Colon Adenocarcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16a (cga svn revision 43808).

Summary

There were 413 tumor samples used in this analysis: 23 significant arm-level results, 24 significant focal amplifications, and 44 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 - 24 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
--- | --- | --- | --- | ---
20q12 | 1.3235e-38 | 5.1667e-22 | chr20:40208877-40360023 | 1
8q24.21 | 9.982e-20 | 4.4351e-19 | chr8:128389850-128754688 | 3
20q11.21 | 8.0355e-42 | 2.073e-18 | chr20:26196264-30582729 | 26
17q12 | 6.235e-15 | 3.1004e-14 | chr17:37837542-38021723 | 6
13q12.13 | 2.4167e-17 | 1.5321e-13 | chr13:27521847-27544633 | 0 [USP12]
8p11.23 | 2.1671e-11 | 1.9254e-09 | chr8:38139741-38237581 | 1
11p15.5 | 1.1017e-08 | 1.1017e-08 | chr11:2141587-2241214 | 8
12p13.33 | 1.8032e-08 | 1.8032e-08 | chr12:893819-4699385 | 34
13q22.1 | 4.5244e-09 | 1.0418e-06 | chr13:73616064-74055302 | 1
5q22.3 | 7.6859e-06 | 7.6859e-06 | chr5:114756122-114759166 | 0 [FEM1C]
8p11.21 | 1.2524e-09 | 3.0762e-05 | chr8:41614677-42365372 | 9
20p11.21 | 2.7494e-17 | 0.00034115 | chr20:25355954-25483163 | 3
6p21.1 | 0.0011395 | 0.0011395 | chr6:40092319-44407505 | 90
20q13.32 | 1.7472e-05 | 0.0017944 | chr20:51458068-59778131 | 64
19q13.11 | 0.0036395 | 0.0036395 | chr19:32351550-33019554 | 3
8q12.1 | 0.00015648 | 0.0066792 | chr8:42932479-70211670 | 103
19p13.2 | 0.012987 | 0.012987 | chr19:7300056-7398264 | 0 [INSR]
5p13.2 | 0.014546 | 0.014546 | chr5:27059148-50133343 | 91
16q12.1 | 0.042739 | 0.097549 | chr16:51098275-52648730 | 5
17q24.1 | 0.0028785 | 0.10022 | chr17:63179119-68650398 | 39
20p11.23 | 0.00045836 | 0.10207 | chr20:19907399-20680922 | 6
2q33.1 | 0.12362 | 0.12362 | chr2:199627908-199644614 | 0 [SATB2]
16p11.2 | 0.050389 | 0.14361 | chr16:30572436-31003843 | 22
20p12.3 | 0.11979 | 0.1604 | chr20:1490029-11108958 | 94

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q12.

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

Genes
CHD6

Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
LOC727677

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.21.

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

Genes
hsa-mir-3193
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
MLLT10P1
LINC00028
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
PSIMCT-1
MIR3193

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
IKZF3
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

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

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

Genes
WHSC1L1

Genes in Wide Peak

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

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

Genes
hsa-mir-483
IGF2
INS
TH
IGF2-AS1
MIR483
INS-IGF2
MIR4686

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
CCND2
CACNA1C
FGF6
FKBP4
FOXM1
RAD52
TEAD4
TULP3
FGF23
DYRK4
RAD51AP1
TSPAN9
ERC1
ITFG2
PRMT8
PARP11
C12orf4
C12orf5
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
EFCAB4B
CACNA2D4
FBXL14
DCP1B
LOC283440
LRTM2
LOC100271702
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

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

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

Genes
KLF5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
ANK1
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
AP3M2
DKK4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.21.

