIP
SYT7
SART1
USP2
SLC6A5
FIBP
HTR3B
ZW10
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
MMP20
UBE4A
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MED17
MAPK8IP1
TP53I11
EI24
PITPNM1
RIN1
MTL5
FEZ1
MICAL2
CTR9
CEP57
ARHGAP32
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
TRIM66
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
TSPAN32
TSSC4
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
MRVI1
TRIM22
PRG3
IFITM3
YAP1
SPON1
RBM14
CDC42EP2
EIF3M
NXF1
DEAF1
KAT5
HYOU1
IPO7
SSSCA1
HTATIP2
IFITM2
DRAP1
TRIM3
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
OR7E14P
OR7E12P
NEU3
ME3
GPR83
LYVE1
YIF1A
SRSF8
EHD1
C11orf58
STIP1
CLP1
KCNQ1OT1
SF3B2
CCDC85B
B3GNT1
ADAMTS8
PRSS23
PLA2G16
TREH
PKP3
HPS5
PTGDR2
SLCO2B1
RRAS2
CEP164
ZP1
SHANK2
KDM2A
IGSF9B
ENDOD1
SWAP70
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
DENND5A
NUP160
NCAPD3
FNBP4
RRP8
SIK3
SIRT3
CLCF1
OR52A1
VSIG2
BACE1
FAM89B
SNHG1
ARFIP2
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
C11orf41
PRDX5
POU2F3
ABTB2
BRMS1
C11orf20
CHRDL2
PAMR1
C11orf51
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
DAK
ODZ4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
PPP1R14B
OR8G2
OR8B8
OR8G1
OR10A3
FXC1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
ACAD8
B3GAT1
DKK3
RBMXL2
RAB30
PGAP2
PRPF19
DCPS
C11orf54
C11orf67
MACROD1
SLC43A3
ZBTB44
THYN1
COMMD9
DDX25
C11orf21
PACSIN3
TRPM5
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
UBQLN3
KCNK4
RNF141
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
SUV420H1
HSD17B12
IGF2-AS1
TMEM216
BET1L
CEND1
CHCHD8
SLC15A3
PHF21A
MS4A4A
WT1-AS
TRAPPC4
PPME1
CABP2
C11orf73
CWC15
TRMT112
TMEM138
PCF11
MRPL48
CYB5R2
RSF1
SPA17
FXYD6
C11orf24
TRIM34
CDHR5
CNTN5
SIAE
TOLLIP
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39A
TRIM44
BTG4
FAM55D
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
USP47
VPS37C
ANO1
TRIM68
NADSYN1
FAM86C1
C11orf57
NAT10
CCDC87
PPP6R3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
PIDD
ELMOD1
KCNQ1DN
SOX6
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
PARVA
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
MMP26
TMPRSS4
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
GPR137
IFT46
C11orf75
C11orf30
PRDM10
PRDM11
CABP4
CHRNA10
SLC17A6
TRIM49
PNPLA2
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
CARNS1
SYT13
USP28
PHRF1
LRRC4C
SCUBE2
POLD4
KRTAP5-8
PLEKHB1
MS4A7
ZBED5
CREBZF
CARD18
SIGIRR
CCDC90B
CCDC81
AASDHPPT
ALX4
RIC8A
MRPL17
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
EPS8L2
KLC2
TUT1
MRPL11
TMEM135
STK33
KCTD14
C11orf95
CHID1
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
TAF1D
RNF26
OR51G1
OR51B4
OR51B2
OR52N1
FAM118B
RIC3
DYNC2H1
NLRX1
C11orf61
C11orf80
NARS2
E2F8
SLC25A22
CCDC82
ALG9
ZNF408
CLMP
NAA40
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
ATHL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
PTDSS2
MOB2
GDPD5
CLPB
UNC93B1
SBF2
RAB1B
KIF18A
PUS3
MFRP
C11orf68
MS4A8B
JAM3
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
FAM160A2
RNASEH2C
FAR1
TMEM126A
DCUN1D5
BTBD10
EIF1AD
NUDT22
ARFGAP2
KIAA1826
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
SPRYD5
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
MICALCL
RELT
UBASH3B
C11orf70
LGALS12
TRIM5
TNKS1BP1
DIXDC1
KIAA1731
ZC3H12C
GAL3ST3
NAV2
ATG16L2
GLB1L2
