Skin Cutaneous Melanoma: Copy number analysis (GISTIC2)
(BRAF_Hotspot_Mutants cohort)
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 99 tumor samples used in this analysis: 19 significant arm-level results, 14 significant focal amplifications, and 22 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 - 14 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
--- | --- | --- | --- | ---
3p13 | 2.5245e-08 | 2.5245e-08 | chr3:69742187-70087344 | 1
7q34 | 6.9714e-06 | 1.3363e-05 | chr7:140360645-140746356 | 5
1q43 | 0.0074517 | 0.0074517 | chr1:233951521-249250621 | 132
12q14.3 | 0.02034 | 0.02034 | chr12:67369366-69374775 | 13
19p13.2 | 0.032586 | 0.032586 | chr19:7296453-7398264 | 0 [INSR]
15q26.2 | 0.037896 | 0.037896 | chr15:96964574-97231548 | 0 [NR2F2]
5p15.33 | 0.042211 | 0.042211 | chr5:1-1287702 | 23
2q36.2 | 0.063941 | 0.063941 | chr2:225481923-226025854 | 2
17q24.3 | 0.095607 | 0.095607 | chr17:45634386-81195210 | 515
8q24.21 | 0.041071 | 0.096414 | chr8:96826502-146364022 | 301
6p25.3 | 0.097778 | 0.097778 | chr6:1-43038705 | 585
22q13.32 | 0.10945 | 0.10945 | chr22:46335313-51304566 | 70
7q21.11 | 0.03645 | 0.21774 | chr7:57921705-106117961 | 378
8q21.13 | 0.23047 | 0.23407 | chr8:78718362-84367165 | 20

Genes in Wide Peak

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

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

Genes
MITF

Genes in Wide Peak

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

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

Genes
BRAF
NDUFB2
MRPS33
ADCK2
LOC100134713

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q43.

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
ACTN2
ADSS
CHML
LYST
CHRM3
GNG4
HNRNPU
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
ZNF124
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZNF238
SDCCAG8
RBM34
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
PPPDE1
SCCPDH
ARID4B
KIF26B
HEATR1
ZNF692
ERO1LB
FMN2
ZNF695
ZP4
TFB2M
GREM2
SMYD3
ZNF669
ZNF672
SH3BP5L
OR2G3
OR2G2
OR2C3
EFCAB2
ZNF496
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
EDARADD
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR2W5
OR13G1
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LGALS8-AS1
MIR1537
LINC00184
MIR3123
MIR3124
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4677
MIR4671

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.3.

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

Genes
MDM2
CPM
IFNG
RAP1B
DYRK2
IL22
SLC35E3
IL26
CAND1
MDM1
NUP107
SNORA70G
LOC100507250

Genes in Wide Peak

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

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

Genes
SDHA
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4456
MIR4635

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q36.2.

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

Genes
DOCK10
MIR4439

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.3.

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

Genes
CD79B
CLTC
COL1A1
DDX5
HLF
PRKAR1A
ASPSCR1
BRIP1
MSI2
CANT1
hsa-mir-3186
hsa-mir-1250
hsa-mir-4316
hsa-mir-636
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
hsa-mir-4315-2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
hsa-mir-3185
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
ATP5G1
CA4
CACNG1
CD7
CDK3
CHAD
COX11
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
DLX3
DLX4
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
GIP
GNGT2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
HOXB1
HOXB2
HOXB3
HOXB4
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
ICAM2
ICT1
FOXK2
ITGA3
ITGB4
KCNJ2
KCNJ16
KPNB1
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NFE2L1
NGFR
NME1
NME2
NPTX1
P4HB
PDE6G
PDK2
PECAM1
PHB
SEPT4
PRKCA
MAP2K6
PRPSAP1
PSMC5
PSMD12
PYCR1
PCYT2
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF1
SRSF2
SGCA
SGSH
SMARCD2
SUMO2
SOX9
SP2
SRP68
SSTR2
SUPT4H1
TBCD
TBX2
TIMP2
TK1
TRIM25
VEZF1
COIL
AKAP1
EPX
AXIN2
SPOP
PPM1D
DGKE
CBX4
SKAP1
DNAH17
ABCC3
RGS9
GALR2
SPHK1
CACNA1G
SOCS3
SPAG9
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
NOG
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
NPEPPS
AATK
TBKBP1
KIAA0195
EIF4A3
MRC2
HELZ
MED13
TOM1L1
TOB1
ALYREF
SLC35B1
DCAF7
CALCOCO2
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
HOXB13
APPBP2
ST6GALNAC2
IGF2BP1
GNA13
SEPT9
CD300C
CBX1
RAB40B
TLK2
KAT7
POLG2
NXPH3
SNF8
CD300A
TMC6
DDX42
ZNF652
PPM1E
ARSG
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
MMD
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
SNX11
TBX21
NT5C
CDR2L
MRPS7
UTP18
RNFT1
HN1
TUBD1
DCXR
TACO1
ABI3
COPZ2
MRPL27
AMZ2
ANAPC11
SIRT7
MRPS23
PTRH2
LUC7L3
SDK2
FAM20A
MBTD1
BCAS3
TMEM104
RNF43
MKS1
LINC00483
C17orf80
CCDC40
EPN3
WIPI1
PNPO
SMG8
TMEM100
RSAD1
LRRC59
MSX2P1
NPLOC4
PRR11
ST6GALNAC1
TEX2
GPRC5C
TEX14
WDR45L
CA10
CCDC47
CBX8
MIF4GD
INTS2
CASKIN2
RPTOR
BAHCC1
USP36
RNF213
TNRC6C
PCTP
SCPEP1
SLC25A19
UBE2O
HEATR6
DUS1L
FN3K
XYLT2
DNAI2
SMURF2
ENGASE
SPATA20
MRPL38
UBE2Z
CARD14
MFSD11
PRR15L
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
C17orf101
ZNF750
NUP85
MYO15B
ACSF2
C17orf70
CDK5RAP3
SP6
LIMD2
KCNH6
FAM117A
VMP1
TSPAN10
MYCBPAP
QRICH2
PRAC
KIF2B
USP32
PPP1R9B
CBX2
FAM104A
MGC16275
FBF1
UNK
LRRC46
SCRN2
CEP95
TRIM47
ANKRD40
STRADA
C17orf72
MAFG-AS1
OTOP2
TTYH2
CYGB
RNF157
OSBPL7
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
WFIKKN2
FLJ40194
B4GALNT2
MRPL10
TBC1D16
AFMID
DYNLL2
MGAT5B
C17orf56
B3GNTL1
RBFOX3
CD300LF
C17orf77
TCAM1P
EFCAB3
LOC146880
EME1
NOTUM
TMC8
ANKFN1
MARCH10
TMEM92
PHOSPHO1
CEP112
SAMD14
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MTVR2
STXBP4
LOC253962
TAC4
MYADML2
NPB
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
TTLL6
LOC284080
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
LINC00482
TMEM105
METRNL
RAB37
METTL2A
C17orf67
ENPP7
C17orf90
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
HOXB13-AS1
HILS1
LRRC37A3
RNF126P1
YPEL2
C17orf82
BTBD17
AATK-AS1
FLJ43681
LOC400604
KCNJ2-AS1
LINC00511
LOC400620
FLJ45079
TEX19
CUEDC1
LOC404266
MIR10A
MIR142
MIR152
MIR196A1
MIR21
MIR301A
MXRA7
TBC1D3P2
PLEKHM1P
LOC440461
FLJ90757
MIR338
CPSF4L
C17orf109
LOC645638
TBC1D3P1-DHX40P1
LOC653653
NME1-NME2
LINC00338
SCARNA20
SCARNA16
SNORA76
SNORD1A
SNORD1B
SNORD1C
SNORD104
MIR634
MIR635
MIR636
MIR657
FLJ45513
LOC729683
PRCD
MIR454
SNORA38B
C17orf110
LOC100131096
CD300LD
TEN1
C17orf99
LOC100287042
LOC100294362
MIR1203
MIR1250
MIR4316
MIR3065
MIR548W
MIR3186
MIR4315-2
MIR3185
MIR4315-1
LOC100499466
LOC100499467
MIR3614
MIR3678
MIR3615
LOC100506650
LOC100506779
LOC100507218
LOC100507246
LOC100507351
LOC100507410
TEN1-CDK3
MIR4739
MIR4729
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524A
MIR4730
MIR3064
MIR5047
LOC100653515