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

Genes
GINS1
NINL
ABHD12

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
CCND3
TFEB
BYSL
CDC5L
SLC29A1
GUCA1A
GUCA1B
HSP90AB1
MDFI
MEA1
NFKBIE
NFYA
PEX6
PGC
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
NCR2
MED20
POLR1C
MAD2L1BP
CUL7
C6orf108
CNPY3
FRS3
SLC22A7
APOBEC2
CAPN11
CUL9
UBR2
KIAA0240
ZNF318
YIPF3
USP49
GNMT
PRICKLE4
MRPL2
TREM2
TREM1
GTPBP2
MRPS18A
MRPS10
TMEM63B
TRERF1
LRFN2
AARS2
XPO5
MRPL14
DLK2
TREML2
TTBK1
RRP36
ABCC10
KLC4
TJAP1
FOXP4
KLHDC3
TAF8
PTCRA
TCTE1
SPATS1
C6orf223
RSPH9
LRRC73
TREML2P1
LOC221442
C6orf130
TSPO2
UNC5CL
TREML4
RPL7L1
TREML1
TREML3
SLC35B2
FLJ41649
CRIP3
C6orf226
TMEM151B
ATP6V0CP3
C6orf132
TDRG1
LOC100132354
TOMM6
MIR4647
MIR4641
MIR4642

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.32.

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

Genes
GNAS
hsa-mir-646
hsa-mir-298
hsa-mir-4325
ATP5E
BMP7
CSTF1
CTSZ
CYP24A1
EDN3
MC3R
PCK1
PFDN4
PPP1R3D
AURKA
TFAP2C
ZNF217
RAE1
BCAS1
STX16
VAPB
SYCP2
SPO11
SLMO2
TH1L
C20orf43
PPP4R1L
RBM38
DOK5
PMEPA1
CASS4
RAB22A
CDH26
FAM217B
NPEPL1
TUBB1
ZBP1
FAM210B
PHACTR3
TSHZ2
C20orf85
ZNF831
GCNT7
CBLN4
CTCFL
LOC149773
GNAS-AS1
APCDD1L
FAM209A
C20orf197
LOC284757
FAM209B
SUMO1P1
MIR296
MIR298
MIR4325
MTRNR2L3
LOC100506384
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4532
MIR4533
MIR5095

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
ZNF507
DPY19L3
LOC400684

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q12.1.

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

Genes
PLAG1
TCEA1
CHCHD7
hsa-mir-124-2
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
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100287846
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.2.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
C6
C7
C9
CDH6
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
WDR70
BRIX1
C5orf22
CCL28
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
LOC340113
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC643401
LOC646719
LOC648987
MIR580
LOC729862
CCDC152
LOC100132356
MIR4279
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4

Genes in Wide Peak

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

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

Genes
SALL1
TOX3
LOC388276
LOC643714
LOC100505619

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.1.

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

Genes
PRKAR1A
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
APOH
CACNG1
BPTF
KCNJ2
KCNJ16
KPNA2
PRKCA
MAP2K6
PSMD12
AXIN2
RGS9
SLC16A6
HELZ
ABCA10
ABCA9
ABCA8
ARSG
ABCA6
ABCA5
NOL11
PITPNC1
CACNG5
CACNG4
AMZ2
FAM20A
WIPI1
CEP112
C17orf58
KCNJ2-AS1
LOC440461
MIR634
MIR635
SNORA38B
LOC100499466
MIR4524A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.23.

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

Genes
INSM1
C20orf26
NAA20
CRNKL1
RIN2
RALGAPA2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

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

Genes
hsa-mir-762
CTF1
PHKG2
BCL7C
SETD1A
RNF40
SRCAP
ZNF629
FBXL19
FBRS
PRR14
HSD3B7
C16orf93
ORAI3
STX1B
ZNF689
ZNF785
ZNF688
FBXL19-AS1
SNORA30
MIR762
MIR4519

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p12.3.

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

Genes
hsa-mir-103-2-as
hsa-mir-1292
ADRA1D
JAG1
AVP
BMP2
CDC25B
CENPB
CHGB
GNRH2
IDH3B
ITPA
OXT
PCNA
PDYN
PLCB4
PRNP
PTPRA
SIGLEC1
SNAP25
SNRPB
TGM3
MKKS
ATRN
CDS2
ProSAPiP1
RASSF2
SLC23A2
SIRPB1
NOP56
RNF24
UBOX5
PLCB1
PRND
LAMP5
SPEF1
C20orf194
SNORD57
SNORD56
C20orf30
TRMT6
HAO1
SMOX
CRLS1
C20orf27
C20orf29
SIRPG
FERMT1
TMX4
GPCPD1
CPXM1
PAK7
MAVS
EBF4
FASTKD5
ANKRD5
GFRA4
VPS16
FAM113A
MRPS26
DDRGK1
ZNF343
PANK2
ADAM33
SLC4A11
MCM8
HSPA12B
TMC2
SIRPD
C20orf141
PROKR2
C20orf94
SIRPA
STK35
PRNT
LOC149837
C20orf196
LRRN4
TGM6
MIR103A2
LOC643406
SNORA51
SNORD86
SNORD110
LOC728228
SNORD119
LOC100131208
LOC100134015
TMEM239
LOC100289473
MIR1292
MIR103B2
PCNA-AS1
LOC100507629

