SNP6 Copy number analysis (GISTIC2)
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 2.0.23.

Summary

There were 80 tumor samples used in this analysis: 41 significant arm-level results, 3 significant focal amplifications, and 18 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 - 3 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
--- | --- | --- | --- | ---
8q24.22 | 6.8573e-12 | 7.8824e-12 | chr8:113697713-145138636 | 263
6p24.3 | 0.0002226 | 0.0002226 | chr6:1-18226591 | 133
8q11.22 | 1.2335e-08 | 0.00073354 | chr8:43078230-69295680 | 119

Genes in Wide Peak

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

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

Genes
EXT1
MYC
RECQL4
ADCY8
ANXA13
ADGRB1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
POU5F1B
PTK2
PVT1
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
JRK
EIF3H
DGAT1
GPAA1
WISP1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
COLEC10
KHDRBS3
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
MTBP
AGO2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
HGH1
KCNK9
THEM6
FAM49B
CHRAC1
EXOSC4
LY6K
TRMT12
WDYHV1
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
RHPN1-AS1
DSCC1
DERL1
SLC52A2
GSDMD
ZNF696
ARHGAP39
ZNF34
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
MAF1
UTP23
PARP10
C8orf76
TIGD5
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
NAPRT
TBC1D31
HPYR1
MFSD3
MAL2
RHPN1
FBXO32
TOP1MT
CCDC26
ZNF572
LYPD2
TMEM71
FER1L6-AS2
TMEM65
LINC00964
FAM84B
FAM91A1
SLC30A8
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LINC01591
ZNF252P
TMED10P1
ZNF252P-AS1
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
WDR97
TMEM249
SPATC1
MROH5
MAFA
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
AARD
LRRC24
MIR151A
NCRNA00250
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
TMEM75
MROH6
SCX
RAD21-AS1
FER1L6
MIR548D1
MIR661
CASC8
MROH1
LINC00977
OC90
LINC01300
MIR937
MIR939
FAM83H-AS1
CDC42P3
LINC00861
CCDC166
FAM83A-AS1
LOC100133669
CASC11
TONSL-AS1
LOC100288181
MIR1302-7
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR1208
MIR3686
MIR548AA1
MIR3610
CCAT1
ASAP1-IT2
MINCR
ZHX1-C8orf76
MIR4662A
MIR4662B
MIR4663
MIR4472-1
MIR4664
PCAT1
MIR5194
LINC00536
CCAT2
PRNCR1
LOC101927513
LOC101927543
LOC101927588
RNF139-AS1
LOC101927657
LINC00824
LOC101927798
LOC101927822
LOC101927845
LOC101927915
LOC101928087
LOC101928160
LOC101928902
MIR6846
MIR6847
MIR6848
MIR7112
MIR6850
MIR548AZ
MIR6844
MIR6893
MIR6845
MIR6849
MIR7848
CASC21
CASC19
PCAT2
LINC01151
MAFA-AS1
LOC105375713
LOC105375734
LOC105375744
LOC105375773
LOC105375787
LOC105375800

Genes in Wide Peak

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

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

Genes
IRF4
DEK
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
NOL7
FAM8A1
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
MCUR1
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
LINC01600
PIP5K1P1
KDM1B
RBM24
RNF182
PHACTR1
SMIM13
SYCP2L
LINC00518
PXDC1
SERPINB9P1
FAM217A
LOC285766
LINC01622
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
NHLRC1
PSMG4
LINC01011
HTATSF1P2
STMND1
C6orf201
ERVFRD-1
LINC00266-3
KU-MEL-3
PPP1R3G
HULC
TMEM170B
SCARNA27
LYRM4-AS1
TFAP2A-AS1
LOC100130357
MIR3691
LOC100506207
ELOVL2-AS1
JARID2-AS1
LOC100507194
LOC100507506
GMDS-AS1
BLOC1S5-TXNDC5
EEF1E1-BLOC1S5
MIR4639
MIR4645
MIR5689
MIR5683
LOC101927691
FOXCUT
LOC101927730
LOC101927759
LOC101927950
LOC101927972
LOC101928191
LOC101928253
LOC101928433
LOC101928491
LINC01108
MIR7641-2
MIR6720
MIR7853
LOC102724096
LOC105374952
MIR5689HG
TBC1D7-LOC100130357

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.22.

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

Genes
PLAG1
TCEA1
CHCHD7
ASPH
CA8
CEBPD
CRH
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SPIDR
SGK3
LINC00588
PTTG3P
RNU105C
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
POMK
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
MCMDC2
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
LOC286178
NKAIN3
LINC01289
LINC01299
PPP1R42
C8orf34-AS1
POTEA
FAM150A
LOC401463
MIR124-2
SDR16C6P
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
MIR124-2HG
LOC100130298
SBF1P1
LOC100287846
LINC01602
LINC01301
LINC00967
RRS1-AS1
LINC01592
LOC100507464
LINC00968
LINC01606
C8orf44-SGK3
MIR4470
YTHDF3-AS1
LOC101929217
LOC101929268
LOC101929341
LOC101929415
LOC101929488
LOC101929528
LOC102724612
LOC102724623
LOC102724708
LOC105375843

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 - 18 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
--- | --- | --- | --- | ---
1p36.12 | 0.0016441 | 0.0016441 | chr1:18105008-27386427 | 176
6q25.3 | 0.0016441 | 0.0016441 | chr6:155944963-158007554 | 8
3p25.1 | 0.0035484 | 0.0035484 | chr3:13503739-13651118 | 2
11q24.3 | 0.01013 | 0.010227 | chr11:17383801-133813742 | 1283
3q29 | 0.010826 | 0.010826 | chr3:194310859-194355276 | 1
2q37.2 | 0.01221 | 0.012384 | chr2:225006957-242193529 | 188
3q24 | 0.016688 | 0.017321 | chr3:143210556-143975530 | 2
8p11.22 | 0.037764 | 0.037764 | chr8:38455400-38611162 | 2
1p12 | 0.039767 | 0.039767 | chr1:116766064-119608325 | 25
3p22.2 | 0.045261 | 0.044545 | chr3:38273260-38347639 | 1
16q22.1 | 0.046297 | 0.051696 | chr16:31711094-90338345 | 512
3p25.2 | 0.056191 | 0.054482 | chr3:12767722-12841777 | 3
3q29 | 0.066004 | 0.066004 | chr3:194576042-194646185 | 2
3p14.2 | 0.073099 | 0.07193 | chr3:58633296-67015239 | 34
16q23.3 | 0.09096 | 0.10675 | chr16:82656211-83509230 | 4
18q22.2 | 0.10123 | 0.10675 | chr18:67514632-80373285 | 60
5q23.1 | 0.15322 | 0.15168 | chr5:114562212-158412206 | 448
17q12 | 0.20414 | 0.20414 | chr17:28944822-56486234 | 572

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.12.