Genes in Wide Peak

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

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

Genes
COX6C
EXT1
MYC
RECQL4
hsa-mir-1234
hsa-mir-939
hsa-mir-661
hsa-mir-937
hsa-mir-1302-7
hsa-mir-151
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
ADCY8
ANGPT1
ANXA13
ATP6V1C1
BAI1
CYC1
CYP11B1
CYP11B2
DPYS
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HAS2
HSF1
EIF3E
KCNQ3
KCNS2
LY6E
LY6H
MATN2
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
ENPP2
PLEC
POLR2K
POU5F1B
PTK2
PVT1
RAD21
RPL8
RPL30
SDC2
ST3GAL1
SLA
SNTB1
SPAG1
SQLE
STK3
TAF2
TG
KLF10
TRHR
TRPS1
TSTA3
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
LY6D
JRK
EIF3H
DGAT1
GPAA1
WISP1
FOXH1
EBAG9
LRRC14
TTC35
RIMS2
MTSS1
PTDSS1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
PGCP
COLEC10
KHDRBS3
POP1
PTP4A3
RNF139
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
ARC
BOP1
ZFPM2
SCRIB
LRRC6
DCAF13
RNF19A
RGS22
FBXL6
SNORA72
OPLAH
PABPC1
KCNV1
MTBP
EIF2C2
COMMD5
MRPL13
ATAD2
ASAP1-IT1
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
FAM135B
PHF20L1
ZNF706
VPS28
FAM203A
KCNK9
C8orf55
UBR5
FAM49B
AZIN1
CHRAC1
EXOSC4
LY6K
TRMT12
OXR1
WDYHV1
LAPTM4B
SLC39A4
SYBU
GSDMC
ENY2
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
C8orf51
DSCC1
DERL1
GPR172A
GSDMD
NIPAL2
BAALC
ZNF696
GRHL2
ARHGAP39
ZNF34
SLC25A32
TM7SF4
SHARPIN
EPPK1
SCRT1
TRAPPC9
TATDN1
NACAP1
NCALD
MAF1
UTP23
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
TSPYL5
MED30
ZNF251
KIFC2
MTDH
PKHD1L1
NAPRT1
WDR67
HPYR1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
CTHRC1
OSR2
TOP1MT
ZNF572
ABRA
LYPD2
TMEM71
TMEM65
LOC157381
C8orf56
ANKRD46
FAM84B
VPS13B
TMEM74
FAM91A1
SLC30A8
COL22A1
SNX31
ADCK5
TSNARE1
C8orf47
MAPK15
NSMCE2
ZNF707
BREA2
FAM83H
LOC286094
ZNF252
TMED10P1
C8orf77
C8orf31
ZFP41
FBXO43
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
C8ORFK29
RSPO2
SPATC1
FLJ43860
MAFA
GDF6
SAMD12
MIR30B
MIR30D
C8orf82
FER1L6-AS1
FLJ42969
C8orf85
LRRC24
SAMD12-AS1
ZFAT-AS1
HAS2-AS1
LINC00051
C8orf73
SCXB
RAD21-AS1
FER1L6
MIR599
MIR661
LOC727677
HEATR7A
LOC728724
OC90
LOC731779
MIR875
MIR937
MIR939
LOC100128338
SCXA
LOC100130231
CCDC166
LOC100131726
LOC100133669
LOC100288181
MIR1205
MIR1206
MIR1207
MIR1204
MIR1234
MIR2053
MIR1208
MIR3151
LOC100499183
LOC100500773
MIR3610
LOC100507117
ZHX1-C8ORF76
MIR4663
MIR4472-1
MIR4664
MIR4471
PCAT1
LINC00536

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p25.3.

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

Genes
CCND3
DAXX
FANCE
HMGA1
IRF4
PIM1
POU5F1
TRIM27
DEK
TFEB
HIST1H4I
hsa-mir-1275
hsa-mir-219-1
hsa-mir-1236
hsa-mir-877
hsa-mir-3143
hsa-mir-548a-1
ABCF1
AGER
AIF1
ATP6V1G2
BAK1
CFB
BMP6
BPHL
BTN1A1
BYSL
C2
C4A
C4B
DDR1
CDKN1A
CDSN
CLIC1
CLPS
COL11A2
ATF6B
MAPK14
CSNK2B
CYP21A2
CYP21A1P
DNAH8
DOM3Z
DSP
E2F3
EDN1
SERPINB1
F13A1
FKBP5
FOXF2
FOXC1
GABBR1
GCNT2
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPX5
GRM4
GTF2H4
GUCA1A
GUCA1B
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
HLA-A
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSPA1A
HSPA1B
HSPA1L
ID4
ITPR3
JARID2
KIFC1
LTA
LTB
MAK
MDFI
MEA1
MICB
MLN
MOCS1
MOG
MSH5
RPL10A
NEDD9
NEU1
NFKBIL1
NFYA
NQO2
NOTCH4
PBX2
PEX6
PGC
PHF1
SERPINB6
SERPINB9
PPARD
PPP1R10
PPP2R5D
MAPK13
PRL
PSMB8
PSMB9
RGL2
PRPH2
RING1
BRD2
RNF5
RPS10
RPS18
RREB1
RXRB
VPS52
ATXN1
SRSF3
SKIV2L
SLC17A1
SNRPC
SOX4
SRPK1
SSR1
TAF11
TAP1
TAP2
TAPBP
TBCC
TCF19
TCP11
PPP1R11
TEAD3
TFAP2A
TNF
TNXA
TNXB
TPMT
TUBB2A
TULP1
VARS
ZNF76
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204P
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
OR2H2
RDBP
LST1
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
CMAHP
DHX16
KCNK5
B3GALT4
RIPK1
SYNGAP1
STK19
IER3
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
GCM2
WDR46
ZBTB22
CD83
PPT2
CDYL
NCR2
LY86
MED20
EEF1E1
MDC1
FAM65B
ZSCAN12
CUL7
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
FLOT1
SLC17A2
HCG9
PRSS16
BTN3A3
BTN2A2
ECI2
PFDN6
HMGN4
TRIM38
CAP2
UBD
AGPAT1
SCGN
C6orf10
FARS2
CNPY3
SLC17A3
RPP40
FRS3
HCP5
EHMT2
APOBEC2
TRIM31
BTN3A2
BTN3A1
BTN2A1
NUDT3
NRM
STK38
FTSJD2
ANKS1A
UBR2
SIRT5
DAAM2
KIAA0240
DDAH2
MTCH1
SPDEF
USP49
OR2B6
FAM50B
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
SNORD52
SNORD48
BRPF3
GNMT
MRPS18B
C6orf15
MYLIP
ABT1
PRICKLE4
PACSIN1
ZNRD1
DEF6
C6orf48
SLC35B3
GMNN
MRPL2
TBC1D7
NRN1
NOL7
FAM8A1
DCDC2
ETV7
TMEM14C
TDP2
CUTA
PPIL1
TREM2
TREM1
HCG4
GFOD1
CCHCR1
BTN2A3P
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
MRPS10
LRRC16A
TBC1D22B
EXOC2
SAYSD1
TRERF1
ACOT13
APOM
BTNL2
TRIM39
WRNIP1
DUSP22
LYRM4
VARS2
MRS2
LRFN2
CPNE5
LSM2
C6orf47
LY6G5B
LY6G6D
ZFAND3
SLC22A23
MUTED
CCDC90A
GPSM3
FKBPL
KIF13A
ZNF323
C6orf106
LY6G6E
ZNF322
TREML2
RPP21
ATAT1
ZKSCAN3
ZSCAN16
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRR3
ZNRD1-AS1
PRRT1
EGFL8
HCG4B
TXNDC5
C6orf62
OR5V1
OR2B2
OR12D3
TMEM14B
RIOK1
KCNK16
DTNBP1
MNF1
PGBD1
ADTRP
HIST1H2AH
HIST1H2BK
RRP36
KCNK17
TRIM15
KLC4
POM121L2
FOXQ1
BTBD9
SCAND3
FOXP4
KLHDC3
SLC26A8
MAS1L
IP6K3
TAF8
HUS1B
TRIM40
DPCR1
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
CCDC167
PSORS1C1
PSORS1C2
PPP1R18
PTCRA
TRIM39-RPP21
TUBB
PIP5K1P1
TREML2P1
LOC221442
C6orf130
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
TOB2P1
FAM217A
HCG27
RNF144B
HIST1H2BA
GPX6
NCR3
LY6G6F
MDGA1
ZNF311
LOC285768
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
HCG22
LOC285847
PNPLA1
TREML4
RPL7L1
RNF5P1
MYLK4
IFITM4P
CLPSL1
TREML1
TREML3
ZNF391
ZFP57
TUBB2B
C6orf52
HCG26
KAAG1
NHLRC1
ZKSCAN4
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
SFTA2
CLPSL2
C6orf222
MUC21
DKFZP686I15217
FLJ23152
LINC00340
LOC401242
MCCD1
SAPCD1
LINC00336
FLJ41649
C6orf201
ERVFRD-1
MIR219-1
HCG23
HCG25
HCG18
C6orf226
OR2B3
OR2J3
OR14J1
OR10C1
ATP6V0CP3
GGNBP1
HCG11
LOC554223
C6orf132
PPP1R3G
SNORA38
SNORD32B
SNORD84
SNORD117
MIR548A1
HULC
LOC729177
TDRG1
TMEM170B
SCARNA27
MIR877
LOC100129636
LOC100130275
LOC100130357
PSORS1C3
LOC100131047
LOC100131289
LINC00240
TOMM6
LOC100270746
LOC100293534
LOC100294145
MIR1275
MIR1236
MIR3143
MIR3925
MIR3691
LOC100506207
LOC100506409
LOC100507173
LOC100507194
LOC100507362
MICA
LOC100507463
LOC100507547
LOC100507584
MUC22
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
RPS10-NUDT3
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4641
MIR4646
MIR4640
MIR4639
MIR4645
MIR4462

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q13.32.

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

Genes
hsa-mir-3201
hsa-let-7b
ACR
ARSA
CHKB
CPT1B
TYMP
PPARA
MAPK11
MAPK12
SBF1
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
FAM19A5
NCAPH2
GTSE1
MOV10L1
TTC38
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR3201
MIR3619
MIR4763
MIR4535

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.11.