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 - 44 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
--- | --- | --- | --- | ---
16p13.3 | 1.0203e-111 | 1.0203e-111 | chr16:5144019-7771745 | 1
20p12.1 | 2.9373e-39 | 2.9373e-39 | chr20:14302876-16036135 | 3
6q26 | 6.8107e-38 | 6.8107e-38 | chr6:161693099-163153207 | 1
4q22.1 | 1.2319e-34 | 4.1796e-32 | chr4:91148280-93240505 | 1
16q23.1 | 8.7676e-31 | 8.7676e-31 | chr16:78129058-79627770 | 1
1p33 | 1.1997e-33 | 1.3174e-29 | chr1:49193395-50514967 | 1
3p14.2 | 7.3559e-31 | 3.4012e-29 | chr3:59034763-61547330 | 1
5q11.2 | 1.3597e-26 | 3.5557e-24 | chr5:58260298-59787985 | 3
1p36.11 | 1.0266e-24 | 2.1062e-20 | chr1:26527443-27650365 | 25
6p25.3 | 5.4412e-18 | 5.5239e-18 | chr6:1608837-2252425 | 2
18q21.2 | 1.8837e-23 | 3.0783e-17 | chr18:48472083-48705371 | 2
4q35.1 | 5.7239e-19 | 1.9379e-15 | chr4:178911874-186507186 | 38
3q26.31 | 1.6296e-13 | 1.5375e-13 | chr3:173999806-175760559 | 2
10q11.23 | 1.0823e-14 | 2.4259e-13 | chr10:53057593-53461574 | 3
8p22 | 4.0177e-14 | 1.6325e-11 | chr8:15092726-16024383 | 1
10q23.31 | 1.2379e-11 | 2.6268e-07 | chr10:89313008-90348818 | 6
5q21.2 | 4.7115e-16 | 4.0659e-06 | chr5:96090301-107194910 | 22
15q11.2 | 7.1548e-09 | 2.5791e-05 | chr15:1-27218028 | 136
7q31.1 | 3.7095e-05 | 3.6732e-05 | chr7:109599468-111366370 | 2
21q11.2 | 6.9086e-05 | 7.0045e-05 | chr21:1-19290232 | 36
5q23.1 | 4.1535e-11 | 0.00013958 | chr5:104425581-122432489 | 62
18q12.2 | 2.3063e-14 | 0.00020458 | chr18:35235531-39060470 | 4
17p12 | 0.00026924 | 0.00027844 | chr17:10740609-12456081 | 6
19p13.3 | 0.00029057 | 0.00029057 | chr19:1033227-1907478 | 36
18q22.1 | 3.4788e-17 | 0.00036298 | chr18:65565142-66383463 | 1
15q21.1 | 5.2369e-08 | 0.00047107 | chr15:44851245-45299932 | 5
8p23.3 | 5.8939e-10 | 0.0019634 | chr8:1-6361015 | 17
15q22.33 | 0.00046246 | 0.0032362 | chr15:67067796-67549628 | 2
18p11.31 | 0.020911 | 0.019953 | chr18:3277692-5144550 | 5
8p11.21 | 0.036768 | 0.071512 | chr8:42883855-47753079 | 4
14q32.11 | 0.070361 | 0.071512 | chr14:56763887-107349540 | 490
10q25.2 | 9.13e-06 | 0.07565 | chr10:93788727-135534747 | 383
17q24.3 | 0.08261 | 0.081268 | chr17:68173089-70595192 | 2
9p21.3 | 0.085606 | 0.086699 | chr9:1-26841183 | 115
4p16.2 | 0.094766 | 0.098665 | chr4:1-9830219 | 132
2q37.2 | 0.10779 | 0.10653 | chr2:214015746-243199373 | 282
3p26.1 | 0.022363 | 0.11802 | chr3:1-21447833 | 133
1p13.1 | 0.00031462 | 0.13587 | chr1:55347880-149898950 | 499
10p15.3 | 0.13304 | 0.13587 | chr10:1-11047562 | 59
22q13.32 | 0.17374 | 0.17374 | chr22:48668761-51304566 | 46
13q14.13 | 0.2118 | 0.2118 | chr13:34539992-74263053 | 165
8p11.22 | 0.089515 | 0.22935 | chr8:35650656-41119553 | 37
1q43 | 0.23327 | 0.23117 | chr1:228032960-249250621 | 189
12p13.2 | 0.2377 | 0.23117 | chr12:4486970-17826819 | 214