SYT8
TSPAN18
ESAM
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
PRKCDBP
VPS26B
GLB1L3
CDCA5
RPLP0P2
SAAL1
ODF3
SLC22A9
SNORD15B
TIRAP
CARD16
OSBPL5
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
LRRC56
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRE
MRGPRF
ART5
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
SLC36A4
FAT3
TRIM64
TMEM45B
CYP2R1
DBX1
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
LOC120824
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
XRRA1
UBQLNL
MUC15
LOC143666
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
AMOTL1
SLC5A12
CCDC67
PATE1
C11orf65
LDHAL6A
C11orf42
GPHA2
ADAMTS15
NLRP6
NS3BP
B3GNT6
METTL15
MPZL3
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
MRPL21
TPCN2
SPATA19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
PPP1R32
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
LOC254100
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
TMEM151A
OR51F1
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
KRT8P41
LOC283104
CSNK2A1P
OR51V1
LOC283116
H19
C11orf85
SLC25A45
NEAT1
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
OR9G4
LOC283194
LINC00301
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
EFCAB4A
TMEM80
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
ANKRD42
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
OR10A2
OVCH2
TBX10
PDDC1
C11orf34
RTN4RL2
GALNTL4
B7H6
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
KRTAP5-10
SLC22A25
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
SLC22A10
SPDYC
LIPT2
VSTM5
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
NAV2-AS4
HNRNPKP3
FAM180B
PCNXL3
FLJ42102
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
OR4C45
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR210
MIR34B
MIR34C
DDI1
BLID
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
LOC440040
LOC440041
SLC22A20
KRTAP5-7
KRTAP5-11
CARD17
LINC00167
LOC441601
OR5B3
MIR326
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
MS4A13
OR8U8
OR9G9
SCARNA9
MIR483
SNORA3
SNORA52
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
BTBD18
LOC643733
PGA3
PGA4
LOC643923
LOC644656
CLDN25
RASSF10
FAM86C2P
TRIM64C
LOC646813
LOC649133
RPL23AP64
LOC650368
LOC653486
SNORA8
SNORA1
SNORA18
SNORA23
SNORA40
SNORA45
SNORA54
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
SNORD97
MIR610
MIR611
MIR612
INS-IGF2
MUC5B
LOC729013
TRIM49L1
LOC729799
METTL12
C11orf83
MIR675
MIR708
LOC100126784
LOC100128239
LOC100129216
MRVI1-AS1
LOC100130348
LOC100130987
C11orf91
LOC100132078
FAM99B
LOC100133161
LOC100133315
MRPL23-AS1
PATE3
LOC100288077
LOC100288346
MIR1304
MIR1908
MIR1237
MIR548K
MIR670
SNORA70E
BACE1-AS
MIR4300
MIR3160-2
MIR3160-1
MIR4301
MIR3162
MIR3167
MIR3165
MIR1260B
MIR4298
MIR4299
MTRNR2L8
LOC100499227
MIR3654
MIR3920
MIR3656
MIR3664
MIR3680-1
LOC100500938
MIR210HG
LOC100506233
LOC100506305
LOC100506368
LOC100506540
DCDC5
CASP12
LOC100507050
LOC100507205
LOC100507300
LOC100507392
LOC100507401
RBM14-RBM4
LOC100526771
TMX2-CTNND1
SAA2-SAA4
ARL2-SNX15
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
HNRNPUL2-BSCL2
MIR4486
MIR4697
MIR4686
MIR4490
MIR4485
MIR4489
MIR4690
MIR3973
MIR4493
MIR4491
MIR4688
MIR4492
MIR4696
MIR4691
MIR4692
MIR4694
MIR1343
MIR4687
MIR4693
MIR4488
LOC100652768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q32.1.