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

Genes
CDK6
ELN
HIP1
AKAP9
SBDS
hsa-mir-548o
hsa-mir-4285
hsa-mir-106b
hsa-mir-591
hsa-mir-489
hsa-mir-1285-1
hsa-mir-590
hsa-mir-4284
hsa-mir-4283-2
ACHE
ASL
ASNS
AZGP1
CACNA2D1
CALCR
KRIT1
CD36
AP1S1
COL1A2
CLDN4
CLDN3
CUX1
CYP3A7
CYP3A4
CYP3A5
CYP51A1
DLX5
DLX6
DYNC1I1
EPHB4
EPO
ERV3-1
GNAI1
GNB2
GNG11
GNGT1
GRM3
GTF2I
GTF2IP1
GUSB
HGF
AGFG2
HSPB1
LIMK1
LRCH4
MCM7
MDH2
NPTX2
OCM2
ORC5
SERPINE1
PCOLCE
PDK4
PEX1
CDK14
ABCB1
ABCB4
PMS2P1
PMS2L2
PMS2P4
PMS2P5
PMS2P3
POLR2J
PON1
PON2
PON3
POR
RELN
PSMC2
PTPN12
RFC2
CCL24
SRI
SRPK2
STX1A
SYPL1
TAC1
TAF6
TFR2
TRIP6
VGF
ZAN
EIF4H
CLIP2
LAT2
YWHAG
ZNF3
ZKSCAN1
ZSCAN21
ZNF138
ZP3
MTERF
SHFM1
TFPI2
TRRAP
FZD1
FZD9
TPST1
FKBP6
BUD31
SGCE
PLOD3
BAZ1B
CLDN12
AP4M1
BCL7B
PMPCB
ATP5J2
GTF2IRD1
SEMA3E
MAGI2
POM121
DMTF1
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
BET1
CCL26
SEMA3A
ZNHIT1
SEMA3C
ARPC1A
SH2B2
STAG3
ZNF273
FGL2
CPSF4
DBF4
COPS6
TP53TG1
PDAP1
LMTK2
POMZP3
PEG10
ZKSCAN5
CLDN15
BRI3
TECPR1
PTCD1
AUTS2
FBXO24
TBL2
STEAP1
DNAJC2
CRCP
RABGEF1
PCLO
PILRB
PILRA
FIS1
MLXIPL
ZNF117
ACTL6B
ZNF107
SRRT
STYXL1
ASB4
ADAM22
PION
STAG3L1
ANKIB1
PUS7
CROT
ALKBH4
SAMD9
ZCWPW1
C7orf42
TYW1
C7orf43
PPP1R9A
CCDC132
NSUN5
MLL5
BAIAP2L1
SLC25A40
MEPCE
SLC12A9
ACN9
SMURF1
PHTF2
RHBDD2
CCDC146
GATAD1
RINT1
WBSCR17
MOSPD3
GIGYF1
RABL5
CYP3A43
CASD1
STAG3L4
ZNF655
PVRIG
C7orf23
STEAP4
GAL3ST4
PRKRIP1
C7orf63
ORAI2
UPK3B
OR2AE1
WBSCR16
TSC22D4
TRIM56
ABHD11
CALN1
ARMC10
TMEM120A
RBM48
ZNF394
GTF2IRD2
MYH16
DNAJC30
MGC16142
TMEM60
GTPBP10
TRIM4
MYL10
DTX2
WBSCR22
WBSCR28
TRIM50
EMID2
SRCRB4D
MUC17
RUNDC3B
VKORC1L1
KCTD7
WBSCR27
SBDSP1
VPS37D
NSUN5P1
ZNF92
ZNF679
BHLHA15
ABHD11-AS1
SAMD9L
C7orf62
ZNF804B
ZNF498
FAM200A
PPP1R35
GPC2
SRRM3
RSBN1L
KIAA1324L
LRWD1
FAM185A
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
MBLAC1
FAM133B
NSUN5P2
STEAP2
INTS4L1
LINC00174
DLX6-AS1
ZNF789
ZNF680
GNAT3
MOGAT3
GJC3
DPY19L2P2
GATS
TRIM73
NAT16
SLC26A5
LHFPL3
TRIM74
SPDYE8P
GATSL1
GTF2IRD2B
MGC72080
C7orf59
RPL13AP17
GTF2IRD2P1
LRRD1
FLJ42280
KPNA7
C7orf61
UFSP1
MIR106B
MIR25
MIR93
LOC441242
TYW1B
SPDYE7P
DTX2P1-UPK3BP1-PMS2P11
SPDYE3
SPDYE2
ZNF727
DPY19L2P4
STAG3L3
STAG3L2
SPDYE5
LOC493754
LOC541473
POLR2J3
MIR489
FDPSL2A
LOC641746
CCT6P3
CCT6P1
LOC643955
INTS4L2
LOC645591
AZGP1P1
LOC649395
NCF1
NCF1B
NCF1C
SNORA14A
SNORA22
MIR590
MIR591
LOC723809
MIR653
LOC728066
ZNF736
LOC729156
GATSL2
SPDYE6
ZNF735
LOC100093631
POM121C
RPL19P12
LOC100129845
EFCAB10
LOC100132832
LOC100133091
UPK3BL
LOC100216545
LOC100216546
LOC100287704
LOC100287834
LOC100289187
LOC100289561
SPDYE2L
MIR548M
SAP25
MIR4283-2
MIR4285
MIR4283-1
MIR4284
MIR3609
MIR3914-1
MIR3914-2
LOC100505854
MAGI2-AS3
LOC100506050
LOC100506136
ATP5J2-PTCD1
MIR4653
MIR4652
MIR4651
MIR4650-1
MIR4650-2
MIR4467
MIR4658
LOC100630923
CYP3A7-CYP3AP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q21.13.

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

Genes
FABP4
FABP5
IL7
IMPA1
PMP2
PKIA
TPD52
STMN2
HEY1
MRPS28
ZC2HC1A
PAG1
SNX16
ZBTB10
ZFAND1
CHMP4C
SLC10A5
ZNF704
FABP9
FABP12

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 - 22 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 5.3742e-88 | 5.3742e-88 | chr9:21959052-21997722 | 2
10q23.31 | 5.6847e-08 | 5.2903e-07 | chr10:89617158-90034038 | 2
11q22.3 | 6.833e-05 | 6.833e-05 | chr11:103906053-128463796 | 255
4q34.3 | 7.0015e-05 | 7.0015e-05 | chr4:178911874-183060693 | 1
15q21.1 | 0.0015584 | 0.0015584 | chr15:36216473-54921359 | 195
1p22.1 | 0.0016279 | 0.0025474 | chr1:76538397-114523464 | 259
2q37.3 | 0.0059136 | 0.0059136 | chr2:234677660-243199373 | 86
6q25.2 | 8.0176e-05 | 0.0060067 | chr6:101844516-171115067 | 380
1p36.31 | 0.00086889 | 0.0069719 | chr1:1-13739155 | 234
5q31.3 | 0.0063705 | 0.0093291 | chr5:133558221-158916359 | 295
6q27 | 2.9564e-05 | 0.016207 | chr6:127756786-171115067 | 256
14q31.1 | 0.039393 | 0.038428 | chr14:78263652-107349540 | 293
10q11.23 | 0.020088 | 0.047185 | chr10:38987170-66592074 | 139
16q23.3 | 0.052187 | 0.051275 | chr16:73418707-90354753 | 154
4p16.3 | 0.071319 | 0.073957 | chr4:1-6915319 | 96
12q24.32 | 0.079884 | 0.081818 | chr12:69750840-133851895 | 466
19p13.3 | 0.081818 | 0.081818 | chr19:1-3814391 | 139
3p26.1 | 0.084199 | 0.087198 | chr3:1-81811783 | 585
9q21.2 | 0.088185 | 0.087198 | chr9:38614979-88357924 | 118
17q12 | 0.13922 | 0.13987 | chr17:13971526-61507293 | 775
3q27.2 | 0.2092 | 0.20446 | chr3:109128554-198022430 | 604
5q11.2 | 0.082369 | 0.23008 | chr5:1-180915260 | 1050

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
VWA5A
MCAM
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
MPZL3
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
LOC100652768

Genes in Wide Peak

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

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

Genes
LINC00290

Genes in Wide Peak

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

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

Genes
BUB1B
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
B2M
CAPN3
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
MYO5A
PLCB2
MAPK6
RAD51
SLC12A1
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
SECISBP2L
LCMT2
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
CEP152
MAPKBP1
RTF1
MGA
DMXL2
VPS39
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PLDN
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
TRPM7
PPP1R14D
FLJ10038
HAUS2
FAM82A2
DNAJC17
MYO5C
FAM214A
PAK6
DTWD1
CASC5
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
SPRED1
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
FAM98B
PLA2G4D
GLDN
MRPL42P5
USP50
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
MIR626
MIR627
LOC728758
OIP5-AS1
MIR147B
LOC100129387
LOC100131089
ANKRD63
LOC100132724
JMJD7
PLA2G4B
MIR1266
MIR1282
LOC100306975
MIR4310
LOC100505648
SERF2-C15ORF63
MIR4510
MIR4716
MIR4713
MIR4712

Genes in Wide Peak

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

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

Genes
BCL10
RBM15
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP5F1
BRDT
CAPZA1
CD53
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
OVGP1
PRKACB
PKN2
PSMA5
PTGFR
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
TAF13
TGFBR3
VCAM1
WNT2B
EVI5
CDC7
BCAR3
LMO4
CDC14A
RTCD1
FUBP1
SLC16A4
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
PIGK
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
IFI44L
DNAJB4
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
PTPN22
AK5
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
TTLL7
RPAP2
DENND2D
RPF1
ST6GALNAC5
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
FAM40A
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
MGC27382
RP11-165H20.1
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
SPP2
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
MSL3P1
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
FLJ43879
MIR149
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.2.