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
FLRT3
MACROD2
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

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

Genes
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p33.

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

Genes
BEND5

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
ARID1A
hsa-mir-1976
CD52
SFN
HMGN2
RPS6KA1
SLC9A1
NR0B2
NUDC
WDTC1
GPN2
AIM1L
PIGV
GPATCH3
CEP85
LIN28A
DHDDS
SH3BGRL3
ZDHHC18
UBXN11
FAM46B
C1orf172
ZNF683
TRNP1
MIR1976

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
SMAD4
ELAC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
hsa-mir-1305
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ENPP6
C4orf38
RWDD4
CCDC111
CCDC110
ANKRD37
LOC389247
HELT
FAM92A3
C4orf47
SLED1
LINC00290
LOC728175
LOC731424
CLDN24
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

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

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

Genes
hsa-mir-605
CSTF2T
MIR605

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p22.

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

Genes
TUSC3

Genes in Wide Peak

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

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

Genes
PTEN
PAPSS2
RNLS
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.2.

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

Genes
hsa-mir-548p
CHD1
EFNA5
LNPEP
PAM
ST8SIA4
RAB9BP1
PPIP5K2
ERAP1
GIN1
RIOK2
ERAP2
NUDT12
C5orf30
SLCO6A1
LIX1
RGMB
FAM174A
SLCO4C1
FLJ35946
LOC100133050
LOC100289230

Genes in Wide Peak

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

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

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
NBEAP1
GABRA5
GABRB3
IPW
NDN
SNRPN
UBE3A
MKRN3
PAR5
SNURF
CYFIP1
C15orf2
MAGEL2
ATP10A
NIPA2
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
LOC503519
CHEK2P2
LOC646214
CXADRP2
REREP3
LOC653061
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8DP
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
LRRN3
IMMP2L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

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

Genes
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
POTED
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37

Genes in Wide Peak

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

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

Genes
APC
hsa-mir-1244-2
hsa-mir-548f-3
CAMK4
CDO1
AP3S1
DMXL1
EFNA5
FER
HSD17B4
KCNN2
LOX
MAN2A1
MCC
PGGT1B
PPIC
SNX2
SRP19
REEP5
ATG12
NREP
RAB9BP1
SNCAIP
PJA2
TNFAIP8
SNX24
TMED7
PRR16
COMMD10
FLJ11235
TRIM36
FEM1C
SEMA6A
EPB41L4A
FBXL17
YTHDC2
TSSK1B
TSLP
SLC25A46
FTMT
EPB41L4A-AS1
ZNF474
STARD4
WDR36
SRFBP1
CCDC112
DCP2
AQPEP
DTWD2
FAM170A
TICAM2
TMEM232
LOC644100
SNORA13
LOC728342
LOC100289673
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
LOC100505678
LOC100505841

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

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

Genes
hsa-mir-924
hsa-mir-4318
LOC647946
MIR4318

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

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

Genes
MAP2K4
hsa-mir-744
DNAH9
ZNF18
SHISA6
MIR744

Genes in Wide Peak

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

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

Genes
STK11
TCF3
hsa-mir-1909
ATP5D
CIRBP
EFNA2
GAMT
GPX4
POLR2E
RPS15
APC2
ABCA7
UQCR11
SBNO2
HMHA1
DAZAP1
MBD3
PCSK4
C19orf24
REXO1
FAM108A1
KLF16
MUM1
MIDN
REEP6
PLK5
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
ADAMTSL5
NDUFS7
ONECUT3
MEX3D
LOC100288123
MIR1909

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

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

Genes
TMX3

Genes in Wide Peak

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

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

Genes
B2M
SPG11
TRIM69
C15orf43
PATL2

Genes in Wide Peak

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

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

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
MCPH1
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53
MIR596
LOC100287015

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q22.33.