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
BCR
EP300
EWSR1
MN1
MYH9
NF2
PDGFB
SMARCB1
CLTCL1
CHEK2
MKL1
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
hsa-mir-33a
hsa-mir-1281
hsa-mir-659
hsa-mir-3200
hsa-mir-3199-2
hsa-mir-548j
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ACR
ACO2
ADORA2A
ADRBK2
ADSL
AP1B1
ARSA
ARVCF
ATF4
ATP6V1E1
BID
BIK
TSPO
MPPED1
CHKB
COMT
CPT1B
CRKL
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
CSF2RB
CSNK1E
CYP2D7P1
CYP2D6
DDT
CYB5R3
TYMP
FBLN1
XRCC6
GGT1
GGT3P
GGT5
GNAZ
GP1BB
MCHR1
GSC2
GSTT1
GSTT2
H1F0
SERPIND1
HMOX1
IGLL1
IL2RB
KCNJ4
LGALS1
LGALS2
LIF
LIMK2
MB
MCM5
MFNG
MGAT3
MIF
MMP11
MPST
NAGA
NCF4
NDUFA6
DRG1
NEFH
NHP2L1
OSM
PI4KA
PMM1
SEPT5
POLR2F
PPARA
MAPK1
MAPK11
PRODH
PVALB
RAC2
RANBP1
RANGAP1
RFPL1
RPL3
MAPK12
SBF1
SLC5A1
SMTN
SLC5A4
SLC7A4
SLC25A1
SNRPD3
SOX10
SREBF2
SSTR3
ST13
TBX1
TCF20
TCN2
TEF
TIMP3
CLDN5
TOP1P2
TST
HIRA
UBE2L3
UFD1L
UPK3A
VPREB1
WNT7B
XBP1
YWHAH
ZNF70
ZNF74
DGCR6
LZTR1
DGCR14
SYN3
CDC45
PLA2G6
TPST2
GALR3
NIPSNAP1
APOL1
THOC5
EIF3D
MTMR3
CACNA1I
TOP3B
P2RX6
SYNGR1
LARGE
SNAP29
GRAP2
PICK1
GAL3ST1
GTPBP1
APOBEC3B
RAB36
CELSR1
PPM1F
DEPDC5
PPP6R2
SFI1
ZBED4
JOSD1
RBX1
DGCR2
SCO2
HMGXB4
TOM1
DNAL4
SF3A1
PKDREJ
CACNG2
TAB1
SLC25A17
DDX17
TXNRD2
RASL10A
GAS2L1
RFPL3-AS1
RFPL3
RFPL2
RFPL1-AS1
NUP50
TOB2
KDELR3
IFT27
TRIOBP
CDC42EP1
DMC1
RABL2B
PACSIN2
USP18
MORC2
TNRC6B
HIC2
GRAMD4
TTLL12
MLC1
ZC3H7B
KIAA0930
TTC28
SPECC1L
GCAT
CBX6
NPTXR
PES1
CBX7
CABIN1
PRAME
SLC16A8
SEC14L2
MAPK8IP2
RBFOX2
SEZ6L
RASD2
PATZ1
SH3BP1
TSSK2
PLXNB2
SDF2L1
PPIL2
PITPNB
PISD
OSBP2
MAFF
IL17RA
BRD1
ARHGAP8
APOL2
AP1B1P1
ANKRD62P1-PARP4P3
POTEH
BCL2L13
TFIP11
C22orf31
TBC1D22A
GSTTP1
C22orf24
CBY1
SUN2
DGCR11
DGCR9
FBXO7
RHBDD3
TTLL1
POM121L1P
SAMM50
ATXN10
FAM19A5
TXN2
TMEM184B
SULT4A1
GGA1
RIBC2
DGCR5
DGCR10
FBXW4P1
ARFGAP3
SNORD43
TRMT2A
INPP5J
SMC1B
CYTH4
RTDR1
CSDC2
RRP7A
MCAT
APOBEC3C
PPPDE2
SGSM3
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L9P
CARD10
PARVB
NCAPH2
UQCR10
POM121L8P
YPEL1
ZDHHC8
VPREB3
PLA2G3
C22orf43
EIF3L
C22orf28
GTSE1
MTFP1
MED15
UPB1
TUBA8
CECR1
A4GALT
MOV10L1
SMCR7L
DGCR8
GNB1L
TUG1
FAM118A
TTC38
C22orf26
MIOX
PRR5
PEX26
TRMU
ZMAT5
SEPT3
SUSD2
EIF4ENIF1
PANX2
TOMM22
PDXP
ASPHD2
MICAL3
APOBEC3G
XPNPEP3
PARVG
CERK
EFCAB6
MRPL40
RTN4R
SLC2A11
CENPM
ALG12
NOL12
CRELD2
C22orf46
C22orf29
KCTD17
CCDC134
ADM2
FOXRED2
BAIAP2L2
SCUBE1
TRABD
PNPLA3
THAP7
APOL6
APOL5
APOL4
APOL3
OR11H1
C22orf13
SELO
SLC25A18