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
ACAT2
AIM1
AMD1
ARG1
CCR6
COL10A1
CTGF
EPB41L2
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GJA1
GPR6
GPR31
GRIK2
GRM1
HDAC2
HIVEP2
HSF2
IFNGR1
IGF2R
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PLN
PREP
PKIB
PSMB1
PTPRK
REV3L
RPS6KA2
RPS12
SGK1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
NR2E1
TPD52L1
TSPYL1
UTRN
EZR
VIP
EPM2A
STX7
PEX3
DDO
RNASET2
STX11
SNX3
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
AKAP7
ATG5
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
ZBTB24
FIG4
UST
TRDN
CITED2
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
RAB32
KATNA1
BVES
SEC63
SCAF8
CDK19
TAB2
TSPYL4
SASH1
SYNE1
HEY2
HEBP2
BRD7P3
ASF1A
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
SESN1
DLL1
OSTM1
MRPL18
DSE
CLDN20
NOX3
HDDC2
TFB1M
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
SOBP
PHF10
QRSL1
VNN3
C6orf70
ECHDC1
AGPAT4
TULP4
HYMAI
PDSS2
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
SERINC1
HACE1
TMEM181
ZBTB2
BEND3
C6orf115
PBOV1
TRMT11
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
FAM184A
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RNF146
SF3B5
TAAR8
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
FNDC1
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
REPS1
PPIL4
SLC22A16
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
FAM54A
SFT2D1
TMEM200A
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
BVES-AS1
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
C6orf191
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
RSPH4A
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
LIN28B
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FAM26F
FLJ46906
LOC441177
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
MIR548B
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
BET3L
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100289495
NHEG1
MIR1913
LOC100422737
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
RPL22
TNFRSF14
PRDM16
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
RERE
CA6
TNFRSF8
CDK11B
CLCN6
CORT
DFFA
DFFB
DVL1
MEGF6
ENO1
MTOR
GABRD
GNB1
ZBTB48
TNFRSF9
MTHFR
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLOD1
EXOSC10
PRKCZ
SCNN1D
SKI
SLC2A5
SRM
TNFRSF1B
TP73
TNFRSF4
MMP23B
MMP23A
KCNAB2
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CEP104
KLHL21
SLC35E2
MFN2
ANGPTL7
UBE4B
MAD2L2
MASP2
UTS2
RER1
PARK7
ACOT7
CLSTN1
KIF1B
CAMTA1
TARDBP
ICMT
CHD5
NOC2L
FBXO2
FBXO6
OR4F3
ARHGEF16
SSU72
UBIAD1
WRAP73
SLC45A1
SDF4
ERRFI1
MXRA8
HES2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
VPS13D
ATAD3A
PANK4
DNAJC11
AJAP1
CTNNBIP1
AGTRAP
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
HES4
MIIP
NMNAT1
VWA1
PRAMEF1
PRAMEF2
NADK
MMEL1
OR4F5
NOL9
LINC00115
MORN1
GPR157
SPSB1
GLTPD1
TAS1R1
OR4F16
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
SLC25A33
LZIC
C1orf170
KIAA1751
KIAA2013
THAP3
C1orf158
FBXO44
LOC115110
RBP7
ACAP3
UBE2J2
AADACL3
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
SLC2A7
CALML6
TMEM201
C1orf86
ATAD3C
LOC254099
TTLL10
NPHP4
FAM41C
LOC284661
C1orf174
KLHL17
TMEM240
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
C1orf187
AGRN
APITD1
GPR153
FAM132A
HES5
LOC388588
RNF207
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PRAMEF4
PRAMEF13
RNF223
PRAMEF3
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC649330
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
PRAMEF14
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
NPPA-AS1
MIR4251
MIR4252
ENO1-AS1
APITD1-CORT
MIR4689
MIR4632
MIR4417

Genes in Wide Peak

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

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

Genes
CD74
EBF1
ITK
PDGFRB
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
ADRB2
ANXA6
ATOX1
CAMK2A
CAMLG
CD14
CDC25C
CDX1
CSF1R
CSNK1A1
CTNNA1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EGR1
ETF1
FAT2
FGF1
GFRA3
GLRA1
GM2A
GPX3
GRIA1
NR3C1
HARS
HSPA9
NDST1
HTR4
IK
IL9
IL12B
LECT2
SMAD5
MFAP3
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPP2R2B
PURA
RPS14
SGCD
SLC6A7
SPARC
SPINK1
SPOCK1
TAF7
TCOF1
TGFBI
UBE2B
UBE2D2
WNT8A
NME5
EIF4EBP3
PCDHGB4
CDC23
ADAM19
HDAC3
CNOT8
HAND1
MED7
MYOT
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
KIF20A
G3BP1
APBB3
TNIP1
SEC24A
C5orf4
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
SOX30
SYNPO
ABLIM3
HMGXB3
ARHGAP26
PHF15
LARP1
HARS2
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
IL17B
MRPL22
PCDHB1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
LARS
CXXC5
KDM3B
RBM27
PCDHB18
PCDHB17
WDR55
ANKHD1
THG1L
TMCO6
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
TRPC7
KCTD16
PCDHB16
HMHB1
SIL1
ARAP3
PCYOX1L
SH3TC2
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
C5orf32
SPINK7
HAVCR2
C5orf62
FCHSD1
CDKN2AIPNL
TIMD4
ZNF300
MYOZ3
SLC35A4
SCGB3A2
PPARGC1B
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
UBLCP1
C5orf24
C5orf20
SLC36A2
SPINK13
SLC25A48
LOC153469
ZMAT2
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
SPATA24
DNAJC18
STK32A
SLC36A1
RELL2
LOC285626
LOC285627
SLC36A3
KIF4B
TMEM173
LOC340073
LOC340074
ARSI
IRGM
CATSPER3
NIPAL4
DND1
FLJ38109
LOC389332
C5orf65
C5orf46
ARHGEF37
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
SPINK14
FNDC9
IGIP
TIFAB
ECSCR
GRXCR2
SPINK9
SNHG4
MIR143HG
LOC729080
VTRNA2-1
MIR874
C5orf52
MIR3141
MIR3655
MIR3661
LOC100505658
MIR4461

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MLLT4
MYB
TNFAIP3
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
ACAT2
ARG1
CCR6
CTGF
EPB41L2
EYA4
ESR1
FUCA2
GPR31
GRM1
HIVEP2
IFNGR1
IGF2R
KIF25
LAMA2
LPA
MAS1
MAP3K4
MAP3K5
NMBR
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PLAGL1
PLG
PSMB1
PTPRK
RPS6KA2
RPS12
SGK1
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
STX7
PEX3
RNASET2
STX11
SYNJ2
VNN2
VNN1
TAAR5
MAP7
LATS1
TAAR2
TAAR3
MED23
QKI
AKAP7
TBPL1
WTAP
AKAP12
KIAA0408
PHACTR2
BCLAF1
UST
CITED2
HBS1L
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
HEBP2
CCDC28A
MTHFD1L
MOXD1
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
PDE7B
DLL1
MRPL18
CLDN20
NOX3
TFB1M
AIG1
SNX9
VTA1
BRP44L
HECA
IL20RA
UNC93A
MTRF1L
AHI1
RMND1
PHF10
VNN3
C6orf70
AGPAT4
TULP4
HYMAI
GPR126
KIAA1244
NHSL1
PLEKHG1
ARID1B
TMEM181
ZBTB2
C6orf115
PBOV1
PERP
SMOC2
ALDH8A1
ULBP3
OR2A4
C6orf211
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
TAAR8
RSPH3
TTLL2
FBXO30
L3MBTL3
FAM120B
FNDC1
LRP11
LTV1
SERAC1
REPS1
PPIL4
LINC00473
ARHGAP18
SYTL3
FAM54A
SFT2D1
TMEM200A
C6orf72
IL22RA2
C6orf192
TAGAP
ADAT2
TAAR9
TAAR1
STXBP5
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
LOC154449
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
C6orf191
WDR27
SHPRH
LINC00326
LOC285740
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
ECT2L
NUP43
C6orf58
RAET1G
HMGA1P7
SUMO4
C6orf174
C6orf120
THEMIS
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
FLJ46906
LOC441177
SNORD101
SNORD100
SNORA33
CTAGE9
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LINC00271
LOC100132735
LOC100289495
NHEG1
MIR1913
MIR3145
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.1.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
GALC
GTF2A1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
MTA1
RPS6KA5
NRXN3
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
PTPN21
RCOR1
PACS2
PPP1R13B
FLRT2
KIF26A
C14orf109
PRO1768
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
ADCK1
UNC79
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
CEP128
TTC7B
C14orf49
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
CCDC85C
ITPK1-AS1
SERPINA9
LINC00226
LINC00221
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
MIR1247
MIR1185-1
MIR1185-2
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392
LOC100628307

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.23.