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

Genes
SMAD3
AAGAB

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.31.

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

Genes
TGIF1
DLGAP1
LOC201477
LOC284215
FLJ35776

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.21.

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

Genes
FNTA
SGK196
HGSNAT
POTEA

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.11.

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

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
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
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
NDUFB1
SIX6
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
TIMM9
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
C14orf101
CDCA4
C14orf102
ATG2B
UBR7
C14orf105
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
ACTR10
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
C14orf149
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
C14orf37
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
SLC35F4
COX8C
ASPG
RAB15
FLJ31306
TOMM20L
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
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
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
C14orf38
LOC731223
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
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.2.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HELLS
HHEX
HMX2
HPS1
IDE
INPP5A
KIF11
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
DPCD
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
PLCE1
CHST15
ACSL5
EXOC6
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
CWF19L1
PI4K2A
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
WDR96
LRRC27
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
OPALIN
SYCE1
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
FRA10AC1
SFXN2
PDZD8
C10orf32
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
NKX2-3
SLC35G1
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
PIPSL
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
LOC283038
LOC283089
O3FAR1
KCNK18
CYP26C1
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
C10orf62
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
DUX4L2
LOC728558
LOC729020
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100169752
DNMBP-AS1
LOC100289509
MIR1287
MIR1307
MIR2110
MIR378C
MIR4297
MIR3157
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4483
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

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

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

Genes
SOX9
LOC100499467

Genes in Wide Peak

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

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

Genes
JAK2
MLLT3
NFIB
CD274
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
PLIN2
CDKN2A
CDKN2B
DMRT1
ELAVL2
FOXD4
MLANA
GLDC
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
INSL4
MTAP
PTPRD
RFX3
RLN1
RLN2
RPS6
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TYRP1
VLDLR
MPDZ
CER1
KIAA0020
RCL1
DMRT2
RRAGA
PSIP1
INSL6
KDM4C
KANK1
SLC24A2
RANBP6
AK3
C9orf53
BNC2
HAUS6
CNTLN
KIAA1797
C9orf68
CDC37L1
DENND4C
C9orf46
CBWD1
KLHL9
KIAA1432
DMRT3
DMRTA1
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
C9orf66
TTC39B
FAM154A
FREM1
KIAA2026
KCNV2
GLIS3
C9orf93
TUSC1
LURAP1L
IFNE
ZDHHC21
ACER2
LOC389705
FLJ35024
FLJ41200
PTPLAD2
PPAPDC2
MIR101-2
MIR31
FLJ35282
MIR31HG
MIR491
FAM138C
SCARNA8
CDKN2B-AS1
C9orf146
WASH1
MIR3152
LOC100506422
MIR4473
MIR4665
MIR4474

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.2.

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

Genes
FGFR3
WHSC1
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
KIAA0232
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
D4S234E
GPR78
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
CNO
STK32B
LYAR
TBC1D14
SORCS2
KIAA1530
ZFYVE28
AFAP1
TNIP2
HAUS3
ABCA11P
GRPEL1
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
ZNF595
JAKMIP1
FAM53A
METTL19
ZBTB49
ZNF721
ZNF718
CCDC96
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
USP17L6P
USP17
C4orf48
LOC402160
ZNF876P
DEFB131
LOC650293
ZNF732
SCARNA22
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
LOC100507266
MIR378D1
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
TIMP4
NR2C2
WNT7A
BRPF1
COLQ
CAMK1
BHLHE40
KAT2B
SH3BP5
VGLL4
EDEM1
TBC1D5
TATDN2
IQSEC1
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LSM3
LINC00312
LMCD1
C3orf32
TRNT1
CRBN
C3orf19
GHRL
ARL8B
SETD5
TMEM40
TMEM111
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
HDAC11
TSEN2
GRIP2
C3orf20
JAGN1
GHRLOS2
IL17RC
EAF1
OXNAD1
C3orf24
GALNTL2
KCNH8
CHCHD4
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
FGD5
CIDECP
CNTN4
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC339862
COL6A4P1
TPRXL
LHFPL4
LOC401052
LOC440944
SNORA7A
MIR563
MIR885
EGOT
GHRLOS
LOC100129480
LOC100132526
LOC100288428
MIR4270
MIR3714
FGD5-AS1
LOC100505696
LOC100507582
ARPC4-TTLL3
MIR4791
MIR4790