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

Genes
PAX7
ARID1A
MDS2
ALPL
C1QA
C1QB
C1QC
CAPZB
RUNX3
CDA
CDC42
CD52
CNR2
DDOST
E2F2
ECE1
EPHA8
EPHB2
EXTL1
FUCA1
GALE
SFN
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
NBL1
PAFAH2
PLA2G2A
PLA2G5
RAP1GAP
RHCE
RHD
RPL11
RPS6KA1
SLC9A1
TCEA3
TCEB3
SLC30A2
LUZP1
NR0B2
FCN3
AKR7A2
ALDH4A1
EIF4G3
MAP3K6
ZBTB40
CELA3A
HNRNPR
SRRM1
CNKSR1
NUDC
SRSF10
RCAN3
LYPLA2
AKR7A3
KDM1A
WDTC1
EMC1
OTUD3
UBR4
CELA3B
TMEM50A
CLIC4
SYF2
LDLRAP1
PLA2G2D
LINC00339
PLA2G2E
HP1BP3
ZNF593
MRTO4
WNT4
RNF186
GPN2
PQLC2
AIM1L
TMEM57
CAMK2N1
ASAP3
PNRC2
PIGV
MTFR1L
RSRP1
PITHD1
MAN1C1
NIPAL3
SEPN1
KIF17
GRHL3
IL22RA1
GPATCH3
PLA2G2F
CEP85
PINK1
AUNIP
MUL1
LIN28A
FAM110D
DHDDS
ZNF436
TAS1R2
SH3BGRL3
TMEM222
USP48
NBPF3
ZDHHC18
TRIM63
SYTL1
IGSF21
STPG1
UBXN11
FAM46B
KDF1
IFFO2
MYOM3
KLHDC7A
VWA5B1
UBXN10
ZNF436-AS1
PDIK1L
IFNLR1
FAM43B
PAQR7
AKR7L
TMCO4
ZNF683
LOC284632
LINC01141
CATSPER4
TRNP1
CD164L2
PLA2G2C
SH2D5
NCMAP
LDLRAD2
MINOS1
RPS14P3
ACTG1P20
LACTBL1
LOC646471
C1orf234
MIR1256
MIR1976
MIR1290
MIR3115
MIR4253
MIR3917
LOC100506730
LOC100506801
TCEB3-AS1
LOC100506985
MINOS1-NBL1
MIR4695
MIR4419A
MIR4425
MIR4684
MIR4418
MIR378F
RCAN3AS
PINK1-AS
LINC01355
LOC101927895
UBXN10-AS1
LOC101928043
LOC101928163
LOC101928303
LOC101928324
LOC101928728
MIR6084
MIR6731
MIR6127
LOC105378614

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.3.

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

Genes
SNX9
ARID1B
ZDHHC14
TMEM242
MIR1202
MIR3692
MIR4466
SYNJ2-IT1

Genes in Wide Peak

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

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

Genes
FBLN2
SNORA93

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CCND1
CBL
DDB2
DDX6
DDX10
EXT2
FANCF
FLI1
LMO2
MEN1
NUMA1
PAFAH1B2
POU2AF1
SDHD
WT1
PICALM
PCSK7
ARHGEF12
MAML2
CREB3L1
ACAT1
ACP2
ACRV1
ACTN3
GRK2
APLNR
ALDH3B1
ALDH3B2
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
ARHGAP1
PHOX2A
ARL2
ARRB1
FXYD2
BAD
BBS1
BDNF
CXCR5
SERPING1
CAPN5
VPS51
MRPL49
ZNHIT2
MPPED2
MYRF
TMEM258
DAGLA
CAPN1
CASP1
CASP4
CASP5
CAT
SERPINH1
CD3D
CD3E
CD3G
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CFL1
CTSC
CHEK1
CHKA
CHRM1
CHRM4
CLNS1A
CNTF
COX8A
CPT1A
CRY2
CRYAB
CST6
CSTF3
CTNND1
CTSW
DDB1
DHCR7
DLAT
DLG2
DPAGT1
DRD2
EEF1G
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
HMBS
SLC29A2
HSPA8
HSPB2
DNAJC4
HTR3A
IGHMBP2
IL10RA
IL18
INCENP
INPPL1
STT3A
CD82
KCNA4
KCNC1
KCNJ1
KCNJ5
KCNJ11
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
VWA5A
LRP4
LRP5
LTBP3
CAPRIN1
MAP6
MCAM
MDK
SCGB2A1
SCGB2A2
MAP3K11
KMT2A
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYBPC3
MYO7A
MYOD1
NCAM1
NDUFC2
NDUFS3
NDUFV1
NDUFS8
NELL1
NFRKB
NNMT
NPAT
NRGN
OMP
OPCML
OSBP
OVOL1
P2RX3
P2RY2
P2RY6
PAK1
PAX6
PC
PDE2A
PGA5
PGR
PLCB3
POLR2G
PPP1CA
PPP2R1B
PPP2R5B
PRCP
PRG2
THAP12
PSMC3
PTPRCAP
PTPRJ
PTS
NECTIN1
PYGM
RAB3IL1
RAB6A
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RDX
RELA
DPF2
SNORD15A
ROM1
RPS3
RPS6KB2
RPS25
SAA1
SAA2
SAA3P
SAA4
SC5D
SCN2B
SCN4B
ST3GAL4
SIPA1
SLC1A2
SLC3A2
SLN
SORL1
SPI1
SPTBN2
SRPRA
SSRP1
ST14
STX3
STX5
ABCC8
TAGLN
TCN1
TECTA
THRSP
THY1
TM7SF2
TPH1
TRAF6
TRPC6
TSG101
TYR
UCP2
UCP3
SCGB1A1
UPK2
UVRAG
VEGFB
BEST1
WNT11
SF1
ZFPL1
ZBTB16
ZNF202
CSRP3
PDHX
FOSL1
CUL5
FZD4
BBOX1
PPFIA1
SLC43A1
DGKZ
CHST1
BARX2
API5
MADD
OR7E2P
JRKL
CTSF
EED
FADD
BANF1
ZPR1
MTMR2
RPS6KA4
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
TESMIN
FEZ1
CEP57
ARHGAP32
ATG13
SPCS2
CKAP5
ARHGEF17
GAB2
C2CD2L
FCHSD2
FGF19
CCS
RCE1
NAALAD2
NAALADL1
KCNE3
NR1H3
IL18BP
DPP3
USH1C
KCNK7
HIPK3
RBM7
PRMT3
MPZL2
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
PRG3
YAP1
RBM14
CDC42EP2
EIF3M
NXF1
KAT5
HYOU1
SSSCA1
HTATIP2
DRAP1
TAF6L
ATP5L
SCGB1D2
SCGB1D1
CELF1
POLD3
OR5I1
STARD10
NEU3
ME3
GPR83
YIF1A
SRSF8
EHD1
STIP1
CLP1
SF3B2
CCDC85B
B4GAT1
ADAMTS8
PRSS23
PLA2G16
TREH
HPS5
PTGDR2
SLCO2B1
CEP164
ZP1
SHANK2
KDM2A
ENDOD1
EXPH5
ATG2A
PHLDB1
GANAB
FAM168A
DTX4
SIK2
NUP160
FNBP4
SIK3
CLCF1
VSIG2
BACE1
FAM89B
SNHG1
POLA2
TRIM29
RAB38
CADM1
FLRT1
MTCH2
PANX1
FJX1
KIAA1549L
PRDX5
POU2F3
ABTB2
BRMS1
TEX40
CHRDL2
PAMR1
ANAPC15
ZDHHC5
ATL3
TSKU
HINFP
REXO2
C2CD3
TKFC
TENM4
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
PPP1R14B
OR8G2
OR8B8
OR8G1
TIMM10
TIMM8B
MYEOV
BSCL2
OR8B2
ELP4
CHORDC1
RAB30
PRPF19
DCPS
C11orf54
AAMDC
MACROD1
SLC43A3
ZBTB44
COMMD9
DDX25
PACSIN3
SAC3D1
SNX15
RHOD
EFEMP2
NOX4
KCNK4
NTM
CDON
UBXN1
APIP
TMX2
GAL
SIDT2
KMT5B
HSD17B12
TMEM216
COA4
SLC15A3
PHF21A
MS4A4A
WT1-AS
TRAPPC4
PPME1
CABP2
HIKESHI
CWC15
TRMT112
TMEM138
PCF11
MRPL48
RSF1
SPA17
FXYD6
C11orf24
CNTN5
SIAE
C11orf71
ZDHHC13
ROBO4
WDR74
SLC35F2
RAB39A
TRIM44
BTG4
NXPE4
SYTL2
ANKRD49
MS4A12
MRPL16
SDHAF2
SSH3
TTC12
TMEM132A
HRASLS2
LAMTOR1
VPS37C
ANO1
NADSYN1
FAM86C1
C11orf57
NAT10
CCDC87
PPP6R3
UEVLD
RNF121
LIN7C
ACER3
SLC35C1
TCP11L1
LGR4
ELMOD1
CDC42BPG
FOXRED1
OTUB1
AMBRA1
PACS1
KDM4D
KBTBD4
TTC17
SCN3B
VPS11
TMEM126B
SLC22A11
TEX12
CRTAM
TMPRSS4
GPR137
IFT46
SMCO4
EMSY
PRDM10
PRDM11
CABP4
SLC17A6
TRIM49
CD248
CORO1B
SCYL1
DSCAML1
GRAMD1B
USP35
CEP126
ARHGAP20
CARNS1
SYT13
USP28
LRRC4C
POLD4
KRTAP5-8
PLEKHB1
MS4A7
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
ALX4
PKNOX2
FAM111A
TP53AIP1
ANO3
MMP27
ABCG4
ROBO3
MS4A6A
MS4A5
C11orf1
KLC2
TUT1
MRPL11
TMEM135
KCTD14
C11orf95
LRFN4
AHNAK
ALG8
PRRG4
TMEM223
TMEM109
CCDC86
LBHD1
C11orf49
TRIM48
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
C11orf80
NARS2
E2F8
CCDC82
ALG9
ZNF408
CLMP
NAA40
QSER1
AGBL2
ZBTB3
PDZD3
C11orf63
CPSF7
PRR5L
CCDC15
ASRGL1
MOGAT2
TMEM134
MUS81
PAAF1
PDGFD
INTS5
ZFP91
TMPRSS5
OR8J3
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
GDPD5
CLPB
UNC93B1
RAB1B
KIF18A
PUS3
C11orf68
MS4A8
FERMT3
TRPT1
RBM4B
FRMD8
BCO2
TMEM133
TMPRSS13
RNASEH2C
TMEM126A
DCUN1D5
EIF1AD
NUDT22
ARFGAP2
MSANTD4
SYVN1
KIRREL3
DGAT2
ACCS
MS4A14
TRIM51
BUD13
TMEM25
PTPN5
RPUSD4
TBRG1
RELT
UBASH3B
C11orf70
LGALS12
SNORD14C
SNORD14D
SNORD14E
TNKS1BP1
DIXDC1
CEP295
ZC3H12C
GAL3ST3
NAV2
ATG16L2
TSPAN18
ESAM
AP5B1
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
ALKBH8
FDXACB1
C11orf52
INTS4
GLYATL1
CDCA5
RPLP0P2
SAAL1
SLC22A9
SNORD15B
TIRAP
CARD16
C1QTNF4
C1QTNF5
TMEM123
PTPMT1
BATF2
SLC22A12
PANX3
MRGPRD
APOA5
MRGPRF
ARAP1
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
C11orf74
OR4C46
OR4X2
OR4B1
LARGE2
SLC36A4
FAT3
TRIM64
TMEM45B
DBX1
COLCA2
PIH1D2
NXPE1
NXPE2
JAML
DNAJC24
ARL14EP
OR8I2
LDLRAD3
XRRA1
MUC15
C11orf94
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf84
SPTY2D1
TMEM86A
AMOTL1
SLC5A12
DEUP1
PATE1
C11orf65
LDHAL6A
GPHA2
ADAMTS15
B3GNT6
METTL15
MPZL3
IMMP1L
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
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
OOSP2
MS4A15
VWCE
CYB561A3
PPP1R32
GDPD4
DDIAS
CCDC83
ORAOV1
SHANK2-AS3
LRTOMT
HEPACAM
OAF
TIGD3
FAM181B
CCDC89
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
DEFB108B
PELI3
ANGPTL5
SSSCA1-AS1
EHBP1L1
SNX32
TSGA10IP
RNF169
CNIH2
ZDHHC24
C11orf86
NUDT8
ANKK1
OOSP1
OR4C3
OR4S1
EML3
TMEM151A
RNF214
SVIP
MRGPRX1
NPAS4
C11orf31
AQP11
OR10AG1
OR5J2
OR4C13
OR4C12
TRIM49B
MAJIN
SLC25A45
NEAT1
LOC283140
LINC00900
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
C11orf44
OR9G4
LOC283194
LINC00301
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LINC00294
IGSF22
ALG1L9P
LUZP2
CCDC84
TMEM225
OR8D4
OR5F1
OR5AP2
ANKRD13D
LOC338694
ANKRD42
CSTF3-AS1
OTOG
DCDC1
C11orf53
LOC341056
MS4A10
OR2AT4
HEPHL1
TBX10
PLET1
RTN4RL2
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
DNAJB13
MALAT1
ZFP91-CNTF
KRTAP5-10
SLC22A25
FIBIN
C11orf96
SLC22A10
SPDYC
LIPT2
VSTM5
LOC387810
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
GUCY2EP
TRIM77
IZUMO1R
KDM4E
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
NAV2-AS4
HNRNPKP3
LOC399886
FAM180B
PCNX3
FLJ42102
TRIM49D1
C11orf87
COLCA1
C11orf88
MIR100HG
PATE2
PATE4
ST3GAL4-AS1
SNX19
OR4A47
OR4C45
LOC403312
SCGB1D4
MIRLET7A2
MIR100
MIR125B1
MIR129-2
MIR130A
MIR139
MIR192
MIR194-2
MIR34B
MIR34C
DDI1
BLID
DKFZp686K1684
LOC440040
TRIM51HP
SLC22A20
KRTAP5-7
KRTAP5-11
CASP1P2
CARD17
LINC00167
LOC441601
OR5B3
MIR326
CCDC73
LOC494141
BDNF-AS
MS4A13
OR8U8
SCARNA9
HEPN1
TRIM64B
TRIM53AP
TRIM49C
UBTFL1
C11orf97
BTBD18
LOC643733
PGA3
PGA4
LOC643923
CLDN25
FAM86C2P
LOC646029
LOC646522
TRIM64C
LOC646813
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
SNORD67
SNORA57
MIR610
MIR611
MIR612
MS4A18
TRIM49D2
SEC14L1P1
METTL12
UQCC3
ANO1-AS2
MIR708
LOC100126784
LOC100128386
LOC100128494
LOC100129203
LOC100129216
TMEM262
LOC100130987
C11orf91
ZNF705E
LOC100131626
LOC100132078
LOC100132686
LOC100133315
PATE3
LOC100287896
WTAPP1
NCAM1-AS1
KCTD21-AS1
MIR1261
MIR1304
MIR1908
MIR548L
MIR1237
MIR548K
MIR670
SNORA70E
BACE1-AS
MIR4300
MIR3160-2
MIR3160-1
MIR3164
MIR4301
MIR3162
MIR3167
MIR3165
MIR1260B
MIR3161
MIR3159
MIR3163
MIR3166
USP2-AS1
MIR3654
MIR3920
MIR3656
MIR3664
CCDC179
C11orf72
LOC100506127
RAB30-AS1
LOC100506368
SPTY2D1-AS1
DCDC5
LOC100506675
CASP12
TPBGL
LOC100507144
LOC100507205
MIR670HG
LOC100507283
ALKBH3-AS1
LOC100507384
SENCR
LRP4-AS1
LOC100507431
RBM14-RBM4
TMPRSS4-AS1
TMX2-CTNND1
SAA2-SAA4
ARL2-SNX15
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
HNRNPUL2-BSCL2
MIR4486
MIR4490
MIR548AL
MIR4487
MIR4459
MIR4489
MIR4690
MIR3973
MIR4493
MIR4491
MIR4688
MIR4492
MIR4696
MIR4691
MIR4692
MIR4694
MIR1343
MIR4693
MIR4488
LOC100652768
MIR5579
MIR5582
GRM5-AS1
NAV2-AS5
NAV2-AS2
JRKL-AS1
SHANK2-AS1
KIRREL3-AS2
NTM-IT
LOC100996455
LOC101054525
LINC00678
LOC101927120
LOC101927204
LOC101927495
OVOL1-AS1
LOC101928069
MRGPRF-AS1
LINC01488
LOC101928424
FBXO3-AS1
LOC101928443
LOC101928510
LOC101928535
LINC01493
LINC01537
LOC101928580
LOC101928591
LOC101928812
LOC101928823
LOC101928837
LOC101928847
LOC101928865
LOC101928894
LOC101928896
LOC101928940
LOC101928943
LOC101928944
LOC101928985
MIR4300HG
LOC101929011
LOC101929089
LOC101929208
DISC1FP1
LOC101929227
LOC101929295
LOC101929340
LOC101929427
LOC101929473
LOC101929497
LOC101929517
LOC101929538
LINC01395
NTM-AS1
LOC101929653
C11orf98
MIR6128
MIR6503
MIR6514
MIR6746
MIR6747
MIR6748
MIR6751
MIR6752
MIR6753
MIR6755
MIR6756
MIR6860
MIR7113
MIR7154
MIR7641-1
MIR7641-2
MIR8054
MIR8087
MIR6090
MIR6750
MIR6716
MIR6745
MIR6749
MIR6754
MIR6879
MIR7155
MIR8052
MIR8068
LOC102723330
LINC01495
LINC01499
LOC102723838
LOC102723895
LOC102724064
LOC102724265
LOC102724301
PAUPAR
LOC103312105
LOC103611081
PKNOX2-AS1
BBOX1-AS1
APOA1-AS
LOC105369332
LOC105369340
MIR194-2HG
LOC105369423
LOC105369431
LOC105369438
LOC105369443
LOC105369473
LOC105369486
LOC105369507
LOC105369509
LOC105369532
STT3A-AS1
LOC105376599
LOC105376633
LOC105376671
LINC01616
SNORA88
PCF11-AS1
KCNK4-TEX40

Genes in Wide Peak

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

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

Genes
CPN2

Genes in Wide Peak

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

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

Genes
hsa-mir-1244-1
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SNORD20
SAG
CCL20
SP100
SPP2
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
SH3BP4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
USP40
HJURP
HES6
C2orf83
MFF
ACKR3
RNPEPL1
NYAP2
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
MGC16025
DNER
B3GNT7
SP140L
LOC93463
AGAP1
TWIST2
DIS3L2
NEU4
SPATA3
FBXO36
MTERF4
UBE2F
OTOS
COPS9
OR6B3
LOC150935
LINC01107
LOC151174
ERFE
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
DAW1
C2orf57
TIGD1
LOC200772
C2orf72
RTP5
LOC285095
DUSP28
MROH2A
ESPNL
ECEL1P2
SPATA3-AS1
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
LOC646736
PRSS56
AQP12B
SNORA75
LOC654841
SCARNA6
SCARNA5
MIR562
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR3133
MIR4269
AGAP1-IT1
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441
MIR5001
MIR5702
MIR5703
CAPN10-AS1
LINC01237
LOC101928111
LOC101928881
MIR6811
LOC102723927
LINC01173

Genes in Wide Peak

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

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

Genes
SLC9A9
SLC9A9-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.22.

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

Genes
RNF5P1
C8orf86

Genes in Wide Peak

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

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

Genes
HSD3B1
HSD3B2
PTGFRN
TBX15
TTF2
CD101
WARS2
WDR3
MAN1A2
HAO2
GDAP2
FAM46C
VTCN1
TRIM45
HSD3BP4
SPAG17
LINC00622
MIR942
HAO2-IT1
LOC100996263
LOC101929099
LOC101929147
LINC01525
WARS2-IT1
LOC105378933

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p22.2.

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

Genes
SLC22A14

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.1.

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

Genes
CBFA2T3
CBFB
CDH1
CDH11
CYLD
FANCA
MAF
HERPUD1
hsa-mir-1826
AARS
ADCY7
AP1G1
AFG3L1P
AGRP
AMFR
APRT
ZFHX3
BBS2
GAS8-AS1
CA5A
CA7
CALB2
CBLN1
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CES1
CETP
CNGB1
COX4I1
CSNK2A2
CTRB1
CTRL
CYBA
DHODH
NQO1
DYNC1LI2
DPEP1
E2F4
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
GNAO1
GOT2
HAS3
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
KARS
KIFC3
LCAT
MC1R
CHST6
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
MVD
NFATC3
CHMP1A
PHKB
PLCG2
POLR2C
PSKH1
PSMB10
PSMD7
RBL2
RPL13
RRAD
SALL1
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SPG7
TAT
TERF2
TK2
ZNF19
ZNF23
GAN
SLC7A5
CDK10
TRADD
MBTPS1
CES2
NAE1
NOL3
TAF1C
SLC7A6
USP10
ATP6V0D1
ADGRG1
BCAR1
VPS9D1
N4BP1
NUP93
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
NUTF2
IRX5
DNAJA2
KATNB1
ZNF267
EMC8
TUBB3
CFDP1
CTCF
NFAT5
NUDT21
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
CNOT1
PHLPP2
ZNF423
ZCCHC14
GSE1
ATMIN
RPGRIP1L
COTL1
MLYCD
SF3B3
CES3
ADAT1
CHST5
ARL2BP
ORC6
EDC4
PLA2G15
TP53TG3
COG4
PLEKHG4
DKFZP434H168
LRRC29
CPNE7
VPS4A
IL17C
TOX3
NOB1
CCDC113
TMEM208
CFAP20
FHOD1
BRD7
ANKRD11
ZDHHC1
OSGIN1
PARD6A
PLLP
CKLF
NIP7
FAM96B
GINS2
TPPP3
TRAPPC2L
CES1P1
WWOX
BCO1
TERF2IP
PRMT7
NECAB2
KLHDC4
HYDIN
DEF8
DUS2
CHTF8
LPCAT2
TXNL4B
BANP
HEATR3
PDPR
RFWD3
SLC38A7
OGFOD1
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
ZDHHC7
VAC14
DOK4
VPS35
CMTR2
DDX28
TSNAXIP1
CENPN
CMC2
COQ9
CIAPIN1
THAP11
JPH3
PDP2
ZNF319
RANBP10
VAT1L
TLDC1
WFDC1
NOD2
PDF
DPEP2
DPEP3
PAPD5
AKTIP
MTHFSD
GINS3
NDRG4
ACD
DBNDD1
FTO
FA2H
IRX6
IRX3
FAM65A
TMEM231
TANGO6
USB1
WDR59
ELMO3
KLHL36
FBXO31
SHCBP1
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
CYB5B
CMIP
ITFG1
GFOD2
CDT1
MAP1LC3B
NETO2
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
LONP2
ENKD1
SLC7A6OS
NLRC5
DRC7
CAPNS2
COG8
SPIRE2
MT4
ZNF469
GPT2
B3GNT9
UTP4
ZNRF1
ABCC11
NKD1
CNTNAP4
RSPRY1
MYLK3
MARVELD3
MTSS1L
CENPBD1
ZNF276
CCDC102A
KCNG4
SDR42E1
ABCC12
CMTM1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
NRN1L
CMTM3
C16orf78
SPATA2L
SPATA33
ANKRD26P1
ZC3H18
CDYL2
ZNF720
SNX20
TMEM170A
SLC38A8
ZFP90
CARMIL2
KCTD19
CMTM4
CMTM2
BEAN1
SLC22A31
IL34
TMED6
FRG2DP
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
SNAI3-AS1
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
CPNE2
ADGRG5
PRSS54
CES5A
ADGRG3
CNEP1R1
TERB1
CES4A
EXOC3L1
CASC22
LOC283856
LINC00304
LINC00922
HCCAT5
LINC01566
LOC283922
NUDT7
PDXDC2P
CLEC18C
MT1DP
SNAI3
LOC339059
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
TEPP
SLC6A10P
C16orf87
C16orf97
LOC388282
C16orf86
C16orf47
LOC390705
CES1P2
PABPN1L
FLJ26245
LOC400541
LOC400548
FENDRR
LOC400553
LOC400558
C16orf74
MIR138-2
MIR140
NPIPB15
CTRB2
LOC440390
MIR328
CLEC18B
SNORD68
UBE2MP1
CASC16
LOC643802
CRNDE
MT1IP
APOOP5
LINC00273
KIAA0895L
TP53TG3C
SNORA46
SNORA50A
SNORD71
SNORD111
LOC729159
TP53TG3D
TP53TG3B
LINC00917
SNORD111B
VPS9D1-AS1
LOC100129617
LOC100129697
URAHP
TP53TG3HP
VAC14-AS1
SYCE1L
LOC100131303
TAT-AS1
LOC100287036
HERC2P4
LOC100289580
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
MIR3181
MIR3935
LINC00919
FTO-IT1
LINC00920
LOC100505942
SMG1P7
LOC100506083
LINC01568
LOC100506281
LINC01082
C16orf95
LOC100507534
LOC100507577
CKLF-CMTM1
MIR4720
MIR4722
MIR4719
MIR4426
MIR548AI
MIR5093
MIR5189
LOC100996338
LOC100996345
PRCAT47
FAM157C
LINC01081
ITFG1-AS1
LOC101927132
LOC101927272
LOC101927334
LINC01571
LOC101927480
LOC101927580
LOC101927650
BEAN1-AS1
LOC101927793
LOC101927817
LINC01572
LOC101928035
LOC101928203
LINC01229
LINC01227
LOC101928417
LOC101928446
LOC101928557
LOC101928614
LOC101928659
LOC101928682
LOC101928708
LOC101928737
LOC101928880
MIR6504
MIR6771
MIR6772
MIR6775
MIR7641-2
MIR7854
MIR8058
MIR6773
MIR6774
MIR6863
LOC102467079
MAFTRR
LOC102723373
LOC102723753
LOC102724084
TP53TG3E
TP53TG3F
LOC102724163
LOC102724344
LOC102724467
FOXC2-AS1
ENPP7P13
LOC105371267
LOC105371328
LOC105371335
LOC105371414
LOC105376772
LOC106699570

Genes in Wide Peak

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

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

Genes
RPL32
CAND2
SNORA7A

Genes in Wide Peak

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

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

Genes
TMEM44
TMEM44-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

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

Genes
FHIT
PTPRG
ATXN7
CADPS
MAGI1
PSMD6
LRIG1
FEZF2
ADAMTS9
C3orf14
THOC7
KBTBD8
SLC25A26
FAM3D
C3orf49
SNTN
SYNPR
PRICKLE2
C3orf67
LINC00698
LINC00994
PTPRG-AS1
PSMD6-AS2
ADAMTS9-AS2
PRICKLE2-AS1
MAGI1-AS1
SYNPR-AS1
THOC7-AS1
PRICKLE2-AS2
PRICKLE2-AS3
C3orf67-AS1
ADAMTS9-AS1
MIR548BB
LOC105377143

Genes in Wide Peak

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

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

Genes
MIR3182
LOC101928417
LOC101928446
MIR8058

Genes in Wide Peak

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

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

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
SOCS6
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
SALL3
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
RBFA
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
GTSCR1
DOK6
LOC284241
ZADH2
SMIM21
LINC00908
LOC339298
ATP9B
LOC400655
LINC00909
C18orf65
LINC00683
LOC400661
HSBP1L1
LOC643542
C18orf63
PARD6G-AS1
LOC100131655
LINC01541
LOC100505797
LOC100505817
LOC100505853
RBFADN
MIR548AV
LOC101060542
LOC101927481
LOC101927606
LOC101927651
LINC01029
LOC101927989
LOC102724913
LOC105372179

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q23.1.

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

Genes
CD74
ITK
PDGFRB
hsa-mir-886
hsa-mir-1244-2
ADRB2
ANXA6
ATOX1
ALDH7A1
CAMK2A
CAMLG
CD14
CDC25C
CDO1
CDX1
AP3S1
CSF1R
CSF2
CSNK1A1
CSNK1G3
CTNNA1
DMXL1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EGR1
ETF1
FAT2
FBN2
FGF1
GDF9
GFRA3
GLRA1
GM2A
GPX3
GRIA1
NR3C1
HARS
HINT1
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL13
IRF1
LECT2
LMNB1
LOX
SMAD5
MFAP3
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
PURA
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC22A4
SLC22A5
SNX2
SPARC
SPINK1
SPOCK1
TAF7
TCF7
TCOF1
TGFBI
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
P4HA2
ATG12
CNOT8
HAND1
MED7
MYOT
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
SEC24A
FAXDC2
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
KIF3A
SYNPO
ABLIM3
HMGXB3
ARHGAP26
FSTL4
SEPT8
ACSL6
JADE2
LARP1
HARS2
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
IL17B
SLC27A6
SNX24
MRPL22
PCDHB1
TMED7
ISOC1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
LARS
CXXC5
RAPGEF6
KDM3B
PHAX
RBM27
PCDHB18P
PCDHB17P
ZCCHC10
WDR55
ANKHD1
THG1L
TMCO6
TRIM36
GALNT10
RBM22
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
SIL1
ARAP3
GRAMD3
PCYOX1L
SH3TC2
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
CYSTM1
MEGF10
SPINK7
HAVCR2
SMIM3
FCHSD1
LYRM7
CDKN2AIPNL
TIMD4
ZNF300
MYOZ3
PRDM6
FTMT
FNIP1
SLC35A4
MARCH3
LEAP2
SCGB3A2
PPARGC1B
PRRC1
ZNF474
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
SOWAHA
SHROOM1
C5orf24
DCANP1
MGC32805
SLC36A2
SPINK13
CEP120
SLC25A48
SRFBP1
JAKMIP2-AS1
ZMAT2
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
ADAMTS19
SPATA24
DNAJC18
STK32A
LVRN
SLC36A1
LOC255187
DTWD2
RELL2
SLC36A3
KIF4B
CHSY3
TMEM173
FAM170A
C5orf66-AS2
LOC340074
ARSI
IRGM
CATSPER3
NIPAL4
TICAM2
DND1
SAP30L-AS1
TEX43
LOC389332
PROB1
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
SPINK14
FNDC9
C5orf56
IGIP
MIR378A
TIFAB
LOC553103
CTXN3
ECSCR
GRXCR2
SPINK9
ARL14EPL
LOC644762
LINC01184
CCNI2
MIR584
SNHG4
CARMN
LINC00992
CCDC192
MEIKIN
LOC729080
VTRNA2-1
MIR874
KIAA1024L
LOC100130172
C5orf52
MIR1289-2
MIR1294
MIR1303
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
MIR3141
MIR3655
MIR3936
MIR3661
LINC01024
LOC100505658
HNCAT21
LOC100505841
MIR4633
MIR4461
MIR4454
MIR378H
MIR4460
SPRY4-IT1
LOC100652758
MIR5197
MIR5692C1
MIR5706
P4HA2-AS1
ARHGAP26-AS1
PPP2R2B-IT1
ARHGAP26-IT1
C5orf66
LOC101926905
LOC101926941
LOC101926975
LOC101927059
CTB-113P19.1
LOC101927100
CTB-12O2.1
LINC01470
LOC101927190
SEMA6A-AS1
HRAT56
LOC101927357
LOC101927379
LOC101927421
LOC101927460
LOC101927488
LOC101927697
TH2LCRR
LOC101927934
C5orf66-AS1
LOC101929696
LOC101929719
MIR6499
MIR6830
MIR6831
LOC102467217
LOC102467223
LOC102467224
LOC102467225
LOC102467226
LOC102546228
LOC102546229
LOC102546294
LOC102546298
LOC102723557
LOC102724404
ADAMTS19-AS1
LINC01170
LOC105379143
LOC105379176
LOC105379183
LOC105379192
LOC105379194
WSPAR
GRPEL2-AS1
TRPC7-AS2

Genes in Wide Peak

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

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

Genes
BRCA1
COL1A1
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
RARA
TAF15
SUZ12
ACACA
ASIC2
ACLY
AP2B1
AOC2
ARL4D
ATP5G1
ATP6V0A1
BLMH
FMNL1
CACNB1
CDC6
CDC27
CHAD
CCR7
CNP
COX11
CPD
CRHR1
CRYBA1
CSF3
DHX8
DLX3
DLX4
DUSP3
EVI2A
EVI2B
EZH1
GAST
FZD2
G6PC
KAT2A
GFAP
GIP
GNGT2
CCR10
GRB7
GRN
HCRT
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
HSD17B1
IFI35
IGFBP4
ITGA2B
ITGA3
ITGB3
JUP
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LHX1
LIG3
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NSF
OMG
PDK2
PEX12
PHB
PNMT
MED1
PPY
PSMB3
PYY
PSMD3
PSMD11
RAB5C
RAD51D
RNU2-1
RPL19
RPL27
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SGCA
SH3GL1P1
SH3GL1P2
SLC4A1
SLC6A4
SMARCE1
SP2
STAT3
STAT5A
STAT5B
TADA2A
HNF1B
MLX
THRA
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
PCGF2
ZNF207
RND2
PIP4K2B
SPOP
CNTNAP1
TCAP
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
ABCC3
CDK5R1
CACNA1G
HAP1
MAP3K14
SPAG9
TIAF1
ZNHIT3
EFTUD2
RPL23
NPEPPS
GOSR1
CCL4L2
GOSR2
NR1D1
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
TOM1L1
GJC1
TOB1
PSME3
EIF1
NBR2
SLC35B1
CALCOCO2
RAMP2
HOXB13
VAT1
P3H4
HEXIM1
IGF2BP1
CCT6B
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
KAT7
NXPH3
SNF8
SYNRG
CASC3
IKZF3
ZNF652
GPATCH8
KCNH4
MMD
FAM215A
KRT23
TMEM98
TBC1D29
AATF
TUBG2
NKIRAS2
COA3
GIT1
PSMC3IP
SNX11
TBX21
SOCS7
SOST
UTP18
RAPGEFL1
ABI3
COPZ2
MRPL27
PIPOX
ARL17A
CRLF3
SLC25A39
LUC7L3
HIGD1B
CDK12
KRT20
NLE1
FNDC8
MBTD1
CWC25
LINC00483
EPN3
LRRC37A4P
SLFN12
PNPO
KLHL11
TMEM100
RHOT1
RSAD1
COPRS
LRRC59
ADAP2
UTP6
GSDMB
CA10
ATXN7L3
PLXDC1
LYZL6
NUFIP2
TAOK1
ARHGAP23
PCTP
FKBP10
XYLT2
C17orf75
SPATA20
UBE2Z
WNK4
C17orf53
TMUB2
DHX58
MMP28
DHRS11
PRR15L
TEFM
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
FAM117A
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
TTC25
KRTAP4-12
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
RNF135
MIEN1
MRPL45
VPS25
TMEM101
PRAC1
RAB11FIP4
GHDC
KRTAP4-4
KIF2B
PPP1R9B
CORO6
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
SSH2
TP53I13
LRRC46
SCRN2
AOC4P
ANKRD40
ZNF830
SLFN11
RASL10B
G6PC3
ASB16
PGAP3
HSPB9
ORMDL3
PLCD3
TMEM106A
LRRC37B
OSBPL7
NT5C3B
ABHD15
RFFL
ZPBP2
SPATA32
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
FLJ40194
B4GALNT2
SPACA3
SEZ6
ANKRD13B
EFCAB13
MRPL10
GJD3
KRT222
KRT40
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
CRHR1-IT1
LINC00974
WIPF2
KRT25
TMEM99
ANKFN1
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
SPPL2C
KRT28
KRT24
ARHGAP27
ZNF385C
SAMD14
RDM1
GAS2L2
STH
STXBP4
CACNA1G-AS1
TAC4
HEATR9
KANSL1
C17orf105
FAM171A2
MEIOC
TTLL6
LOC284080
PIGW
C17orf78
YWHAEP7
CISD3
GSDMA
KRT42P
PTRF
KLHL10
ASB16-AS1
MSL1
KRT27
SLFN14
LRRC37A11P
STAC2
CCL15-CCL14
KRT26
PRAC2
HILS1
EFCAB5
TMIGD1
CCL4L1
C17orf98
LINC00671
CCDC103
RPRML
ARL5C
KRT39
MYO18A
C17orf102
TOB1-AS1
HOXB-AS3
MIR10A
MIR152
MIR193A
MIR196A1
TBC1D3B
TBC1D3C
CCL3L3
SUZ12P1
LOC440434
GPR179
LOC440446
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
SNORA21
LOC644172
KANSL1-AS1
KRTAP4-11
MRPL45P2
NME1-NME2
SNORD7
MIR632
KRTAP4-8
KRTAP1-4
KRTAP2-2
KRTAP9-1
NSFP1
FLJ45513
TBC1D3
TBC1D3H
KRTAP2-3
MIR365B
MAPT-AS1
MAPT-IT1
LINC00910
LOC100131347
KRTAP4-9
KRTAP4-7
MAP3K14-AS1
C17orf96
RAMP2-AS1
LOC100288866
MIR1203
MIR2117
MIR4315-2
MIR2909
MIR3185
MIR3184
MIR4315-1
LINC00672
LRRC3C
KRTAP9-7
KRTAP16-1
LOC100505782
ARL17B
SP2-AS1
C17orf112
AA06
SLFN12L
KRTAP9-6
RAD51L3-RFFL
KRTAP29-1
LRRC37A8P
MIR4523
MIR4728
MIR4726
MIR4734
MIR4724
MIR4733
MIR4727
MIR4725
MIR548AT
MIR5010
MIR5089
LINC00854
HOXB-AS1
PTGES3L
PTGES3L-AARSD1
TBC1D3G
TBC1D3K
TBC1D3L
LOC101060389
SNORD124
RUNDC3A-AS1
LINC01180
LOC101927166
LOC101927207
LOC101927230
LOC101927239
LOC101927274
RARA-AS1
LOC101929767
MIR378J
MIR6129
MIR6165
MIR6779
MIR6781
MIR6782
MIR6784
MIR6867
MIR6780A
MIR6510
MIR6783
MIR6884
MIR8059
MIR6866
LOC102723471
TBC1D3E
THCAT158
LOC102724532
LOC102724596
TBC1D3I
TMEM92-AS1
CRHR1-IT1-CRHR1
LOC105371730
LOC105371743
LOC105371766
LOC105371789
LOC105371795
THRA1/BTR
LOC105371814
LOC105371824
SNORA90
LOC107133515
LOC107546764
LOC107985033

Arm-level results

Table 3. Get Full Table Arm-level significance table - 41 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 | Del z-score | Del q-value
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1p | 3092 | 0.01 | 0.02 | -1.63 | 0.988 | 0.21 | 0.22 | 5.26 | 7.42e-07
1q | 2863 | 0.12 | 0.13 | 2.32 | 0.0351 | 0.05 | 0.06 | -0.29 | 0.986
2p | 1500 | 0.12 | 0.12 | 2.6 | 0.0239 | 0.00 | 0.00 | -2.06 | 0.986
2q | 2495 | 0.10 | 0.10 | 1.34 | 0.205 | 0.00 | 0.00 | -2.21 | 0.986
3p | 1531 | 0.00 | 0.00 | -1.52 | 0.988 | 0.53 | 0.53 | 17.9 | 0
3q | 1708 | 0.00 | 0.00 | -1.5 | 0.988 | 0.55 | 0.55 | 18.7 | 0
4p | 693 | 0.10 | 0.10 | 1.95 | 0.0662 | 0.01 | 0.01 | -1.47 | 0.986
4q | 1467 | 0.05 | 0.05 | -0.225 | 0.988 | 0.03 | 0.03 | -1.16 | 0.986
5p | 456 | 0.05 | 0.05 | -0.0151 | 0.902 | 0.01 | 0.01 | -1.5 | 0.986
5q | 2185 | 0.05 | 0.05 | -0.352 | 0.988 | 0.04 | 0.04 | -0.802 | 0.986
6p | 1664 | 0.49 | 0.49 | 16.4 | 0 | 0.00 | 0.00 | -1.59 | 0.986
6q | 1304 | 0.21 | 0.25 | 6.94 | 2.01e-11 | 0.15 | 0.19 | 4.63 | 1.51e-05
7p | 926 | 0.10 | 0.10 | 1.83 | 0.0816 | 0.00 | 0.00 | -2.02 | 0.986
7q | 1717 | 0.09 | 0.09 | 1.1 | 0.295 | 0.00 | 0.00 | -2.13 | 0.986
8p | 795 | 0.39 | 0.42 | 14.2 | 0 | 0.09 | 0.14 | 2.8 | 0.013
8q | 1249 | 0.68 | 0.68 | 24.3 | 0 | 0.01 | 0.04 | -0.386 | 0.986
9p | 621 | 0.05 | 0.06 | 0.135 | 0.832 | 0.10 | 0.11 | 2.09 | 0.0833
9q | 1610 | 0.04 | 0.04 | -0.62 | 0.988 | 0.09 | 0.09 | 1.23 | 0.406
10p | 767 | 0.00 | 0.00 | -2.1 | 0.988 | 0.01 | 0.01 | -1.61 | 0.986
10q | 1968 | 0.00 | 0.00 | -2.25 | 0.988 | 0.01 | 0.01 | -1.79 | 0.986
11p | 1162 | 0.11 | 0.12 | 2.32 | 0.0351 | 0.03 | 0.03 | -1 | 0.986
11q | 2133 | 0.11 | 0.11 | 1.95 | 0.0662 | 0.01 | 0.01 | -1.66 | 0.986
12p | 804 | 0.04 | 0.04 | -0.554 | 0.988 | 0.04 | 0.04 | -0.554 | 0.986
12q | 2055 | 0.04 | 0.04 | -0.825 | 0.988 | 0.03 | 0.03 | -1.28 | 0.986
13q | 1092 | 0.07 | 0.08 | 0.887 | 0.384 | 0.04 | 0.04 | -0.542 | 0.986
14q | 1829 | 0.04 | 0.04 | -0.806 | 0.988 | 0.01 | 0.01 | -1.72 | 0.986
15q | 2082 | 0.03 | 0.03 | -1.24 | 0.988 | 0.06 | 0.06 | 0.116 | 0.986
16p | 1378 | 0.04 | 0.04 | -0.575 | 0.988 | 0.09 | 0.09 | 1.3 | 0.396
16q | 1070 | 0.01 | 0.02 | -1.4 | 0.988 | 0.19 | 0.19 | 5.28 | 7.42e-07
17p | 937 | 0.11 | 0.12 | 2.44 | 0.033 | 0.04 | 0.04 | -0.436 | 0.986
17q | 2298 | 0.12 | 0.13 | 2.37 | 0.0351 | 0.01 | 0.01 | -1.66 | 0.986
18p | 212 | 0.01 | 0.01 | -1.49 | 0.988 | 0.03 | 0.03 | -0.991 | 0.986
18q | 644 | 0.01 | 0.01 | -1.56 | 0.988 | 0.03 | 0.03 | -1.07 | 0.986
19p | 1331 | 0.03 | 0.03 | -1.16 | 0.988 | 0.04 | 0.04 | -0.685 | 0.986
19q | 2402 | 0.03 | 0.03 | -1.33 | 0.988 | 0.04 | 0.04 | -0.889 | 0.986
20p | 583 | 0.10 | 0.10 | 1.98 | 0.0662 | 0.01 | 0.01 | -1.45 | 0.986
20q | 1092 | 0.11 | 0.11 | 2.26 | 0.0374 | 0.00 | 0.00 | -2.03 | 0.986
21q | 750 | 0.17 | 0.18 | 5 | 2.32e-06 | 0.03 | 0.03 | -0.817 | 0.986
22q | 1258 | 0.07 | 0.07 | 0.743 | 0.447 | 0.00 | 0.00 | -2.09 | 0.986
Xp | 945 | 0.12 | 0.14 | 3.34 | 0.00284 | 0.14 | 0.16 | 3.82 | 0.000394
Xq | 1533 | 0.11 | 0.13 | 2.65 | 0.0238 | 0.15 | 0.17 | 4.03 | 0.000191

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 = /cromwell_root/fc-2289d790-de74-4808-9b0a-cefafc34d859/8c831002-810c-4524-bfdd-ace10bdcaed8/aggregate_data_workflow/ed996cd3-9cd8-4590-9a90-cbc8a12b1df7/call-aggregate_data/TCGA-UVM-TP.CNV__snp6.seg.txt

- Markers File = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/snp6.na35.remap.hg38.subset.noFreqCNV_As_Of_GDC_DR_12_v20180723.txt

- Reference Genome = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/gistic2.refgene.hg38.UCSC.add_miR.160920.mat

- CNV Files = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg38_GDC_SNP6_CNV_list.161107.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 80 Input Tumor Samples.

Tumor Sample Names
TCGA-RZ-AB0B-01A-11D-A39V-01
TCGA-V3-A9ZX-01A-11D-A39V-01
TCGA-V3-A9ZY-01A-11D-A39V-01
TCGA-V4-A9E5-01A-11D-A39V-01
TCGA-V4-A9E7-01A-11D-A39V-01
TCGA-V4-A9E8-01A-11D-A39V-01
TCGA-V4-A9E9-01A-11D-A39V-01
TCGA-V4-A9EA-01A-11D-A39V-01
TCGA-V4-A9EC-01A-11D-A39V-01
TCGA-V4-A9ED-01A-11D-A39V-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.

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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