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

Genes
RET
NCOA4
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
hsa-mir-4294
hsa-mir-3156-1
ALOX5
ANXA8L2
ANK3
ANXA2P3
CDK1
CHAT
CTSL1P2
EGR2
ERCC6
GDF2
GDF10
HNRNPF
MBL2
MSMB
PPYR1
PRKG1
MAPK8
RBP3
CXCL12
SLC18A3
TFAM
UBE2D1
ZNF22
ZNF32
ZNF33B
CCDC6
ZNF239
PARG
GPRIN2
BMS1
RHOBTB1
HNRNPA3P1
C10orf10
ZWINT
ZNF365
DKK1
CSTF2T
PTPN20B
A1CF
NRBF2
FXYD4
CSGALNACT2
FAM21B
OGDHL
CISD1
ASAH2
WDFY4
ARHGAP22
PCDH15
OR13A1
BICC1
SYT15
RASSF4
ARID5B
PHYHIPL
LOC84856
ADO
LOC84989
ZFAND4
C10orf71
ZNF488
AGAP4
FRMPD2
FAM170B
C10orf128
ANTXRL
VSTM4
C10orf107
TMEM26
RTKN2
SLC16A9
FAM13C
MARCH8
C10orf25
TMEM72-AS1
ZNF485
RASGEF1A
REEP3
JMJD1C
IPMK
FAM21C
SGMS1
PGBD3
C10orf53
C10orf40
LOC283033
FLJ31813
LOC338579
FAM21A
ACTR3BP5
LOC399753
BMS1P5
AGAP6
ZNF32-AS3
FAM35B
C10orf136
FAM35B2
LOC441666
LRRC18
AGAP9
ZNF487P
LOC642826
TMEM72
LOC643650
FAM25C
DRGX
PTPN20A
ANXA8
AGAP7
ASAH2B
MIR605
BMS1P1
ANXA8L1
AGAP8
LOC728407
LOC728640
LOC728643
FRMPD2P1
ZNF37BP
FAM25B
FAM25G
LOC100133308
TIMM23
MIR1296
MIR4294
MIR3156-1
MTRNR2L5
MIR3924
LOC100506733
LOC100506835
LOC100506939
M1

Genes in Wide Peak

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

Table S26. 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
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
BANP
RFWD3
ZDHHC7
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
MLKL
ZNF778
ACSF3
LINC00304
LOC283922
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
CTRB2
CLEC18B
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
SYCE1L
LOC100287036
MIR1910
MIR3182
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
EVC
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
NOP14
FAM193A
KIAA0232
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
D4S234E
STX18
FGFRL1
CYTL1
PIGG
CNO
STK32B
LYAR
KIAA1530
ZFYVE28
TNIP2
HAUS3
ABCA11P
MFSD7
TMEM175
TMEM128
C4orf42
TMEM129
MRFAP1
LOC93622
MRFAP1L1
EVC2
OTOP1
ZNF595
JAKMIP1
FAM53A
ZBTB49
ZNF721
ZNF718
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
C4orf48
LOC402160
ZNF876P
ZNF732
SCARNA22
MIR943
LOC100129917
LOC100130872
LOC100133461
TMED11P
LOC100507266
MIR378D1
MIR4800
HTT-AS1

Genes in Wide Peak

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

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

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
CNOT2
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PTPRB
PTPRR
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
YEATS4
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CCT2
CAMKK2
ZNF268
FRS2
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
RAB21
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
KCNMB4
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
TRHDE
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
RAB3IP
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
TPH2
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
BEST3
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
LOC283392
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
LRRC10
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
MRS2P2
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3913-2
MIR3913-1
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

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

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

Genes
GNA11
STK11
TCF3
FSTL3
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
MATK
GADD45B
NFIC
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
SGTA
TBXA2R
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
APBA3
MED16
APC2
ABCA7
HMG20B
UQCR11
SBNO2
PIP5K1C
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
TJP3
SLC39A3
THEG
FZR1
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
NCLN
SPPL2B
WDR18
REXO1
ZNF77
C19orf29
CELF5
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
LMNB2
RAX2
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
MRPL54
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
C19orf26
CSNK1G2-AS1
C19orf77
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
C19orf29-AS1
FAM138F
LINGO3
FAM138A
C19orf71
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.1.

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

Genes
CTNNB1
FANCD2
FHIT
MITF
MLH1
MYD88
PPARG
RAF1
VHL
XPC
BAP1
SRGAP3
FOXP1
SETD2
PBRM1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
ATP2B2
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CAV3
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DAZL
DNASE1L3
DOCK3
DUSP7
CELSR3
FBLN2
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
GRM7
HRH1
HYAL1
IL5RA
IMPDH2
IRAK2
ITGA9
ITIH1
ITIH3
ITIH4
ITPR1
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
OGG1
OXTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RAB5A
RARB
SNORA62
ROBO1
ROBO2
RPL15
RPL29
RPL32
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
SLC6A1
SLC6A6
SLC6A11
SMARCC1
STAC
NEK4
SYN2
TCTA
TDGF1
TGM4
TGFBR2
THRB
TIMP4
TKT
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
UBA7
UBE2E1
UBE2E2
UBP1
USP4
UQCRC1
VIPR1
WNT5A
WNT7A
ZNF35
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
COLQ
ACOX2
EOMES
HYAL3
CAMK1
BHLHE40
CADPS
HYAL2
SUCLG2
HESX1
KAT2B
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SH3BP5
SLC4A7
VGLL4
EDEM1
VPRBP
TBC1D5
TATDN2
IP6K1
EPM2AIP1
PSMD6
TRANK1
IQSEC1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ARPC4
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
CXCR6
CSPG5
CHL1
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CAND2
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
LARS2
RYBP
CAPN7
MKRN2
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
HACL1
TTLL3
GNL3
CNTN6
LSM3
RBMS3
NKIRAS1
SPCS1
PRSS50
RBM15B
GMPPB
LINC00312
LMCD1
ARHGEF3
VILL
C3orf32
TRNT1
ABHD5
DYNC1LI1
C3orf18
CRBN
SS18L2
C3orf19
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
GHRL
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
ARL8B
SETD5
TMEM40
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
TMEM111
BRK1
ZNF167
LMOD3
RAD18
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
LRRN1
SELK
PROK2
RNF123
CIDEC
ZFYVE20
KIF9
AZI2
MTMR14
MRPS25
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CRELD1
CAMKV
TMEM43
LRRC2
FYCO1
CCDC51
ZNF385D
HDAC11
THOC7
WDR82
TSEN2
GRIP2
RTP3
C3orf20
ID2B
ATRIP
NICN1
MON1A
JAGN1
KBTBD8
GHRLOS2
IL17RC
ABHD14B
C3orf39
EAF1
DCLK3
UCN2
ZNF502
RFT1
OXNAD1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
C3orf24
LRRC3B
GALNTL2
GPR62
KCNH8
FAM3D
LYZL4
KBTBD5
TRIM71
CHCHD4
TMEM42
METTL6
TAMM41
IL17RE
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
SGOL1
PP2D1
EFHB
CPNE9
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
FGD5
CIDECP
CNTN4
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC285401
EIF4E3
CCDC36
LOC339862
C3orf35
GADL1
PRSS42
ZNF860
COL6A4P1
TPRXL
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VENTXP7
LOC401052
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
MIR425
SNORA6
SNORA7A
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR563
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
MIR885
EGOT
GHRLOS
C3orf74
LOC100128640
NRADDP
LOC100129480
ZNF717
LOC100132146
LOC100132526
BSN-AS2
PRSS46
LOC100287879
LOC100288428
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
MIR3938
MIR3714
FGD5-AS1
LOC100505696
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4791
MIR4790
MIR548AC
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.2.

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

Genes
GNAQ
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
ALDH1A1
ANXA1
APBA1
KLF9
FXN
GCNT1
HNRNPK
NTRK2
PCSK5
PGM5
PRKACG
RORB
TLE1
TLE4
ZFAND5
PIP5K1B
FAM189A2
TJP2
GDA
GNA14
SMC5
VPS13A
AGTPBP1
TMEM2
ZNF658
FAM75A7
OSTF1
PSAT1
UBQLN1
PCA3
FAM108B1
C9orf95
C9orf40
RFK
KIF27
SLC28A3
CNTNAP3
RMI1
TRPM3
GKAP1
CEP78
ANKRD20A1
C9orf64
FAM122A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
TRPM6
RASEF
FAM201A
PRUNE2
C9orf71
CBWD5
MAMDC2
FRMD3
LOC286297
FOXD4L3
FAM75D5
FOXD4L4
AQP7P1
PTAR1
KGFLP1
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
FAM74A1
FAM74A4
ZNF658B
MIR204
MIR7-1
C9orf103
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
FOXB2
CBWD3
LOC494558
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920
LOC100286938
MIR548H3
LOC100507244
LOC100507299