Genes in Wide Peak

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

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

Genes
BCL9
JAK1
JUN
NOTCH2
NRAS
BCL10
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
ABCA4
ACADM
ADORA3
AGL
AK4
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
C8A
C8B
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
CTH
CYP2J2
DAB1
DBT
GADD45A
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FCGR1B
FMO5
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
IL12RB2
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
LEPR
TACSTD2
MOV10
MSH4
NFIA
NGF
NHLH2
ROR1
OVGP1
PDE4B
PDZK1
PGM1
PIN1P1
PRKAA2
PRKAB2
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPE65
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
USP1
VCAM1
WNT2B
BSND
CSDE1
EVI5
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
TTF2
ITGA10
LMO4
CDC14A
PPAP2B
RTCD1
FPGT
PEX11B
FUBP1
DIRAS3
SLC16A4
SRSF11
CD101
SEP15
ZRANB2
ARHGAP29
SEC22B
CHD1L
CLCA3P
CLCA2
HS2ST1
DNAJC6
LRIG2
LPPR4
SV2A
RBM8A
INSL5
PIGK
TSPAN2
INADL
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
CD160
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
SLC35D1
LPHN2
KIAA1107
USP24
ITGB3BP
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
ZZZ3
SERBP1
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
FOXD3
CHIA
RNF115
ANGPTL3
GPSM2
ALG6
SLC25A24
DNTTIP2
TMED5
BOLA1
TNNI3K
SH3GLB1
HAO2
ACP6
HOOK1
SNX7
GPR89B
DPH5
GPR88
CCDC76
L1TD1
RSBN1
ZNHIT6
LEPROT
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RAVER2
FGGY
MCOLN3
SLC22A15
RNPC3
LRRC40
DEPDC1
LRIF1
CTTNBP2NL
FAM212B
GNG12
CCBL2
TMEM167B
OLFML3
FAM91A2
AMIGO1
ODF2L
KIAA1324
LRRC7
CACHD1
MIER1
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
DLEU2L
EPS8L3
VTCN1
TTLL7
WDR78
RPAP2
DENND2D
WLS
RPF1
SIKE1
TRIM45
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
TM2D1
REG4
SYDE2
ZNF644
LRRC8C
SGIP1
POLR3GL
PROK1
EFCAB7
PSRC1
ATP1A1OS
ATG4C
FAM40A
DOCK7
ZNF697
NEXN
DNAJA1P5
HENMT1
MYSM1
GNRHR2
OMA1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
C1orf87
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
UBE2U
HFE2
ANKRD35
SLC30A7
MGC27382
IL23R
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
KANK4
SASS6
PPIAL4A
HFM1
UBL4B
PDIA3P
ALG14
LINC00466
C1orf168
TMEM61
NBPF11
NUDT17
TCTEX1D1
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
NEGR1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
ZNF326
BTBD8
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
FAM73A
LOC375010
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
UOX
FRRS1
C1orf141
GBP1P1
FLJ27354
MIR137HG
NBPF9
MIR101-1
MIR137
MIR186
MIR197
LHX8
C1orf180
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
PGCP1
GEMIN8P4
RBMXL1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC646626
EMBP1
SRGAP2P2
LOC648740
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
SNORD45C
MIR548D1
MIR553
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
HSD52
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130000
LOC100131060
LOC100131564
NBPF10
FCGR1C
ZRANB2-AS1
LOC100286793
LOC100287722
LOC100289178
LOC100289211
MIR320B1
MIR1262
MIR3117
MIR4256
MIR3671
MIR548AA1
LOC100505768
LOC100506343
LOC100507634
FPGT-TNNI3K
TMEM56-RWDD3
MIR4422
MIR4794
MIR4711
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2