L3MBTL2
TBC1D10A
HDAC10
KREMEN1
ZNRF3
ASCC2
TMEM191A
LDOC1L
POLDIP3
C22orf23
MYO18B
PHF5A
KLHL22
KIAA1644
SHANK3
DGCR6L
KIAA1656
RIMBP3
MICALL1
TUBGCP6
KIAA1671
HPS4
LOC90834
SCARF2
GGTLC2
LMF2
GUSBP11
DERL3
IGLL3P
LRP5L
RNF185
ISX
RPS19BP1
C22orf32
RRP7B
SERHL
LOC96610
PHF21B
MGC16703
KLHDC7B
PIK3IP1
FAM83F
ELFN2
C1QTNF6
TNFRSF13C
RNU86
SNORD83A
SNORD83B
GAB4
C22orf39
C22orf25
ZNF280A
SGSM1
EMID1
ANKRD54
APOBEC3D
SELM
ZNF280B
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
C22orf15
HSCB
CCDC117
HORMAD2
DUSP18
MORC2-AS1
C22orf42
ENTHD1
DNAJB7
CHADL
MEI1
FAM109B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
CCDC116
CABP7
TMPRSS6
APOBEC3H
WBP2NL
POLR3H
RNF215
APOBEC3A
APOBEC3F
PRR14L
SERHL2
BPIFC
TMEM211
SEC14L3
POM121L4P
RGL4
RNU12
ATP5L2
LOC284865
LOC284889
TTC28-AS1
SEC14L4
LOC284933
RPL23AP82
SLC35E4
LOC339666
C22orf33
BK250D10.8
LOC339685
C22orf34
PI4KAP2
SDC4P
CHKB-CPT1B
TPTEP1
LOC388849
FAM211B
LOC388906
LINC00207
LOC391322
LOC400891
BCRP2
CHCHD10
LOC400927
MIRLET7BHG
FLJ46257
IL17REL
SRRD
MIRLET7A3
MIRLET7B
MIR130B
MIR185
MIR33A
LINC00229
FAM116B
PIM3
THAP7-AS1
P2RX6P
RIMBP3B
PIWIL3
MIAT
SHISA8
ODF3B
CCDC157
PRR5-ARHGAP8
BCRP3
SYCE3
TMEM191C
C22orf45
POM121L10P
LOC646851
LOC648691
CES5AP1
GATSL3
GSTTP2
GSTT2B
MIR648
MIR650
MIR658
MIR659
TMEM191B
PI4KAP1
LOC729444
SEC14L6
LOC730668
DDTL
SNORD125
MIR301B
LOC100128531
LOC100128946
CECR7
CECR5-AS1
LOC100130899
LOC100132273
LOC100144603
FLJ41941
LOC100271722
MIR1286
MIR1249
MIR1306
MIR1281
MIR548J
MIR3200
MIR3201
MIR3199-2
MIR3198-1
MIR3199-1
IGLL5
MIR3909
MIR3619
MIR3653
MIR3618
MIR3928
LOC100506195
LOC100506241
LOC100506472
LOC100506714
SEPT5-GP1BB
MIR4763
MIR4534
MIR4762
MIR4766
MIR4764
MIR4761
MIR4535

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Arm-level results

Table 2. Get Full Table Arm-level significance table - 18 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.01 | -0.942 | 0.932 | 0.00 | -1.45 | 0.976
1q | 1955 | 0.04 | 3.16 | 0.00345 | 0.00 | -1.42 | 0.976
2p | 924 | 0.01 | -0.942 | 0.932 | 0.03 | 1.58 | 0.572
2q | 1556 | 0.00 | -1.45 | 0.954 | 0.02 | 1.09 | 0.976
3p | 1062 | 0.01 | -0.463 | 0.932 | 0.00 | -1.47 | 0.976
3q | 1139 | 0.01 | -0.965 | 0.932 | 0.01 | -0.965 | 0.976
4p | 489 | 0.01 | 0.0246 | 0.932 | 0.00 | -1.48 | 0.976
4q | 1049 | 0.01 | 0.0461 | 0.932 | 0.00 | -1.47 | 0.976
5p | 270 | 0.05 | 5.06 | 4.25e-06 | 0.00 | -1.96 | 0.976
5q | 1427 | 0.04 | 4.14 | 0.000156 | 0.00 | -1.94 | 0.976
6p | 1173 | 0.01 | -0.969 | 0.932 | 0.00 | -1.47 | 0.976
6q | 839 | 0.00 | -1.47 | 0.954 | 0.01 | 0.038 | 0.976
7p | 641 | 0.04 | 4.08 | 0.000156 | 0.00 | -1.96 | 0.976
7q | 1277 | 0.05 | 5.14 | 4.25e-06 | 0.00 | -1.94 | 0.976
8p | 580 | 0.02 | 0.0357 | 0.932 | 0.01 | -0.969 | 0.976
8q | 859 | 0.02 | 0.0464 | 0.932 | 0.01 | -0.961 | 0.976
9p | 422 | 0.00 | -1.47 | 0.954 | 0.02 | 1.04 | 0.976
9q | 1113 | 0.01 | -0.931 | 0.932 | 0.03 | 2.1 | 0.239
10p | 409 | 0.01 | -0.991 | 0.932 | 0.00 | -1.49 | 0.976
10q | 1268 | 0.01 | -0.967 | 0.932 | 0.00 | -1.47 | 0.976
11p | 862 | 0.02 | 0.0617 | 0.932 | 0.02 | 0.0617 | 0.976
11q | 1515 | 0.01 | -0.421 | 0.932 | 0.02 | 0.593 | 0.976
12p | 575 | 0.04 | 4.07 | 0.000156 | 0.00 | -1.96 | 0.976
12q | 1447 | 0.04 | 4.14 | 0.000156 | 0.00 | -1.94 | 0.976
13q | 654 | 0.01 | -0.423 | 0.932 | 0.03 | 2.59 | 0.0949
14q | 1341 | 0.03 | 1.58 | 0.169 | 0.00 | -1.96 | 0.976
15q | 1355 | 0.00 | -1.97 | 0.976 | 0.01 | 0.0504 | 0.976
16p | 872 | 0.04 | 3.6 | 0.000796 | 0.00 | -1.44 | 0.976
16q | 702 | 0.03 | 2.58 | 0.0177 | 0.01 | -0.937 | 0.976
17p | 683 | 0.04 | 3.12 | 0.00363 | 0.02 | 0.101 | 0.976
17q | 1592 | 0.04 | 3.65 | 0.000743 | 0.00 | -1.42 | 0.976
18p | 143 | 0.01 | -0.988 | 0.932 | 0.01 | -0.487 | 0.976
18q | 446 | 0.01 | -0.979 | 0.932 | 0.01 | -0.477 | 0.976
19p | 995 | 0.01 | -0.452 | 0.932 | 0.01 | -0.452 | 0.976
19q | 1709 | 0.01 | 0.0642 | 0.932 | 0.00 | -1.97 | 0.976
20p | 355 | 0.03 | 1.53 | 0.169 | 0.00 | -1.98 | 0.976
20q | 753 | 0.03 | 1.55 | 0.169 | 0.00 | -1.98 | 0.976
21q | 509 | 0.01 | -0.971 | 0.932 | 0.02 | 0.033 | 0.976
22q | 921 | 0.01 | -0.716 | 0.932 | 0.17 | 20.4 | 0
Xq | 1312 | 0.03 | 1.62 | 0.169 | 0.02 | 0.102 | 0.976

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.

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/THCA/1709067/2.GDAC_MergeDataFiles.Finished/THCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 3. Get Full Table First 10 out of 268 Input Tumor Samples.

Tumor Sample Names
TCGA-BJ-A0YZ-01A-11D-A10T-01
TCGA-BJ-A0Z0-01A-11D-A10T-01
TCGA-BJ-A0Z2-01A-11D-A10T-01
TCGA-BJ-A0Z3-01A-11D-A13V-01
TCGA-BJ-A0Z5-01A-11D-A10T-01
TCGA-BJ-A0Z9-01A-11D-A10T-01
TCGA-BJ-A0ZA-01A-11D-A10T-01
TCGA-BJ-A0ZB-01A-11D-A10T-01
TCGA-BJ-A0ZC-01A-12D-A13V-01
TCGA-BJ-A0ZE-01A-11D-A10T-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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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