Genes in Wide Peak

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

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

Genes
BRCA1
CLTC
COL1A1
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
RARA
TAF15
SUZ12
BRIP1
MSI2
hsa-mir-633
hsa-mir-21
hsa-mir-301a
hsa-mir-142
hsa-mir-3185
hsa-mir-196a-1
hsa-mir-10a
hsa-mir-1203
hsa-mir-152
hsa-mir-4315-1
hsa-mir-2117
hsa-mir-2909
hsa-mir-632
hsa-mir-365-2
hsa-mir-3184
hsa-mir-144
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
ACACA
ACCN1
ACLY
ADORA2B
AP2B1
ALDH3A1
ALDH3A2
ALDOC
AOC2
ARL4D
ATP5G1
ATP6V0A1
BLMH
FMNL1
CA4
CACNB1
CDC6
CDC27
CHAD
CCR7
CNP
COX10
COX11
CPD
CRHR1
CRYBA1
CSF3
DHX8
DLX3
DLX4
DRG2
DUSP3
EVI2A
EVI2B
EZH1
FOXO3B
FLII
FLOT2
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
KCNJ12
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LGALS9
LHX1
LIG3
LLGL1
LPO
NBR1
MAPT
ADAM11
MEIS3P1
MEOX1
MFAP4
MPO
MPP2
MPP3
TRIM37
MYL4
MYO1D
NAGLU
NEUROD2
NFE2L1
NGFR
NME1
NME2
NMT1
NOS2
NSF
OMG
PDK2
PEX12
PHB
PMP22
PNMT
SEPT4
MED1
PPY
MAPK7
MAP2K3
PRPSAP2
PSMB3
PYY
PSMD3
PSMD11
RAB5C
RAD51C
RAD51D
RPL19
RPL23A
RPL27
RPS6KB1
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SRSF1
SGCA
SH3GL1P1
SH3GL1P2
SHMT1
SLC4A1
SLC6A4
SMARCE1
SP2
SREBF1
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
TADA2A
TBX2
HNF1B
MLX
THRA
TNFAIP1
TOP2A
TOP3A
DNAJC7
TUBG1
UBB
UBTF
VTN
WNT3
WNT9B
PCGF2
TRIM25
VEZF1
RNF112
ZNF207
RND2
COIL
AKAP1
EPX
PIP4K2B
SPOP
FOXN1
PPM1D
CNTNAP1
DGKE
COPS3
TCAP
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
ABCC3
TMEM11
KSR1
CDK5R1
CACNA1G
HAP1
MAP3K14
SPAG9
SLC13A2
UNC119
MTMR4
TIAF1
NOG
BZRAP1
ZNHIT3
EFTUD2
RPL23
PIGL
TBX4
NPEPPS
GOSR1
CCL4L1
GOSR2
NR1D1
NCOR1
TRAF4
KIAA0100
ULK2
CCDC144A
TBKBP1
PLEKHM1
MED24
LRRC37A
MRC2
HS3ST3B1
MED13
HDAC5
TOM1L1
GJC1
TOB1
PSME3
EIF1
NBR2
SLC35B1
CALCOCO2
RAMP2
PEMT
HOXB13
VAT1
APPBP2
FBXW10
LEPREL4
HEXIM1
SPAG5
TRIM16
IGF2BP1
CCT6B
RAI1
GRAP
C1QL1
RUNDC3A
STARD3
CBX1
TLK2
DDX52
DUSP14
KAT7
AKAP10
NXPH3
SNF8
SYNRG
CASC3
IKZF3
ZNF652
PPM1E
EPN2
SARM1
GPATCH8
MPRIP
USP22
KCNH4
TNFRSF13B
MMD
FAM215A
PPY2
PYY2
DHRS7B
KRT23
TMEM98
POLDIP2
TBC1D29
TANC2
WSB1
ERAL1
AATF
OR4D1
SNORD4B
SNORD4A
SNORD49A
SNORD42B
SNORD42A
B9D1
TUBG2
TMEM97
NKIRAS2
CCDC56
GIT1
PSMC3IP
SNX11
TBX21
SOCS7
SOST
FAM18B1
UTP18
RNFT1
MYO15A
TUBD1
RAPGEFL1
ABI3
COPZ2
MRPL27
PIPOX
ARL17A
CRLF3
TRPV2
SLC25A39
MRPS23
PTRH2
RASD1
NLK
LUC7L3
HIGD1B
CDK12
KRT20
NLE1
FNDC8
MBTD1
BCAS3
CWC25
ALKBH5
RNF43
TTC19
MKS1
LINC00483
EPN3
LRRC37A4
MED9
SLFN12
PNPO
KLHL11
SMG8
SLC47A1
TMEM100
RHOT1
RSAD1
C17orf79
LRRC59
MSX2P1
C17orf63
PRR11
ADAP2
UTP6
GSDMB
TEX14
CA10
NT5M
ATXN7L3
PLXDC1
LYZL6
ZNF286A
ZNF287
INTS2
NUFIP2
ZNF624
TAOK1
ARHGAP23
PHF12
PCTP
SCPEP1
FKBP10
HEATR6
XYLT2
C17orf75
TEKT3
SPATA20
UBE2Z
WNK4
C17orf53
C17orf39
TMUB2
DHX58
MMP28
DHRS11
PRR15L
DHX40
TEFM
ACBD4
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
FAM106A
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
FAM117A
VMP1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
LRRC48
TTC25
KRTAP4-12
RAB34
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
RNF135
MIEN1
MRPL45
VPS25
TMEM101
PRAC
RAB11FIP4
GHDC
KRTAP4-4
KIF2B
USP32
PPP1R9B
MGC12916
CORO6
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
SSH2
TP53I13
IFT20
LRRC46
SCRN2
AOC4
ANKRD40
ZNF830
SLFN11
RASL10B
ATPAF2
SPECC1
G6PC3
ASB16
PGAP3
PIGS
HSPB9
ORMDL3
CDRT7
PLCD3
SLC46A1
TMEM106A
LRRC37B
OSBPL7
NT5C3L
ABHD15
TLCD1
RFFL
HSF5
OR4D2
ZPBP2
C17orf64
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
WFIKKN2
FLJ40194
B4GALNT2
SPACA3
SGK494
SEZ6
ANKRD13B
C17orf57
MRPL10
GJD3
KRT222
KRT40
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
DYNLL2
SMCR5
SMCR8
SMCR9
TOM1L2
EFCAB3
SLC47A2
CDRT15
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
TMEM199
PROCA1
DHRS13
C17orf69
LOC147093
TRIM16L
LRRC37BP1
WIPF2
KRT25
TMEM99
ANKFN1
MARCH10
SLFN5
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
IMP5
KRT28
USP32P1
KRT24
FAM18B2
CENPV
FLCN
PLD6
ARHGAP27
ZNF385C
SAMD14
C17orf108
RDM1
USP32P2
GAS2L2
STH
MTVR2
STXBP4
LOC253962
TBC1D28
TAC4
CDRT15L2
C17orf103
C17orf66
CDRT4
CCDC144B
KIAA1267
C17orf105
FAM171A2
C17orf104
TTLL6
LOC284080
C17orf47
KRT18P55
NEK8
PIGW
C17orf78
LOC284100
CISD3
GSDMA
KRT42P
PTRF
FAM27L
FLJ36000
GDPD1
LGALS9B
KLHL10
METTL2A
CCDC144NL
C17orf65
C17orf67
LOC339240
C17orf51
MSL1
NACA2
KRT27
SLFN14
FLJ43826
STAC2
SKA2
CCL14-CCL15
CCDC144C
TBC1D26
KRT26
HOXB13-AS1
HILS1
CDRT1
EFCAB5
RNF126P1
FAM211A
TMIGD1
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
YPEL2
C17orf82
ARL5C
KRT39
MYO18A
KRT16P2
GRAPL
C17orf102
LOC400604
MGC57346
CUEDC1
LOC404266
MIR10A
MIR142
MIR144
MIR152
MIR193A
MIR196A1
MIR21
MIR301A
TBC1D3B
TBC1D3C
CCL3L3
TBC1D3P5
SUZ12P
LOC440434
GPR179
TBC1D3P2
LRRC37A2
FBXO47
MIR423
ARGFXP2
DPRXP4
MIR451A
SNORA21
LOC644172
LOC644246
CDRT15P2
FAM83G
KRT16P3
EVPLL
LOC645638
SEBOX
KRTAP4-11
MRPL45P2
TBC1D3P1-DHX40P1
LOC653653
TBC1D3G
LGALS9C
NME1-NME2
SCARNA20
SNORA59B
SNORA59A
SNORD7
SNORD49B
SNORD65
MIR33B
MIR632
KRTAP4-8
KRTAP2-2
KRTAP9-1
NSFP1
FLJ45513
ZNF286B
TBC1D3
TBC1D3H
LOC730755
MIR454
SNORD124
MIR365B
LOC100128977
FAM106CP
LOC100130148
LOC100130581
LOC100131347
KRTAP4-9
KRTAP4-7
LOC100133991
KCNJ18
C17orf96
LOC100190938
MIR1288
MIR1203
MIR1180
MIR2117
MIR548W
MIR4315-2
MIR2909
MIR3185
MIR3184
MIR4315-1
MTRNR2L1
MIR3614
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
SPAG5-AS1
LOC100506650
AA06
SLFN12L
LOC100506779
RAD51L3-RFFL
FAM18B2-CDRT4
MIR4523
MIR4731
MIR4728
MIR4726
MIR4734
MIR4729
MIR4737
MIR4736
MIR4724
MIR4733
MIR451B
MIR4522
MIR4732
MIR4723
MIR4727
MIR4725
RAB34

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q27.2.