Genes in Wide Peak

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

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

Genes
GATA3
hsa-mir-3155
ADARB2
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PRKCQ
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
KIN
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
IDI2-AS1
SFMBT2
ASB13
TUBAL3
ITIH5
AKR1E2
TAF3
FBXO18
RBM17
IDI2
UCN3
SFTA1P
LOC254312
LOC282980
LOC338588
AKR1CL1
TUBB8
tAKR
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf108
LOC439949
ADARB2-AS1
LOC100216001
MIR3155A
LOC100507034
LOC100507127
MIR3155B

Genes in Wide Peak

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

Table S60. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-3201
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC284933
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR3201
MIR4535

Genes in Wide Peak

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

Table S61. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LCP1
RB1
LHFP
TTL
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
ATP7B
KLF5
RCBTB2
CPB2
DACH1
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
PCDH9
RFXAP
ATXN8OS
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
ITM2B
MTRF1
UTP14C
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
PIBF1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
DIS3
KIAA0564
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
PCDH20
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
LINC00284
CSNK1A1L
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
LINC00550
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ALG11
MZT1
TSC22D1-AS1
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR548F5
MIR759
MIR320D1
MIR4305
MIR3169
MIR3613
OR7E37P
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4703
LOC100616668

Genes in Wide Peak

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

Table S62. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FGFR1
WHSC1L1
ADRB3
ADAM3A
EIF4EBP1
ADAM2
IDO1
STAR
TACC1
ADAM18
ADAM9
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
BRF2
C8orf4
PLEKHA2
ZMAT4
ZNF703
RAB11FIP1
TM2D2
PPAPDC1B
GOT1L1
LETM2
KCNU1
IDO2
HTRA4
ADAM32
ADAM5P
RNF5P1
C8orf86
LOC728024
LOC100130964

Genes in Wide Peak

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

Table S63. 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
hsa-mir-1182
ACTA1
ACTN2
ADSS
AGT
ARF1
CHML
LYST
CHRM3
GALNT2
GNG4
GUK1
HNRNPU
KCNK1
LGALS8
MTR
NID1
RAB4A
RGS7
RYR2
TARBP1
TBCE
GPR137B
TSNAX
WNT9A
ZNF124
HIST3H3
GNPAT
KMO
EXO1
GGPS1
TOMM20
URB2
CEP170
AKT3
ZNF238
SPHAR
CAPN9
SDCCAG8
COG2
RBM34
ABCB10
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
TAF5L
DISC2
DISC1
PPPDE1
SCCPDH
TRIM17
ARID4B
EGLN1
KIAA1383
KIF26B
HEATR1
ZNF692
NUP133
ERO1LB
FMN2
ZNF695
GJC2
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
SMYD3
ARV1
C1orf35
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
ZNF496
C1orf198
WNT3A
HIST3H2A
ZNF670
NLRP3
FAM36A
C1orf96
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
EXOC8
RNF187
CNST
PLD5
C1orf100
IBA57
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
FAM89A
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
OR2W5
OR13G1
DUSP5P
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
MIR3123
MIR3124
MIR3620
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ETV6
ZNF384
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
KCNA1
KCNA5
KCNA6
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NOP2
NTF3
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTMS
PTPN6
PTPRO
PEX5
PZP
SCNN1A
SLC2A3
VAMP1
TNFRSF1A
TPI1
VWF
MFAP5
USP5
MLF2
KLRC4
CSDA
DYRK4
GPRC5A
CD163
GDF3
CLSTN3
NCAPD2
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
RAD51AP1
KLRAP1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
TAPBPL
MAGOHB
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
ANO2
C12orf4
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
PLBD1
NANOG
DUSP16
APOLD1
GSG1
CDCA3
RBP5
ACRBP
SPSB2
RERG
HTR7P1
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf53
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
CLEC9A
C12orf36
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
SCARNA12
SCARNA11
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
KLRC4-KLRK1
PRH1-PRR4
MIR3974

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.06 | -2.81 | 1 | 0.24 | 8.18 | 6.34e-16
1q | 1955 | 0.17 | 2.99 | 0.00706 | 0.16 | 2.57 | 0.0187
2p | 924 | 0.17 | -1.33 | 1 | 0.02 | -8.21 | 1
2q | 1556 | 0.17 | 0.868 | 0.514 | 0.02 | -6.75 | 1
3p | 1062 | 0.10 | -4.06 | 1 | 0.12 | -3.15 | 1
3q | 1139 | 0.14 | -2.03 | 1 | 0.08 | -4.91 | 1
4p | 489 | 0.02 | -8.58 | 1 | 0.30 | 3.41 | 0.00131
4q | 1049 | 0.04 | -6.79 | 1 | 0.26 | 3.94 | 0.000178
5p | 270 | 0.15 | -3.97 | 1 | 0.16 | -3.87 | 1
5q | 1427 | 0.09 | -3.39 | 1 | 0.20 | 1.99 | 0.0671
6p | 1173 | 0.20 | 1.07 | 0.406 | 0.11 | -3.43 | 1
6q | 839 | 0.18 | -0.898 | 1 | 0.14 | -2.95 | 1
7p | 641 | 0.55 | 16.4 | 0 | 0.01 | -6.84 | 1
7q | 1277 | 0.50 | 17.7 | 0 | 0.02 | -5.81 | 1
8p | 580 | 0.34 | 4.54 | 1.64e-05 | 0.49 | 11.7 | 0
8q | 859 | 0.50 | 14.5 | 0 | 0.18 | -0.9 | 1
9p | 422 | 0.19 | -2.16 | 1 | 0.15 | -3.77 | 1
9q | 1113 | 0.17 | -0.75 | 1 | 0.14 | -2.23 | 1
10p | 409 | 0.08 | -6.83 | 1 | 0.16 | -3.39 | 1
10q | 1268 | 0.05 | -6.2 | 1 | 0.16 | -0.511 | 1
11p | 862 | 0.12 | -3.67 | 1 | 0.13 | -3.24 | 1
11q | 1515 | 0.13 | -1.25 | 1 | 0.15 | -0.00454 | 1
12p | 575 | 0.23 | 0.387 | 0.822 | 0.11 | -4.98 | 1
12q | 1447 | 0.21 | 2.84 | 0.00997 | 0.12 | -2.05 | 1
13q | 654 | 0.59 | 18.2 | 0 | 0.06 | -4.95 | 1
14q | 1341 | 0.12 | -2.23 | 1 | 0.32 | 8.19 | 6.34e-16
15q | 1355 | 0.04 | -5.39 | 1 | 0.35 | 9.84 | 0
16p | 872 | 0.25 | 2.31 | 0.0384 | 0.08 | -5.53 | 1
16q | 702 | 0.24 | 1.35 | 0.274 | 0.07 | -6.27 | 1
17p | 683 | 0.07 | -4.92 | 1 | 0.56 | 16.6 | 0
17q | 1592 | 0.20 | 2.57 | 0.0203 | 0.17 | 1.44 | 0.201
18p | 143 | 0.10 | -4.83 | 1 | 0.58 | 15 | 0
18q | 446 | 0.07 | -4.92 | 1 | 0.61 | 18 | 0
19p | 995 | 0.16 | -1.72 | 1 | 0.12 | -3.62 | 1
19q | 1709 | 0.18 | 2.09 | 0.0617 | 0.11 | -1.71 | 1
20p | 355 | 0.57 | 14.7 | 0 | 0.30 | 2.14 | 0.05
20q | 753 | 0.70 | 24 | 0 | 0.18 | -0.879 | 1
21q | 509 | 0.07 | -6.68 | 1 | 0.28 | 2.52 | 0.0197
22q | 921 | 0.04 | -6.59 | 1 | 0.31 | 5.94 | 7.21e-09
Xq | 1312 | 0.18 | 0.773 | 0.549 | 0.15 | -0.886 | 1

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/COAD/1971042/2.GDAC_MergeDataFiles.Finished/COAD.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 413 Input Tumor Samples.

Tumor Sample Names
TCGA-A6-2670-01A-02D-0819-01
TCGA-A6-2671-01A-01D-1549-01
TCGA-A6-2672-01A-01D-1549-01
TCGA-A6-2674-01A-02D-1549-01
TCGA-A6-2675-01A-02D-1717-01
TCGA-A6-2676-01A-01D-1549-01
TCGA-A6-2677-01A-01D-1549-01
TCGA-A6-2678-01A-01D-1549-01
TCGA-A6-2679-01A-02D-1549-01
TCGA-A6-2680-01A-01D-1549-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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