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

Genes
BCL6
FOXL2
EIF4A2
ETV5
GATA2
LPP
MLF1
PIK3CA
RPN1
SOX2
TFRC
GMPS
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
AADAC
ACPP
ACTL6A
ADCY5
ADPRH
AGTR1
AHSG
APOD
ATP1B3
ATP6V1A
ATR
BCHE
BDH1
CASR
CD80
CD86
AP2M1
CLCN2
CP
CPA3
CPB1
CPN2
CRYGS
CSTA
DGKG
DLG1
DRD3
DVL3
ECT2
EHHADH
EIF4G1
EPHB1
EPHB3
MECOM
FGF12
GAP43
GHSR
GOLGB1
GP5
GP9
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRG
HES1
IL1RAP
IL12A
ITGB5
KNG1
KPNA1
KPNA4
LSAMP
TM4SF1
MBNL1
MCM2
MFI2
MME
CD200
MUC4
MYLK
NCK1
NDUFB4
NDUFB5
OPA1
CLDN11
P2RY1
PAK2
PCCB
PCYT1A
PFN2
SERPINI1
SERPINI2
PIK3CB
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
POLR2H
PPP1R2
PPP2R3A
PRKCI
MASP1
PSMD2
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
RPL35A
RYK
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC15A2
SLCO2A1
HLTF
SSR3
SST
TERC
TF
TFDP2
THPO
SEC62
TM4SF4
TRH
TRPC1
UPK1B
UMPS
CLRN1
ZIC1
CNBP
ZNF80
ZNF148
RAB7A
KCNAB1
FXR1
SOX14
BFSP2
RUVBL1
TP63
CHRD
B4GALT4
B3GALNT1
SNX4
TNFSF10
NR1I2
EIF2B5
MBD4
H1FX
USP13
KALRN
CLDN1
MAP3K13
SLC33A1
COPB2
ADIPOQ
CHST2
STXBP5L
RNF7
IQCB1
KIAA0226
ECE2
TSC22D2
P2RY14
SMC4
ABCC5
COX17
TNK2
ALG3
CD96
KCNMB2
STAG1
IGF2BP2
CLDN16
POLQ
ALDH1L1
PDIA5
TOPBP1
FSTL1
MRPL3
PDCD10
RNF13
MGLL
MRAS
COPG
SLITRK3
NLGN1
NCBP2
PLCH1
TMCC1
TNIK
MCF2L2
PLXND1
ATP11B
DNAJC13
U2SURP
VPS8
C3orf27
ACAP2
ANAPC13
ARMC8
C3orf17
WWTR1
PVRL3
TIPARP
UBXN7
ARHGEF26
ZBTB20
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
SERP1
GOLIM4
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
GPR171
SEC61A1
SCHIP1
PIK3R4
PODXL2
NMD3
COMMD2
A4GNT
DBR1
ZNF639
CLDN18
TIMMDC1
RSRC1
PLA1A
AMOTL2
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
P2RY13
IL20RB
GPR87
DCUN1D1
SEMA5B
XRN1
WDR5B
PARP14
GRAMD1C
ROPN1
KLHL24
SIDT1
SLC41A3
PIGX
SLC35A5
MSL2
TBCCD1
FAIM
SLC25A36
LEPREL1
TMEM39A
ABCF3
LSG1
ABHD10
PARL
CDV3
MFN1
YEATS2
IFT122
WDR52
EAF2
MYNN
EIF5A2
MUC13
SUCNR1
MCCC1
LXN
C3orf37
MRPS22
POGLUT1
CCNL1
PLSCR2
PLSCR4
HRASLS
MRPL47
ISY1
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
SLC7A14
SRPRB
SENP2
GNB4
BPESC1
EEFSEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZMAT3
ATG3
MFSD1
CCDC14
FNDC3B
P2RY12
TMEM108
ZXDC
ZBED2
ATP13A3
HSPBAP1
C3orf52
VEPH1
QTRTD1
TBL1XR1
ZBBX
LRRC31
CCDC48
NEK11
UBA5
MAP6D1
PHC3
C3orf36
ARL14
NAA50
PIGZ
CEP63
CEP70
ABTB1
TMEM22
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
ZIC4
ACAD11
IQCG
ATP13A4
FYTTD1
CHCHD6
HPS3
ARPM1
SLC12A8
MGC2889
LRCH3
DIRC2
CEP19
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
LOC90246
C3orf25
TMEM41A
BOC
SPSB4
ACPL2
TMEM44
EGFEM1P
CAMK2N2
TXNRD3
OSBPL11
LRRC58
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
CPNE4
CCDC58
DNAJC19
OTOL1
FAM131A
CD200R1
ZDHHC19
LRRC15
FAM43A
TPRA1
UROC1
FAM194A
NUDT16
COL6A6
GRK7
TMEM207
RTP1
RPL32P3
H1FOO
PISRT1
TTC14
DTX3L
PPM1L
WDR49
LRRC34
CCDC80
BTLA
MB21D2
XXYLT1
ROPN1B
C3orf22
C3orf55
C3orf79
CCDC50
PYDC2
SPICE1
NUDT16P1
LOC152217
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
RNF168
CHST13
KBTBD12
DHX36
HTR3C
DZIP1L
ALG1L
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
PTPLB
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
LOC253573
NAALADL2
ZDHHC23
NUP210P1
TCTEX1D2
C3orf43
SDHAP1
COL6A5
GK5
PLCXD2
GCET2
UTS2D
LSAMP-AS3
SLC9A9
DNAJB8-AS1
HTR3E
RABL3
IGSF10
C3orf33
SLC9A10
C3orf70
TPRG1
ILDR1
TRIM59
TRIM42
RAB43
CCDC39
KY
LOC339874
LOC339894
LOC339926
LPP-AS2
H1FX-AS1
LRRIQ4
SAMD7
AADACL2
GPR149
TMPRSS7
CD200R1L
PAQR9
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
CCDC37
NPHP3-AS1
ANKRD18DP
NMNAT3
LRRC33
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
FLJ25363
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
MIR198
ARGFX
SNORD2
SNORA4
ALG1L2
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
LOC653712
IQCJ
SCARNA7
SNORA7B
SNORA58
SNORA81
SNORD66
MIR551B
MIR567
MIR568
MIR569
MIR570
SDHAP2
FAM157A
FAM86HP
PRR23A
LOC730091
LOC100125556
MIR922
MIR944
LOC100128023
WWTR1-AS1
LOC100128164
LOC100129550
ZBTB20-AS1
LOC100131551
LOC100131635
SNAR-I
MIR1224
TIPARP-AS1
LOC100289361
MIR1248
MIR1280
MIR548I1
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100505687
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
LOC100507032
MFI2-AS1
LOC100507086
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
NPHP3-ACAD11
ISY1-RAB43
TM4SF19-TCTEX1D2
MIR4796
MIR4797
MIR4788
MIR4789
MIR4446

Genes in Wide Peak

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

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

Genes
APC
CD74
EBF1
IL6ST
ITK
LIFR
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
hsa-mir-887
hsa-mir-4278
hsa-mir-4277
ADCY2
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
C6
C7
C9
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDH6
CDH9
CDH10
CDH12
CDH18
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
CTNND2
DAB2
DAP
DBN1
DMXL1
DHFR
DIAPH1
DNAH5
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGF10
FGFR4
FOXD1
FOXI1
FLT4
FYB
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GDNF
GFRA3
GHR
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
GZMA
GZMK
HARS
HEXB
HINT1
HK3
HMGCR
HMGCS1
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL7R
IL9
IL12B
IL13
IRF1
ISL1
ITGA1
ITGA2
KCNMB1
KCNN2
KIF2A
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MFAP3
MGAT1
MOCS2
MSH3
MSX2
MTRR
MYO10
NAIP
NDUFA2
NDUFS4
NDUFS6
NEUROG1
NPR3
NPY6R
OXCT1
PAM
PCDH1
PCDHGC3
PCSK1
PDE4D
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
PRKAA1
MAPK9
PRLR
PROP1
PTGER4
RAD1
PURA
RAD17
RARS
RASA1
RASGRF2
RPL37
RPS14
RPS23
SDHA
SEPP1
SGCD
SKP1
SKP2
SLC1A3
SLC6A3
SLC6A7
SLC9A3
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRD5A1
SRP19
STK10
TAF7
TAF9
TARS
TBCA
TCF7
ZNF354A
TCOF1
TERT
NR2F1
TGFBI
THBS4
TRIO
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ZNF131
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
PPAP2A
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
HSPB3
ATP6V0E1
SEMA5A
ATG12
OSMR
PTTG1
PDLIM7
NREP
TRIP13
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
NUP155
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
PDCD6
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
MARCH6
APBB3
CCNO
TNIP1
GNB2L1
BASP1
NSA2
FST
SLU7
PAIP1
POLR3G
RGS14
SLC12A7
PLK2
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
MRPS30
BRD8
TCERG1
BTNL3
SUB1
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
PAPD7
SOX30
TPPP
ESM1
KIF3A
ADAMTS6
MGAT4B
B4GALT7
EXOC3
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
CCT5
SV2C
HMGXB3
PDZD2
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FBXL7
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
KIAA0947
PPWD1
HARS2
OTP
SKIV2L2
NNT
TTC33
ZNF346
AMACR
SSBP2
BHMT2
TNFAIP8
NIPBL
PP7080
PART1
GEMIN5
PCDHGA12
LRRTM2
FAM169A
RAI14
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
FBXO4
OR4F3
HAVCR1
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
DROSHA
PCDHB1
DMGDH
KCNIP1
ZNF354C
IRX4
TAS2R1
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
SLC45A2
DCTN4
IPO11
MZB1
PAIP2
CDKL3
RXFP3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
ZFR
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
PELO
RBM27
FAM134B
FAM105A
NEURL1B
DHX29
FLJ11235
DDX4
FAM193B
MTMR12
SGTB
ARL15
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
NSUN2
CCDC99
THG1L
WDR70
AGGF1
WDR41
BRIX1
C5orf22
TMCO6
TRIM36
GALNT10
NHP2
RBM22
CEP72
RIOK2
DEPDC1B
BDP1
RNF130
ERBB2IP
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
ANKH
CCL28
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
PRDM9
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
AHRR
ZNF608
KCTD16
SEMA6A
ARRDC3
ZSWIM6
PCDHB16
ANKRA2
HMHB1
C5orf54
GOLPH3
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1P1
ARAP3
C5orf28
RMND5B
FBXL17
YTHDC2
AGXT2
SLC30A5
CENPH
MRPL36
GPBP1
C5orf42
BRD9
GRAMD3
PCYOX1L
FASTKD3
IRX1
CCNJL
SH3TC2
PANK3
PARP8
SAP30L
ANKRD55
TXNDC15
MCTP1
PTCD2
ZDHHC11
LPCAT1
BTNL8
SPEF2
DOK3
ELOVL7
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
CLPTM1L
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
ADAMTS12
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
ROPN1L
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
MED10
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
CARD6
TRIM52
HAVCR2
AGXT2L2
C5orf62
NKD2
TSLP
FCHSD1
UNC5A
FAM105B
C5orf30
ZNF622
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
NDUFAF2
ZNF300
MYOZ3
UBTD2
LMBRD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SNX18
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
C1QTNF3
EPB41L4A-AS1
MARCH3
FCHO2
RAB3C
LYSMD3
C5orf55
LEAP2
SCGB3A2
ZNF354B
C5orf35
IL31RA
EMB
SLCO6A1
C5orf47
PPARGC1B
HEATR7B2
EGFLAM
PRRC1
NADKD1
UGT3A1
CAPSL
JMY
C5orf58
ZNF474
CCDC127
OR2Y1
UBE2QL1
C5orf49
FAM173B
CMBL
POU5F2
DNAJC21
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC38A9
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
LOC153469
PLEKHG4B
ZMAT2
MARVELD2
C5orf38
IRX2
BTNL9
ARSK
FAM81B
TTC23L
LOC153684
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
MIER3
CDC20B
UGT3A2
PAPD4
DCP2
NIM1
LIX1
ZNF366
FAM151B
S100Z
ADAMTS16
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
RANBP3L
LOC202181
CCDC125
C5orf27
GAPT
CMYA5
STK32A
AQPEP
SLC36A1
RICTOR
EIF4E1B
LOC255167
RASGEF1C
ANKRD31
SERINC5
LOC257358
LOC257396
LOC285577
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
C5orf51
SLC36A3
KIF4B
OR2V2
C5orf64
RNF180
SREK1IP1
ZNF454
C5orf60
LOC285692
LOC285696
RGMB
RFESD
CHSY3
SLC6A19
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
LOC340094
LOC340107
LOC340113
ANKRD34B
PFN3
ZNF879
PLCXD3
IRGM
FBLL1
IDAS
ACTBL2
FAM174A
MTX3
CATSPER3
SLC6A18
NIPAL4
HCN1
SLCO4C1
TICAM2
DND1
C5orf34
MAST4
C5orf25
RNF138P1
FLJ38109
LRRC14B
C5orf39
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
FLJ33360
LOC401177
RGS7BP
C5orf63
SPINK6
TAG
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
MARCH11
CRSP8P
FLJ42709
C5orf56
FLJ16171
LOC442132
MIR340
IGIP
GPX8
TIFAB
FLJ35946
LOC553103
MIR449A
CTXN3
SNORD72
SNORD95
SNORD96A
ECSCR
LOC642366
TMEM232
C5orf43
LOC643201
GRXCR2
SPINK9
LOC643401
ZFP62
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
CBY3
LOC646719
LOC647859
LOC648987
ANKRD33B
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR449B
MIR580
MIR581
MIR583
MIR585
SNHG4
MIR143HG
GTF2H2C
LOC728342
GUSBP1
SERF1B
LOC728554
SDHAP3
LOC728613
LOC728723
LOC729080
LOC729506
AACSP1
LOC729678
OR4F29
LOC729862
GTF2H2D
GUSBP9
SNORD123
VTRNA2-1
MIR874
LOC100129716
CCDC152
LRRC70
LOC100130744
LOC100131067
FAM196B
LOC100132062
LOC100132287
LOC100132356
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR4279
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MIR4277
MIR4278
MTRNR2L2
MIR3607
MIR3655
MIR3650
MIR3660
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505738
LOC100505806
LOC100505841
LOC100505894
LOC100506548
OCLN
LOC100506688
LOC100507387
C1QTNF3-AMACR
MIR4458
MIR4804
MIR4633
MIR4634
MIR4461
MIR4454
MIR4457
MIR4637
MIR3977
MIR4460
MIR4636
MIR4638
MIR4803
MIR4456
MIR4635
MIR378E
EGFLAM-AS4
LOC100859930

Arm-level results

Table 3. Get Full Table Arm-level significance table - 19 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.22 | -0.485 | 0.999 | 0.27 | 0.501 | 0.726
1q | 1955 | 0.38 | 2.67 | 0.0255 | 0.21 | -0.794 | 0.999
2p | 924 | 0.31 | 0.437 | 0.999 | 0.22 | -1.36 | 0.999
2q | 1556 | 0.33 | 1.21 | 0.505 | 0.22 | -0.853 | 0.999
3p | 1062 | 0.19 | -1.9 | 0.999 | 0.28 | -0.0752 | 0.973
3q | 1139 | 0.21 | -1.47 | 0.999 | 0.27 | -0.363 | 0.999
4p | 489 | 0.17 | -2.71 | 0.999 | 0.24 | -1.29 | 0.999
4q | 1049 | 0.16 | -2.37 | 0.999 | 0.29 | 0.0167 | 0.973
5p | 270 | 0.26 | -1.12 | 0.999 | 0.31 | -0.0879 | 0.973
5q | 1427 | 0.15 | -2.25 | 0.999 | 0.36 | 1.86 | 0.114
6p | 1173 | 0.34 | 1.12 | 0.525 | 0.42 | 2.7 | 0.023
6q | 839 | 0.18 | -1.72 | 0.999 | 0.59 | 6.25 | 1.66e-09
7p | 641 | 0.74 | 9.22 | 0 | 0.20 | -1.22 | 0.999
7q | 1277 | 0.76 | 10.3 | 0 | 0.18 | -1.17 | 0.999
8p | 580 | 0.41 | 1.88 | 0.151 | 0.36 | 1.04 | 0.429
8q | 859 | 0.55 | 5.52 | 1.73e-07 | 0.11 | -2.82 | 0.999
9p | 422 | 0.19 | -1.41 | 0.999 | 0.73 | 8.75 | 0
9q | 1113 | 0.17 | -1.66 | 0.999 | 0.58 | 6.31 | 1.38e-09
10p | 409 | 0.06 | -3.11 | 0.999 | 0.68 | 7.84 | 2.96e-14
10q | 1268 | 0.00 | -3.1 | 0.999 | 0.75 | 10.4 | 0
11p | 862 | 0.19 | -1.99 | 0.999 | 0.34 | 0.882 | 0.472
11q | 1515 | 0.17 | -1.8 | 0.999 | 0.39 | 2.5 | 0.0355
12p | 575 | 0.23 | -1.59 | 0.999 | 0.14 | -3.2 | 0.999
12q | 1447 | 0.14 | -2.79 | 0.999 | 0.14 | -2.79 | 0.999
13q | 654 | 0.31 | 0.0652 | 0.999 | 0.35 | 0.929 | 0.47
14q | 1341 | 0.14 | -2.47 | 0.999 | 0.38 | 2.18 | 0.0583
15q | 1355 | 0.32 | 0.917 | 0.653 | 0.15 | -2.26 | 0.999
16p | 872 | 0.20 | -1.83 | 0.999 | 0.18 | -2.2 | 0.999
16q | 702 | 0.21 | -1.64 | 0.999 | 0.29 | -0.218 | 0.999
17p | 683 | 0.22 | -1.51 | 0.999 | 0.36 | 1.12 | 0.401
17q | 1592 | 0.21 | -1.2 | 0.999 | 0.25 | -0.253 | 0.999
18p | 143 | 0.24 | -1.35 | 0.999 | 0.44 | 2.32 | 0.0462
18q | 446 | 0.18 | -2.25 | 0.999 | 0.38 | 1.39 | 0.272
19p | 995 | 0.25 | -0.744 | 0.999 | 0.29 | -0.0229 | 0.973
19q | 1709 | 0.27 | 0.241 | 0.999 | 0.28 | 0.43 | 0.741
20p | 355 | 0.52 | 4.17 | 0.000123 | 0.15 | -2.48 | 0.999
20q | 753 | 0.61 | 6.66 | 1.88e-10 | 0.10 | -2.81 | 0.999
21q | 509 | 0.20 | -2.09 | 0.999 | 0.23 | -1.56 | 0.999
22q | 921 | 0.39 | 1.96 | 0.144 | 0.17 | -2.17 | 0.999
Xq | 1312 | 0.12 | -2.71 | 0.999 | 0.38 | 2.31 | 0.0462

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/SKCM-BRAF_Hotspot_Mutants/3154364/GDAC_MergeDataFiles_3154646/SKCM-BRAF_Hotspot_Mutants.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 4. Get Full Table First 10 out of 99 Input Tumor Samples.

Tumor Sample Names
TCGA-D3-A1Q4-06A-11D-A194-01
TCGA-D3-A1Q5-06A-11D-A194-01
TCGA-D3-A1Q6-06A-11D-A194-01
TCGA-D3-A1Q7-06A-11D-A192-01
TCGA-D3-A1Q9-06A-11D-A192-01
TCGA-D3-A1QA-06A-11D-A194-01
TCGA-D3-A2J7-06A-11D-A194-01
TCGA-D3-A2J9-06A-11D-A194-01
TCGA-D3-A2JA-06A-11D-A194-01
TCGA-D3-A2JD-06A-11D-A192-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

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
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle