Stomach 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 2.0.16 (cga svn revision 38839).

Summary

There were 132 tumor samples used in this analysis: 21 significant arm-level results, 23 significant focal amplifications, and 33 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 23 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
--- | --- | --- | --- | ---
17q12 | 5.8384e-18 | 5.8384e-18 | chr17:35058337-35159695 | 7
19q12 | 1.3617e-15 | 1.3617e-15 | chr19:34875012-35091997 | 2
12q15 | 2.1112e-10 | 2.1112e-10 | chr12:66890102-68262466 | 13
12p12.1 | 8.7014e-10 | 8.7014e-10 | chr12:25240084-25405863 | 2
7q21.2 | 3.2044e-10 | 1.0269e-09 | chr7:91993046-92395934 | 5
8p23.1 | 3.6401e-07 | 3.6401e-07 | chr8:11585200-11830754 | 4
20q13.2 | 1.4866e-06 | 1.4866e-06 | chr20:51356899-52100291 | 4
10q26.13 | 3.1278e-06 | 3.1278e-06 | chr10:123230278-123389836 | 1
8q24.21 | 8.0949e-08 | 3.5043e-06 | chr8:128215233-128670383 | 2
7p11.2 | 7.7849e-06 | 7.7849e-06 | chr7:55044034-55507625 | 3
6p21.1 | 0.00019747 | 0.00019747 | chr6:43701946-43788316 | 4
18q11.2 | 0.00037477 | 0.00037477 | chr18:17732023-18152003 | 1
1q42.3 | 0.00039496 | 0.00039496 | chr1:232974712-233190000 | 0 [TOMM20]
11q13.2 | 0.0022695 | 0.0022695 | chr11:68238807-70026660 | 19
13q22.1 | 0.0070376 | 0.0070376 | chr13:72562649-72815854 | 0 [KLF5]
15q26.1 | 0.022264 | 0.022264 | chr15:87481512-92176114 | 47
1p36.22 | 0.040992 | 0.040992 | chr1:10591686-11040730 | 6
11p13 | 0.073597 | 0.073597 | chr11:34391504-35616010 | 9
9p24.1 | 0.082265 | 0.093619 | chr9:4754022-5596715 | 11
3q26.2 | 0.10231 | 0.10231 | chr3:158738746-199501827 | 239
8q21.11 | 0.0082441 | 0.1306 | chr8:77316321-77670309 | 0 [LOC100192378]
7q31.2 | 0.0142 | 0.14031 | chr7:116025877-117087494 | 10
9p13.3 | 0.15615 | 0.21573 | chr9:31466821-37751043 | 98

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
PNMT
TCAP
STARD3
C17orf37
PGAP3

Genes in Wide Peak

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

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

Genes
CCNE1
C19orf12

Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
LYZ
RAP1B
YEATS4
FRS2
CPSF6
IL22
SLC35E3
IL26
MDM1
NUP107

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
LYRM5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
PEX1
C7orf64
MGC16142
FAM133B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p23.1.

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

Genes
CTSB
FDFT1
GATA4
NEIL2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
ZNF217
BCAS1
TSHZ2
SUMO1P1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q26.13.

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

Genes
FGFR2

Genes in Wide Peak

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

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

Genes
POU5F1B
LOC727677

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR
LANCL2
VOPP1

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
MAD2L1BP
GTPBP2
MRPS18A
RSPH9

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
GATA6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
CCND1
hsa-mir-548k
CPT1A
CTTN
FGF3
FGF4
IGHMBP2
PPFIA1
FADD
MTL5
FGF19
SHANK2
MYEOV
ANO1
MRGPRD
MRGPRF
MRPL21
TPCN2
ORAOV1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
IDH2
CRTC3
hsa-mir-9-3
ANPEP
CHD2
FES
MAN2A2
FURIN
PLIN1
POLG
RLBP1
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
ABHD2
GABARAPL3
VPS33B
SLCO3A1
NGRN
RHCG
FANCI
MESP1
UNC45A
RGMA
WDR93
C15orf42
RCCD1
C15orf32
MESP2
LOC254559
LOC283761
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
C15orf58
FAM174B
MIR9-3
TTLL13
LOC100144604

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.22.

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

Genes
PEX14
SRM
MASP2
TARDBP
CASZ1
C1orf127

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
CAT
CD44
ELF5
SLC1A2
PDHX
FJX1
PAMR1
EHF
APIP

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.1.

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

Genes
JAK2
CD274
hsa-mir-101-2
INSL4
RLN1
RLN2
RCL1
INSL6
C9orf46
PDCD1LG2
MIR101-2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
BCL6
EIF4A2
ETV5
LPP
MLF1
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
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
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
IL12A
KNG1
KPNA4
MFI2
MUC4
NDUFB5
OPA1
CLDN11
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RARRES1
RFC4
SNORA63
RPL35A
TRA2B
SHOX2
SI
ST6GAL1
SKIL
SLC2A2
SST
TERC
THPO
SEC62
FXR1
TP63
CHRD
B3GALNT1
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
SMC4
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
SCHIP1
NMD3
ZNF639
RSRC1
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
LXN
HRASLS
MRPL47
NCEH1
IFT80
SLC7A14
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
MFSD1
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
ARL14
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
FYTTD1
ARPM1
MGC2889
LRCH3
C3orf34
GFM1
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
C3orf50
CAMK2N2
TM4SF19
RPL39L
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
PPM1L
WDR49
LRRC34
C3orf59
C3orf21
C3orf55
CCDC50
PYDC2
LOC152217
C3orf57
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
NAALADL2
TCTEX1D2
C3orf43
SDHALP1
UTS2D
HTR3E
C3orf70
TPRG1
TRIM59
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
SOX2OT
WDR53
LOC348840
LRRC33
TMEM212
FLJ42393
MIR15B
MIR16-2
SNORD2
SNORA4
C3orf65
LOC647309
IQCJ
SCARNA7
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHALP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
SNAR-I
MIR1224

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.2.

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

Genes
MET
CAPZA2
CFTR
WNT2
ST7
ST7OT1
ST7OT2
ST7OT3
ASZ1
ST7OT4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
FANCG
PAX5
ACO1
ANXA2P2
NUDT2
AQP3
AQP7
BAG1
CA9
CCIN
CD72
CLTA
CNTFR
GALT
B4GALT1
DNAJA1
IL11RA
NDUFB6
NFX1
NPR2
PRSS3
RMRP
CCL19
CCL21
TESK1
TLN1
TPM2
VCP
RECK
GRHPR
RGP1
MELK
RUSC2
ZBTB5
GNE
TOPORS
SIGMAR1
CREB3
UNC13B
CCL27
PTENP1
DCTN3
FRMPD1
KIAA1045
DDX58
DNAJB5
DCAF12
SPAG8
FBXO10
DNAI1
SIT1
SPINK4
STOML2
UBAP1
CHMP5
TMEM8B
APTX
UBE2R2
SMU1
UBAP2
OR2S2
KIAA1161
GBA2
POLR1E
NOL6
KIAA1539
ZCCHC7
HINT2
C9orf24
PIGO
C9orf100
LOC92973
TAF1L
ARID3C
C9orf23
C9orf131
RNF38
GLIPR2
RG9MTD3
LOC158376
LOC158381
C9orf25
CCDC107
C9orf144B
KIF24
ENHO
C9orf144
C9orf128
OR13J1
TMEM215
TOMM5
LOC415056
SUGT1P
HRCT1
MSMP
FAM166B
SNORD121A
SNORD121B

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 33 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
3p14.2 | 2.6578e-81 | 2.6578e-81 | chr3:59009803-61522370 | 1
16q23.1 | 1.7086e-35 | 1.7086e-35 | chr16:76686559-78185271 | 1
20p12.1 | 9.893e-15 | 9.893e-15 | chr20:14250876-15984135 | 2
5q11.2 | 3.811e-14 | 3.811e-14 | chr5:58296055-59823742 | 3
9p24.1 | 6.8535e-15 | 7.8823e-13 | chr9:7786330-12683402 | 2
9p21.3 | 5.3735e-18 | 4.4058e-12 | chr9:21855498-21986995 | 2
6q26 | 2.1731e-11 | 2.1731e-11 | chr6:161613089-163073197 | 1
6p25.3 | 3.2905e-10 | 3.2905e-10 | chr6:1553836-2569051 | 2
4q22.1 | 1.1542e-10 | 1.391e-09 | chr4:91367303-93459528 | 2
7q31.1 | 4.368e-06 | 8.0801e-06 | chr7:110512908-111163100 | 1
1p36.11 | 1.6331e-05 | 2.0591e-05 | chr1:26773226-27306046 | 11
3q26.31 | 3.0522e-05 | 3.0522e-05 | chr3:175482500-178221491 | 1
4q35.1 | 9.9821e-09 | 0.0018573 | chr4:172968157-186538981 | 47
22q13.31 | 0.0019428 | 0.0019584 | chr22:44619793-49691432 | 62
10q23.31 | 0.0019584 | 0.0063249 | chr10:89302988-90024018 | 5
15q21.3 | 0.014207 | 0.014828 | chr15:54995064-55370592 | 1
2q37.2 | 0.0045486 | 0.015742 | chr2:235626319-237660719 | 5
19p13.3 | 0.015987 | 0.015742 | chr19:1-9438458 | 283
2q33.2 | 0.0019428 | 0.021815 | chr2:204534470-206266883 | 1
1q44 | 0.0046448 | 0.024931 | chr1:243931413-244771113 | 1
2q32.1 | 0.0078867 | 0.024931 | chr2:185509151-187268840 | 2
18q21.2 | 0.01032 | 0.024931 | chr18:46604315-48124308 | 4
21q22.3 | 0.060757 | 0.059287 | chr21:34195676-46944323 | 146
7q36.3 | 0.011714 | 0.074233 | chr7:156902368-158821424 | 10
14q21.3 | 0.068148 | 0.090825 | chr14:44648919-44677557 | 2
11p15.5 | 0.093718 | 0.093718 | chr11:1-11267794 | 261
4q35.2 | 1.0177e-06 | 0.1828 | chr4:152413177-191273063 | 146
10q22.2 | 0.059287 | 0.19298 | chr10:75564411-78299547 | 11
14q32.32 | 0.12215 | 0.19298 | chr14:85064045-106368585 | 266
1q44 | 0.077459 | 0.2192 | chr1:243348890-243980330 | 1
18q12.2 | 0.046417 | 0.2192 | chr18:28340262-76117153 | 169
13q33.1 | 0.24216 | 0.22668 | chr13:34932522-114142980 | 268
1p31.1 | 0.18117 | 0.25585 | chr1:1-247249719 | 2207

Genes in Wide Peak

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

Table S21. 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 16q23.1.

Table S22. 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 20p12.1.

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

Genes
FLRT3
MACROD2

Genes in Wide Peak

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

Table S24. 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 9p24.1.

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

Genes
PTPRD
C9orf123

Genes in Wide Peak

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

Table S26. 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 6q26.

Table S27. 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 6p25.3.

Table S28. 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 4q22.1.

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

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

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

Genes
LRRN3

Genes in Wide Peak

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

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

Genes
ARID1A
SFN
NR0B2
NUDC
GPN2
PIGV
GPATCH3
ZDHHC18
FAM46B
C1orf172
TRNP1

Genes in Wide Peak

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

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

Genes
NAALADL2

Genes in Wide Peak

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

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

Genes
hsa-mir-1305
AGA
SLC25A4
CASP3
DCTD
ACSL1
GPM6A
HMGB2
HPGD
ING2
IRF2
VEGFC
GLRA3
SAP30
HAND2
MORF4
ADAM29
SCRG1
FBXO8
GALNT7
CLDN22
NEIL3
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
C4orf41
MLF1IP
NBLA00301
WWC2
KIAA1712
SNX25
MGC45800
WDR17
SPATA4
ENPP6
ASB5
C4orf38
RWDD4A
CCDC111
LOC285501
HELT
FAM92A3
GALNTL6
SLED1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

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

Genes
hsa-let-7b
ACR
ARSA
CHKB
CPT1B
TYMP
PPARA
MAPK11
MAPK12
SBF1
WNT7B
CELSR1
SAPS2
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
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

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

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

Genes
PTEN
PAPSS2
ATAD1
CFLP1
KILLIN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.3.

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

Genes
TCF12

Genes in Wide Peak

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

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

Genes
GBX2
CXCR7
IQCA1
AGAP1
ASB18

Genes in Wide Peak

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

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

Genes
GNA11
MLLT1
SH3GL1
STK11
TCF3
FSTL3
hsa-mir-220b
hsa-mir-7-3
hsa-mir-637
hsa-mir-1227
hsa-mir-1909
hsa-mir-1302-2
AES
AMH
ATP5D
AZU1
HCN2
BSG
C3
CAPS
CD70
CDC34
CIRBP
CNN2
CSNK1G2
DAPK3
CFD
ARID3A
EEF2
EFNA2
ELANE
ELAVL1
EMR1
FCER2
FUT3
FUT5
FUT6
GAMT
GNA15
GNG7
MKNK2
GPX4
GTF2F1
GZMM
INSR
MATK
MYO1F
GADD45B
HNRNPM
NDUFA7
NFIC
NRTN
OAZ1
PALM
POLR2E
POLRMT
MAP2K2
MAP2K7
PSPN
PRTN3
PTBP1
PTPRS
RFX2
RPS15
RPS28
SAFB
CCL25
SGTA
SNAPC2
STXBP2
TBXA2R
THOP1
TLE2
VAV1
ZNF177
MADCAM1
SF3A2
CLPP
RANBP3
KHSRP
PPAP2C
S1PR4
TNFSF14
TNFSF9
AP3D1
RAB11B
TRIP10
LONP1
APBA3
SAFB2
MED16
CHAF1A
SH2D3A
EBI3
PLIN3
APC2
CLEC4M
ABCA7
HMG20B
TUBB4
TIMM44
SEMA6B
ZNF266
PNPLA6
UQCR
SBNO2
KDM4B
ZFR2
ARHGEF18
PIP5K1C
HMHA1
SHC2
RPL36
TIMM13
DAZAP1
OR7E24
SNORD37
FGF22
TJP3
ITGB1BP3
UHRF1
SLC39A3
CD209
ANGPTL4
MARCH2
CD320
THEG
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
RNF126
CCDC94
C19orf10
RETN
NCLN
GPR108
SPPL2B
DUS3L
XAB2
SHD
MCOLN1
WDR18
REXO1
KIAA1543
ZNF317
ZNF77
C19orf29
BRUNOL5
SLC25A23
FSD1
ZNF557
LASS4
TLE6
LPPR3
DENND1C
ZNF556
LRRC8E
UBXN6
OR4F17
ACSBG2
ADAMTS10
FAM108A1
DOHH
KLF16
PRAM1
ALKBH7
ZNF414
DOT1L
FBN3
ZNF559
KISS1R
CREB3L3
HDGF2
LMNB2
RAX2
MUM1
MPND
ATCAY
MBD3L1
MIDN
DPP9
C19orf22
C19orf6
C19orf20
CRB3
REEP6
PEX11G
MUC16
C19orf36
SCAMP4
ADAT3
ZNF554
EVI5L
GRIN3B
MRPL54
LRG1
OR7D4
OR7G1
OR1M1
ACER1
C19orf70
MBD3L2
TRAPPC5
PCP2
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOBKL2A
C19orf28
GIPC3
NDUFA11
C19orf21
PLK5P
C2CD4C
ZNF358
TICAM1
C19orf23
ZNRF4
ZNF558
C19orf25
ATP8B3
DIRAS1
ZNF555
OR7D2
PRR22
ANKRD24
C19orf59
C19orf26
C19orf34
KANK3
PLAC2
TMEM146
ACTL9
OR2Z1
C19orf77
C19orf30
SLC25A41
MBD3L5
ODF3L2
EMR4P
ADAMTSL5
CLEC4G
TMPRSS9
NDUFS7
C19orf35
HSD11B1L
C19orf45
ZNF699
ONECUT3
OR7G2
OR7G3
MEX3D
FLJ45445
PRSSL1
VMAC
CTXN1
MIR7-3
PLIN5
CLEC4GP1
FLJ25758
FAM138F
LINGO3
ARRDC5
FAM138A
MBD3L4
MBD3L3
FAM138C
MIR637
PLIN4
MIR220B
C19orf71
LOC100128573

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q33.2.

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

Genes
PARD3B

Genes in Wide Peak

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

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

Genes
SMYD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q32.1.

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

Genes
ITGAV
ZC3H15

Genes in Wide Peak

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

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

Genes
SMAD4
ME2
MEX3C
ELAC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
RUNX1
ERG
TMPRSS2
hsa-mir-802
ADARB1
AIRE
ATP5O
PTTG1IP
C21orf2
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
RCAN1
DYRK1A
ETS2
HLCS
HMGN1
PRMT2
ITGB2
KCNE1
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SIM2
SLC5A3
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
TTC3
U2AF1
UBE2G2
WRB
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DOPEY2
KCNE2
DSCR4
DSCR3
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
DNMT3L
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
PCBP3
C21orf58
C21orf57
NCRNA00160
FAM165B
C21orf29
NCRNA00112
NCRNA00111
SETD4
FAM3B
RIPK4
CLIC6
AGPAT3
PRDM15
TMPRSS3
MRPS6
C21orf96
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
C21orf70
RSPH1
UMODL1
C21orf82
C21orf84
C21orf88
C21orf90
MCM3APAS
LCA5L
IGSF5
SIK1
C21orf129
C21orf121
C21orf128
PLAC4
DSCR9
DSCR10
C21orf130
C21orf125
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
NCRNA00162
NCRNA00175
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
NCRNA00114
LOC642852
C21orf122
MIR802

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
hsa-mir-595
hsa-mir-153-2
PTPRN2
VIPR2
NCAPG2
WDR60
ESYT2
LOC154822
MIR153-2
MIR595

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.3.

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

Genes
FKBP3
SNORD127

Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
EIF4G2
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPL27A
RPLP2
RRM1
SCT
SMPD1
TRIM21
ST5
STIM1
TAF10
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
CTR9
TRIM66
TSPAN32
TSSC4
MRVI1
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
LYVE1
KCNQ1OT1
PKP3
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2AS
BET1L
CEND1
CYB5R2
TRIM34
MUPCDH
TOLLIP
TRIM68
LRDD
KCNQ1DN
MMP26
C11orf17
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
HCCA2
SBF2
FAM160A2
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIMP1
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
FLJ46111
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVIN1
OR52K1
OR52I1
OR51D1
OR52A4
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC650368
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
LOC100133545

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-1979
AGA
SLC25A4
ANXA2P1
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112L
PLRG1
PPID
SC4MOL
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SORBS2
SAP30
LRAT
HAND2
RAPGEF2
MFAP3L
MORF4
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
PDGFC
TUBB4Q
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
C4orf41
MLF1IP
NBLA00301
MAP9
WWC2
KIAA1712
SNX25
MND1
TKTL2
CBR4
FHDC1
MGC45800
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
C4orf45
TRIM60
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
RNF175
TRIML1
LOC340017
PRSS48
ANKRD37
TRIM61
TRIM75
HELT
FAM92A3
C4orf47
GALNTL6
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
MIR578
LOC728410
FAM160A1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q22.2.

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

Genes
MYST4
hsa-mir-606
ADK
VDAC2
DUSP13
C10orf11
ZNF503
COMTD1
SAMD8
DUPD1
C10orf41

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.32.

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

Genes
AKT1
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-770
hsa-mir-345
hsa-mir-342
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
GALC
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
RAGE
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
MTA1
RPS6KA5
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
KIAA1409
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
C14orf139
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
C14orf153
HHIPL1
C14orf142
FAM181A
BTBD6
C14orf143
C14orf73
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
C14orf72
GSC
SERPINA12
PRIMA1
TTC7B
C14orf49
EML5
MGC23270
NUDT14
C14orf48
SERPINA11
C14orf86
SNHG10
C14orf177
C14orf68
C14orf70
KIAA0284
C14orf80
CCDC85C
NCRNA00203
SERPINA9
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
FLJ45244
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323
MIR337
MIR342
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR453
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
C14orf184
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORD112
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-3
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-8
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
LOC100133469

Genes in Wide Peak

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

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

Genes
KIF26B

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
hsa-mir-122
hsa-mir-1539
hsa-mir-924
hsa-mir-187
ATP5A1
CDH7
CYB5A
DCC
DTNA
FECH
KDSR
GALR1
GALNT1
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC4R
ME2
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
RAB27B
RIT2
RPL17
SERPINB3
SERPINB4
SLC14A1
SYT4
TCF4
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
TNFRSF11A
MBD2
PSTPIP2
PIAS2
CTDP1
SOCS6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
KIAA0427
TSHZ1
ACAA2
CD226
ZNF271
TXNL4A
MAPRE2
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
SLC39A6
RTTN
C18orf10
SETBP1
KCNG2
SNORD58B
SNORD58A
SALL3
CDH20
CDH19
C18orf55
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
TMX3
DYM
ZCCHC2
MOCOS
RPRD1A
ZNF532
ELP2
ELAC1
ZNF407
CNDP2
BRUNOL4
KIAA1328
KLHL14
KIAA1468
KIAA1632
CCDC102B
C18orf22
PQLC1
FHOD3
CCDC68
ASXL3
NETO1
KATNAL2
C18orf21
MRO
HDHD2
ZNF397
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
HAUS1
ALPK2
LOXHD1
INO80C
FAM69C
STARD6
C18orf25
CCBE1
CBLN2
C18orf54
TCEB3C
FBXO15
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
C18orf20
ZNF396
C18orf26
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
CPLX4
C18orf34
ATP9B
LOC390858
LOC400657
MIR122
MIR187
HSBP1L1
WBP11P1
RNF165
C18orf32
U58
KC6
LOC647946
SCARNA17
SNORA37
TCEB3CL
ZNF397OS
SNORD58C
LOC100130522

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q33.1.

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

Genes
ERCC5
LCP1
RB1
LHFP
hsa-mir-1267
hsa-mir-623
hsa-mir-92a-1
hsa-mir-622
hsa-mir-1297
hsa-mir-15a
hsa-mir-621
hsa-mir-320d-1
ATP4B
ATP7B
KLF5
BTF3L1
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF14
GPC5
FOXO1
GAS6
GPR18
MLNR
GTF2F2
GUCY1B2
HTR2A
ING1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
NEK3
PCCA
PCDH8
PCDH9
POU4F1
DNAJC3
RAP2A
RFXAP
GRK1
ATXN8OS
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
UCHL3
ZIC2
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
DCLK1
ITGBL1
TM9SF2
ITM2B
MTRF1
UTP14C
TBC1D4
GPC6
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
MRPS31
SPRY2
ABCC4
DLEU1
TUBGCP3
PIBF1
OLFM4
POSTN
TNFSF13B
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
FBXL3
INTS6
CKAP2
OR7E37P
NUFIP1
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
NDFIP2
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
NUDT15
KIAA1704
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
THSD1
CYSLTR2
C13orf1
COG6
KLHL1
RBM26
PCDH20
UPF3A
KDELC1
CARS2
RNF219
NARG1L
RNASEH2B
DHRS12
GRTP1
C13orf34
C13orf18
C13orf23
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
SLITRK6
EBPL
TMTC4
ABHD13
ZIC5
A2LD1
KBTBD6
C13orf27
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
C13orf16
LOC121838
LOC121952
CSNK1A1L
SLAIN1
PRR20A
C13orf28
RNF113B
LOC144776
C13orf30
C13orf31
HNRNPA1L2
FAM10A4
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
C13orf39
FAM194B
SPERT
DLEU7
FAM124A
LOC220115
LOC220429
SLC25A30
NALCN
HS6ST3
DAOA
C13orf29
ZNF828
OR7E156P
SUGT1L1
SIAH3
KCNRG
FLJ37307
UBAC2
FREM2
NEK5
FAM70B
THSD1P
KCTD4
NHLRC3
SERP2
C13orf36
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ALG11
C13orf37
FLJ44054
LOC643677
LOC646982
SERPINE3
LOC647288
SNORA31
MIR548A2
MIR621
MIR623
FAM155A
C13orf38
PRR20B
PRR20C
PRR20D
PRR20E
FKSG29
LOC100190939

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.1.

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

Genes
ABL2
ARNT
BCL9
CDKN2C
ELK4
EPS15
FCGR2B
FH
JAK1
JUN
LCK
MDM4
MPL
MUC1
MUTYH
MYCL1
NOTCH2
NRAS
NTRK1
PAX7
PBX1
PRCC
RPL22
SDHB
SDHC
SFPQ
TAL1
TPM3
TPR
ARID1A
TNFRSF14
BCL10
PDE4DIP
THRAP3
TRIM33
PRDM16
RBM15
SLC45A3
MDS2
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-190b
hsa-mir-554
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-101-1
hsa-mir-30c-1
hsa-mir-552
hsa-mir-1976
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
ABCA4
ACADM
ACTA1
ACTN2
ADAR
ADORA1
ADORA3
PARP1
ADSS
AGL
AGT
AK2
AK3L1
ALDH9A1
ALPL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
ARF1
RHOC
ASTN1
SERPINC1
ATF3
RERE
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
ATP5F1
ATP6V0B
AVPR1B
BAI2
BGLAP
BMP8B
BRDT
C1QA
C1QB
C1QC
C4BPA
C4BPB
C8A
C8B
CA6
CACNA1E
CACNA1S
CAPN2
CAPZA1
CAPZB
CASP9
CASQ1
CASQ2
RUNX3
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
TNFRSF8
CD34
CD48
CD53
CD58
CDA
CDC2L1
CDC20
CDC42
CD52
CENPF
RCC1
CHI3L1
CHI3L2
CHIT1
CHML
LYST
CHRM3
CHRNB2
CKS1B
CLCA1
CLCN6
CLCNKA
CLCNKB
CLK2
PLK3
CNN3
CNR2
COL8A2
COL9A2
COL11A1
COL16A1
COPA
CORT
CPT2
CR1
CR1L
CR2
CRABP2
CRP
CRYZ
CSF1
CSF3R
CSRP1
CTBS
CTH
CTPS
CTSE
CTSK
CTSS
CYP2J2
CYP4A11
CYP4B1
DAB1
CD55
DBT
GADD45A
DDOST
DHX9
DFFA
DFFB
DHCR24
DIO1
DPH2
DPT
DPYD
DR1
DVL1
E2F2
ECE1
ECM1
S1PR1
EDN2
PHC2
LGTN
EFNA1
EFNA3
EFNA4
CELSR2
MEGF6
EPHA2
ELAVL4
ELF3
ENO1
ENSA
EPB41
EPHA8
EPHB2
EPHX1
EPRS
ESRRG
ETV3
EXTL1
EXTL2
EYA3
F3
F5
F13B
FAAH
FABP3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FGR
FHL3
FOXE3
FOXD2
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
MTOR
NR5A2
FUCA1
DARC
IFI6
GABRD
GALE
GALNT2
GBA
GBAP
GBP1
GBP2
GBP3
GFI1
GJA4
GJA5
GJA8
GJB3
GJB5
GCLM
GLUL
GNAI3
GNAT2
GNB1
GNG4
GNG5
SFN
GPR3
GPR25
GPX7
GRIK3
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
GUCA2A
GUCA2B
GUK1
H3F3A
HCRTR1
HDAC1
HDGF
CFH
CFHR1
CFHR2
ZBTB48
MR1
HLX
HMGN2
HMGCL
HMGCS2
HNRNPU
HPCA
HSD3B1
HSD3B2
HSD11B1
HSPA6
HSPA7
IGSF3
HSPG2
HTR1D
HTR6
ID3
IFI16
CYR61
IL6R
IL10
IL12RB2
TNFRSF9
ILF2
INPP5B
INSRR
IPP
IRF6
ITPKB
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNH1
KCNJ9
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
STMN1
LBR
LEPR
LGALS8
LMNA
LMX1A
LOR
LY9
TACSTD2
MAGOH
MARK1
MATN1
MCL1
CD46
SMCP
MEF2D
MFAP2
MGST3
MNDA
MOV10
MPZ
MSH4
MTF1
MTHFR
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NASP
NBL1
NCF2
NDUFS2
NDUFS5
NEK2
NFIA
NFYC
NGF
NHLH1
NHLH2
NID1
NIT1
NPPA
NPPB
NPR1
NRD1
YBX1
ROR1
DDR2
NVL
OPRD1
ORC1L
OVGP1
PAFAH2
PRDX1
PCTK3
PDC
PDE4B
PDZK1
PEX10
PEX14
PFDN2
PFKFB2
PGD
PGM1
PIGC
PIGR
PIK3C2B
PIK3CD
PI4KB
PIN1L
PKLR
PKP1
PLA2G2A
PLA2G4A
PLA2G5
PLOD1
PLXNA2
EXOSC10
PRRX1
POU2F1
POU3F1
PPOX
PPP1R8
PPP2R5A
PPT1
PRELP
PRKAA2
PRKAB2
PRKACB
PKN2
PRKCZ
PROX1
PSEN2
PSMA5
PSMB2
PSMB4
PSMD4
PTAFR
PTGER3
PTGFR
PTGFRN
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PTPRF
PEX19
ABCD3
RAB3B
RAB4A
RAB13
RABGGTB
RABIF
RAP1A
RAP1GAP
RBBP4
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RHCE
RHD
RIT1
RLF
RNASEL
RNF2
RNPEP
SNORD21
RORC
RPA2
RPE65
RPL5
RPL11
RPS6KA1
RPS8
RPS27
RSC1A1
RXRG
RYR2
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
SCNN1D
SCP2
XCL1
SELE
SELL
SELP
SFRS4
SHC1
ST3GAL3
STIL
SKI
SLAMF1
SLC1A7
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SLC16A1
SNRPE
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRM
SRP9
TROVE2
SSR2
AURKAPS1
STXBP3
XCL2
SYCP1
TAF12
TAF13
TARBP1
CNTN2
TBCE
TBX15
TCEA3
TCEB3
VPS72
TGFB2
LEFTY2
TGFBR3
THBS3
TCHH
TIE1
TLR5
GPR137B
TNFRSF1B
TNNI1
TNNT2
TNR
TOP1P1
TP53BP2
TP73
TRAF5
CCT3
TSHB
TSNAX
TTC4
TUFT1
TNFSF4
TNFRSF4
UCK2
UQCRH
UROD
USF1
USP1
USH2A
VCAM1
WNT2B
WNT9A
ZSCAN20
ZNF124
ZBTB17
SLC30A1
SLC30A2
LUZP1
PRDM2
DNALI1
LRP8
LAPTM5
BSND
CSDE1
EVI5
DAP3
NPHS2
BTG2
PTP4A2
HIST3H3
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
SNHG3
NR0B2
RAD54L
GNPAT
DYRK3
TTF2
CDC42BPA
RGS5
PPFIA4
PIK3R3
MMP23B
MMP23A
KCNAB2
ITGA10
LMO4
FCN3
BLZF1
CDC14A
DEGS1
KMO
YARS
MKNK1
AKR7A2
PPAP2B
RTCD1
PTCH2
ALDH4A1
EIF3I
EIF4G3
VAMP4
PEA15
B4GALT3
B4GALT2
B3GALT2
TNFRSF25
ADAM15
PABPC4
TNFRSF18
FPGT
PEX11B
CREG1
CD84
PER3
FUBP1
EIF2B3
RAB7L1
SELENBP1
TNFSF18
TAF1A
MPZL1
SH2D2A
ARTN
MAP3K6
ANGPTL1
DIRAS3
TBX19
FCGR2C
SLC16A4
PRPF3
KCNQ4
EXO1
ARHGEF2
DEDD
ZMYM4
ZMYM6
XPR1
FAIM3
DHRS3
MAPKAPK2
GPR37L1
GPR52
SFRS11
VAMP3
ZFYVE9
CD101
SEP15
ZRANB2
SNRNP40
ARHGAP29
AIM2
GGPS1
RASAL2
C1orf38
ADAMTS4
TMEM59
SEC22B
CHD1L
H6PD
SOX13
PRDX6
CLCA3P
CLCA2
ISG15
IKBKE
PLCH2
HS2ST1
IPO13
SDC3
SLC25A44
KIAA0040
KDM4A
CROCC
PUM1
NOS1AP
TMEM63A
KIAA0562
RIMS3
TOMM20
KIAA0494
URB2
ARHGEF11
DNAJC6
CEP350
CEP170
LRIG2
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
KLHL21
SLC35E2
DENND4B
RABGAP1L
TMCC2
FAM20B
ZBTB40
LPGAT1
MFN2
KIF14
RBM8A
NR1I3
AKT3
INSL5
PIGK
SCAMP3
PTPRU
ARPC5
TSPAN2
TSPAN1
CELA3A
PDZK1IP1
WASF2
INADL
PRG4
ANGPTL7
GPA33
STX6
HNRNPR
SRRM1
CNKSR1
SF3B4
ZMPSTE24
UBE4B
BCAS2
AKR1A1
WARS2
BPNT1
CEPT1
PIAS3
TESK2
TIMM17A
LRRN2
PPIE
VAV3
HAX1
MAD2L2
PPIH
ZNF238
C1orf61
CAP1
LRRC41
SEMA6C
HBXIP
SLC19A2
IFI44
POLR3C
IVNS1ABP
TXNIP
PDPN
LEFTY1
SPHAR
PMVK
KHDRBS1
GMEB1
FAM189B
AP4B1
NUDC
PHTF1
MASP2
CAPN9
NES
KDM5B
AHCYL1
SFRS13A
SDCCAG8
CFHR4
CFHR3
WDR3
OCLM
JTB
MTMR11
MAN1A2
UTS2
SF3A3
MLLT11
IFI44L
EBNA1BP2
SLC27A3
KIF2C
IL24
TDRKH
RER1
DNAJB4
ADAM30
RCAN3
FAF1
CD160
GLMN
HHLA3
TNRC4
MSTP2
DDX20
DUSP10
MSTP9
PADI2
PMF1
DUSP12
VPS45
LYPLA2
PARK7
CTRC
ACOT7
COG2
CLCA4
MTF2
DNAJC8
NTNG1
PLEKHA6
CLSTN1
FOXJ3
KIAA0907
WDR47
KIFAP3
ATF6
SCMH1
AKR7A3
TTC39A
SPEN
KDM1A
RBM34
USP33
WDTC1
KIF21B
NMNAT2
KIAA0090
KIF1B
NFASC
POGZ
GLT25D2
MAST2
NCDN
CLCC1
SLC35D1
RGL1
PLEKHM2
SYT11
BAT2D1
FBXO28
RPRD2
OTUD3
KIAA1026
CAMTA1
LPHN2
CAMSAP1L1
KIAA1107
ZCCHC11
KIAA0467
DNAJC16
UBR4
USP24
SRGAP2
SMG5
NCSTN
ATP13A2
CRB1
ITGB3BP
GPR161
TARDBP
CELA3B
SLC35A3
ABCB10
ICMT
MACF1
LRRC8B
ZNF281
SNAPIN
LPAR3
PADI4
DDAH1
TMEM50A
OPN3
PHLDA3
RUSC1
CA14
KPNA6
SSBP3
STX12
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
BRP44
TRIM58
INTS7
OLFML2B
AHCTF1
C1orf43
CLIC4
NSL1
SYF2
RWDD3
PARS2
MMACHC
ZZZ3
ACOT11
CHD5
DNM3
TOR1AIP1
C1orf77
C1orf144
LDLRAP1
SERBP1
NOC2L
OR1C1
PTPN22
PHGDH
FBXO2
LCE2B
OR2M4
OR2L2
OR2L1P
OPTC
FBXO6
PLA2G2D
AK5
MYCBP
OR10J1
HEYL
EIF2C1
OR4F3
OR2T1
RPS6KC1
SNORD81
SNORD79
SNORD80
SNORA66
SNORD47
SNORD45B
SNORD45A
SNORD44
SNORD55
RNU11
RNF11
USP21
FOXD3
C1orf107
TRAPPC3
TAF5L
CACYBP
HSPB7
CHIA
SLC39A1
DISC2
DISC1
ARHGEF16
AHDC1
RNF115
KLHL20
TEKT2
SMPDL3B
ANGPTL3
ROBLD3
FLVCR1
PRO0611
UBE2T
HSPC157
CNIH4
SSU72
TMOD4
GNL2
GPSM2
UBIAD1
PYCR2
NME7
ALG6
NENF
PADI1
IL19
LASS2
SLC25A24
PLA2G2E
DNTTIP2
WDR8
CRNN
G0S2
IL20
SLC45A1
DCAF8
HP1BP3
F11R
TMED5
RRP15
GLRX2
BOLA1
PPPDE1
CELA2B
ZNF593
ZBTB7B
ZNF691
TXNDC12
TNNI3K
C1orf66
ADIPOR1
SCCPDH
SH3GLB1
MECR
APH1A
UTP11L
TRIM17
KCTD3
SDF4
MRTO4
PLEKHO1
HAO2
ACP6
TMEM69
MRPL37
IER5
HOOK1
SNX7
UCHL5
C1orf9
HPCAL4
YTHDF2
GPR89B
HSD17B7
UFC1
DTL
ZCCHC17
METTL13
DPH5
HSPB11
OAZ3
PADI3
CYB5R1
CMPK1
ARID4B
CD244
GPR88
ERRFI1
DPM3
WNT4
YIPF1
FBXO42
MRPS21
CCDC76
TMCO1
ADAMTSL4
CRCT1
RNF186
SPATA6
EGLN1
MXRA8
L1TD1
HES2
KIAA1383
RSBN1
ZNHIT6
GPN2
LEPROT
FBLIM1
MED18
TRIT1
GIPC2
C1orf26
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
PQLC2
CASZ1
LAX1
RHBDL2
DUSP23
ADPRHL2
TRNAU1AP
C1orf27
C1orf109
C1orf56
CPSF3L
C1orf123
C1orf159
MOSC2
AURKAIP1
TTC22
MRPL20
AIM1L
SUSD4
KIF26B
TMEM51
RALGPS2
GPATCH2
BSDC1
XKR8
TMEM39B
PRPF38B
HEATR1
CDCA8
LRRC8D
MSTO1
DARS2
ARHGEF10L
PRMT6
RNF220
VPS13D
FAM176B
GOLPH3L
ATAD3A
TMEM57
KLHDC8A
TRIM62
ETNK2
RAVER2
PANK4
KIRREL
TMEM206
YY1AP1
ECHDC2
FGGY
MCOLN3
SLC22A15
YOD1
CAMK2N1
BATF3
SLC30A10
UBE2Q1
RNPC3
ITLN1
ASAP3
POMGNT1
PNRC2
LRRC40
DEPDC1
PIGV
ZNF692
NBPF1
IARS2
MAP7D1
IPO9
TMEM48
NECAP2
IQCC
C1orf112
HHAT
DNAJC11
ENAH
NUP133
RCOR3
C1orf106
C1orf103
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
RCC2
C1orf183
DMAP1
AJAP1
GNG12
RAG1AP1
C1orf91
FAM54B
SERTAD4
CCBL2
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
TMEM167B
OLFML3
SMYD2
LHX9
OTUD7B
CABC1
CTNNBIP1
C1orf63
AGTRAP
C1orf128
RAB25
PGLYRP4
ZNF695
RHBG
MAN1C1
SCYL3
GJC2
CAMK1G
NIPAL3
SEPN1
ATP8B2
KIAA0495
VANGL2
PBXIP1
S100A14
PLEKHG5
GATAD2B
AMIGO1
LRRC47
ODF2L
CGN
KIAA1324
PTCHD2
IGSF9
LRRC7
SIPA1L2
KIF17
ZNF687
ZSWIM5
POGK
KIAA1522
HCN3
CACHD1
MIER1
KIAA1614
FAM5B
HES4
C1orf114
GRHL3
SLAMF7
ZP4
CADM3
PTBP2
RHOU
PRUNE
DNASE2B
DLGAP3
IL22RA1
HIVEP3
KLHL12
LGR6
GPBP1L1
HAPLN2
MIIP
GAS5
PAPPA2
CELA2A
BCAN
GPATCH3
TNN
MRPS14
DMRTB1
DMRTA2
CLSPN
OXCT2
RRAGC
ELTD1
TINAGL1
SPATA1
LEPRE1
TFB2M
SEMA4A
TOR3A
RFWD2
GREM2
RGS18
PLA2G2F
HIAT1
NUCKS1
SMAP2
ACBD3
SMYD3
ATPAF1
MOSC1
S100PBP
MEAF6
DEM1
CCDC21
ARV1
NMNAT1
ELOVL1
AIDA
VWA1
DCLRE1B
MRPS15
MRPL9
PINK1
JMJD4
MARCKSL1
PRAMEF1
PRAMEF2
INTS3
NADK
ZNF643
C1orf163
PHACTR4
C1orf135
SCNM1
ERI3
C1orf50
WDR77
C1orf116
MGC4473
CCDC28B
C1orf35
EFHD2
MMEL1
C1orf89
FCRL2
DLEU2L
OR4F5
NKAIN1
TTC13
EPS8L3
CDC73
MRPL24
MUL1
PGBD5
TNFAIP8L2
C1orf54
TMEM53
AKIRIN1
HECTD3
BEND5
VTCN1
YRDC
ZYG11B
NOL9
PPCS
LIN28
C1orf113
TTLL7
SNIP1
C1orf115
HHIPL2
VASH2
AGMAT
WDR78
ZMYM1
NCRNA00115
ZNF669
RPAP2
ZNF672
MORN1
GRRP1
KIAA0319L
DHDDS
PAQR6
DENND2D
GPR177
PCNXL2
GPR157
TRIM46
C1orf129
RPF1
SIKE1
ZC3H12A
SPSB1
TARS2
WDR26
TRIM45
EDEM3
FLAD1
TRAF3IP3
GLTPD1
ZNF436
TAS1R2
TAS1R1
SH3BP5L
NPL
GJA9
OR4F16
OR6N2
OR6K2
OR2G3
OR2G2
OR2C3
SYNC
CFHR5
TRIM11
C1orf21
ACTL8
ANKRD13C
PVRL4
SNX27
ANP32E
C1orf14
C1orf25
TSSK3
CCNL2
NUAK2
VANGL1
ST6GALNAC5
ISG20L2
HYI
FCRL5
FCRL4
SH3BGRL3
DDX59
NUF2
RASSF5
SESN2
ESPN
TAS1R3
ATAD3B
HMCN1
GPR61
MIXL1
STK40
C1orf124
TM2D1
FCAMR
REG4
OBSCN
TMEM222
C1orf49
PLEKHN1
HORMAD1
TOMM40L
SYDE2
ZNF644
USP48
ZMYND12
NBPF3
LRRC8C
ZDHHC18
SGIP1
POLR3GL
SLC25A33
TMEM79
C1orf57
EFCAB2
DDI2
ACBD6
LZIC
PROK1
KIAA1804
EFCAB7
ZBTB37
NT5C1A
LCE3D
TRIM63
PSRC1
FAM167B
C1orf97
MGC12982
C1orf170
CROCCL1
FCRLA
ANKRD36BL1
ZNF496
HPDL
C1orf203
AGBL4
MFSD2A
C1orf198
PPP1R15B
ATG4C
MAEL
PRPF38A
SYTL1
IGSF21
LSM10
C1orf94
DISP1
SNHG12
FAM40A
RGS8
DOCK7
KIAA1751
WNT3A
NAV1
SEC16B
AQP10
LHX4
SLAMF9
KIAA2013
THAP3
C1orf201
PYGO2
ANGEL2
SPOCD1
ZNF697
IGFN1
NUP210L
BTF3L4
UBXN11
NEXN
CENPL
DUSP27
RCSD1
MEX3A
C1orf156
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
C1orf158
LEMD1
ZNF670
FBXO44
ATPIF1
SNORD46
SNORD38A
SNORD38B
C1orf85
MED8
KTI12
C1orf212
ADC
TMEM54
C1orf59
TOE1
NLRP3
ERMAP
PGLYRP3
CSMD2
MYSM1
GNRHR2
CROCCL2
FHAD1
SLAMF6
OSBPL9
SLC26A9
LOC115110
OMA1
RAB42
FCRL1
FCRL3
LRRC42
GBP4
GBP5
FAM46B
FMO9P
FAM36A
RBP7
TSEN15
FAM129A
SNAP47
ACAP3
TADA1
THEM4
SH2D1B
SSX2IP
UBE2J2
OLFM3
GABPB2
TCHHL1
RPTN
C1orf231
TDRD10
SHE
C1orf172
C1orf96
AADACL3
PUSL1
B3GALT6
WDR63
KLHDC9
C1orf125
C1orf161
IFFO2
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
ASB17
TYW3
C1orf173
LRRIQ3
TPRG1L
C1orf93
MYOM3
DMBX1
OR10J5
TMCO2
ZNF684
C1orf83
PODN
LRRC39
GJB4
HMGB4
RNF19B
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
UBXN10
C1orf87
ARL8A
SYT2
LOC127841
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
SPATA17
EDARADD
KLF17
TMEM125
C1orf182
IQGAP3
APOA1BP
ARHGEF19
MRPL55
HIST3H2BB
DRAM2
C1orf88
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ACTRT2
MIB2
ITLN2
SYT6
C1orf74
CREB3L4
C1orf127
C1orf58
SAMD11
LOC148413
SAMD13
C1orf52
PHF13
C1orf51
TMEM56
NBPF4
UBE2U
SLC35F3
LOC148696
LOC148709
PTPRV
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
SLC30A7
CCDC27
C1orf213
KNCN
MOBKL2C
GLIS1
LELP1
RC3H1
MGC27382
DCDC2B
ZNF362
DCST1
CNIH3
LOC149134
MANEAL
IL23R
METTL11B
FAM78B
SHISA4
EXOC8
PDIK1L
BNIPL
CLDN19
WDR65
C1orf210
C1orf84
CCDC24
BTBD19
CCDC17
C1orf92
C1orf64
RNF187
LOC149620
PYHIN1
C1orf227
FAM71A
SLC2A7
DENND2C
GBP6
LPPR5
FNDC7
DENND1B
TDRD5
TOR1AIP2
CALML6
IL28RA
CYP4Z2P
CITED4
FLJ40434
C1orf177
SPRR4
KANK4
SASS6
C1orf55
CNST
FAM43B
PPIAL4A
HFM1
PAQR7
TTC24
C1orf65
UBL4B
PDIA3P
EIF2C3
EIF2C4
LCE4A
ALG14
FAM76A
C1orf168
TMEM201
TMEM61
CYP4Z1
C1orf86
CDCP2
SLC5A9
CC2D1B
LOC200030
NUDT17
FLJ23867
TXLNA
TCTEX1D1
PLD5
C1orf100
SPAG17
SLFNL1
KRTCAP2
CRTC2
C1orf126
C1orf69
HIPK1
SLC44A5
ATAD3C
AKR7L
AFARP1
TMEM9
FNDC5
EPHX4
TTLL10
AKNAD1
SLC41A1
OR2T6
LCE5A
TMCO4
MCOLN2
COL24A1
PCSK9
SYT14
ST6GALNAC3
C1orf101
ZNF683
ARHGAP30
C1orf192
NEGR1
ASPM
CYP4X1
MAGI3
TIPRL
NPHP4
BEST4
PGBD2
FAM19A3
C1orf230
THEM5
OR2L13
SLC9A11
OR14A16
CYP4A22
C1orf185
LOC284551
NBPF15
C1orf157
LOC284578
FAM41C
FAM102B
SYPL2
CYB561D1
ANKRD34A
C1orf104
LOC284632
RSPO1
EPHA10
LOC284661
C1orf204
C1orf111
LOC284688
ZNF326
BTBD8
NCRNA00201
RIMKLA
SLC25A34
ESPNP
LIN9
VN1R5
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BA
FAM151A
S100A7A
LINGO4
RXFP4
ANKRD45
C1orf174
KLHL17
C1orf70
TMEM52
FAM5C
MTMR9L
ZBTB8OS
TFAP2E
ZNF678
PRSS38
C1orf110
FAM58B
LOC339524
LOC339535
C1orf228
ZNF642
RD3
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
CCDC18
OR6F1
OR2W3
OR2T8
OR2T3
MYBPHL
OR10R2
FCRL6
KCNT2
BARHL2
HSP90B3P
NBPF7
TCTEX1D4
OR2T29
SERINC2
FAM159A
FAM131C
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
PADI6
RGSL1
BMP8A
IRF2BP2
ZBTB41
CYCSP52
C1orf187
SPATA21
CCDC23
C1orf223
C1orf175
FAM73A
PEAR1
SFT2D2
MIA3
C1orf95
FAM89A
AGRN
RPS10P7
APITD1
CATSPER4
NSUN4
GPR153
ILDR2
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
LDLRAD1
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
FMO6P
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
SKINTL
UOX
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
LOC400752
C1orf141
LOC400759
C1orf226
LOC400794
C1orf220
LOC400804
NBPF20
FAM177B
PRAMEF3
LDLRAD2
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR101-1
MIR137
MIR181B1
MIR186
MIR194-1
MIR197
MIR199A2
MIR200A
MIR200B
MIR205
MIR181A1
MIR214
MIR215
MIR29B2
MIR29C
MIR30C1
MIR30E
MIR34A
MIR9-1
RGS21
LHX8
C1orf180
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
FAM183A
ZYG11A
BCL2L15
HIST2H2BF
ETV3L
LRRC52
C1orf186
TRIM67
MAP1LC3C
LOC440926
LOC441869
PRAMEF7
LOC441897
OR10J3
OR2W5
OR13G1
MIR135B
KPRP
LCE6A
SUMO1P3
LOC492303
RBMXL1
C1orf190
PEF1
MIR429
HIST2H4B
DUSP5P
C1orf133
MIR488
CYB5RL
SNORD74
RPL31P11
FAM138F
LOC642502
LOC642587
LQK1
CYMP
KIAA0754
LOC643837
TMEM88B
PPIAL4G
C1orf200
PPIAL4D
LOC645166
PRAMEF19
PRAMEF20
FAM138A
LOC645676
S100A7L2
LOC646471
LOC646627
LOC647121
LOC648740
LOC649330
ZBTB8A
NBPF6
PPIAL4B
GPR89A
LOC653566
PPIAL4C
HIST2H3D
PRAMEF22
PRAMEF15
WASH5P
TMEM183B
FAM72B
PRAMEF16
PCP4L1
FAM138C
SCARNA3
SCARNA2
SCARNA4
SCARNA1
SNORA14B
SNORA36B
SNORA42
SNORA44
SNORA55
SNORA61
SNORA77
SNORA59B
SNORA59A
SNORA16A
SNORD45C
SNORA16B
SNORD75
SNORD76
SNORD77
SNORD78
SNORD85
SNORD99
SNORD103A
MIR551A
MIR553
MIR554
MIR555
MIR556
MIR557
MIR92B
HIST2H2AA4
ZBTB8B
LOC728448
CCDC30
CDC2L2
LOC728661
LOC728855
LOC728875
NBPF11
GPR89C
NBPF16
PDZK1P1
PPIAL4F
RPS15AP10
LOC728989
LOC729467
PRAMEF14
FAM72A
FLJ37453
OR4F29
PPIAL4E
LOC731275
SNHG3-RCC1
C1orf152
MIR765
MIR942
MIR190B
MIR760
MIR921
LOC100128003
LOC100128071
LOC100128842
C1orf68
MSTO2P
LOC100129534
LOC100130093
LOC100130331
FLJ39609
LOC100130557
TSTD1
LOC100132062
LOC100132111
LOC100132287
NBPF10
FCGR1C
LOC100133331
LOC100133612
C2CD4D
LOC100286793
LOC100288778
LOC100302401
TSNAX-DISC1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 21 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.05 | -0.156 | 1 | 0.09 | 1.74 | 0.161
1q | 1572 | 0.14 | 3.7 | 0.000469 | 0.01 | -2.31 | 1
2p | 753 | 0.05 | -1.77 | 1 | 0.01 | -3.43 | 1
2q | 1235 | 0.04 | -1.64 | 1 | 0.02 | -2.58 | 1
3p | 853 | 0.05 | -1.73 | 1 | 0.08 | -0.6 | 1
3q | 917 | 0.09 | 0.0983 | 1 | 0.04 | -1.91 | 1
4p | 366 | 0.01 | -3.55 | 1 | 0.17 | 1.75 | 0.161
4q | 865 | 0.00 | -3.43 | 1 | 0.14 | 1.94 | 0.145
5p | 207 | 0.18 | 1.84 | 0.127 | 0.10 | -0.827 | 1
5q | 1246 | 0.03 | -2.01 | 1 | 0.14 | 2.72 | 0.0258
6p | 937 | 0.05 | -1.56 | 1 | 0.10 | 0.165 | 0.892
6q | 692 | 0.05 | -2 | 1 | 0.06 | -1.45 | 1
7p | 508 | 0.28 | 6.26 | 1.25e-09 | 0.02 | -2.8 | 1
7q | 1071 | 0.26 | 7.21 | 2.16e-12 | 0.07 | -0.495 | 1
8p | 495 | 0.35 | 7.74 | 4.65e-14 | 0.23 | 3.74 | 0.00181
8q | 697 | 0.45 | 12.6 | 0 | 0.12 | 0.414 | 0.735
9p | 343 | 0.09 | -0.834 | 1 | 0.20 | 2.9 | 0.018
9q | 916 | 0.08 | -0.565 | 1 | 0.12 | 1.15 | 0.349
10p | 312 | 0.15 | 1.13 | 0.417 | 0.08 | -1.35 | 1
10q | 1050 | 0.06 | -0.838 | 1 | 0.06 | -0.838 | 1
11p | 731 | 0.07 | -1.17 | 1 | 0.12 | 0.741 | 0.526
11q | 1279 | 0.06 | -0.629 | 1 | 0.11 | 1.6 | 0.166
12p | 484 | 0.12 | 0.286 | 1 | 0.07 | -1.52 | 1
12q | 1162 | 0.10 | 1.01 | 0.467 | 0.07 | -0.52 | 1
13q | 554 | 0.22 | 3.82 | 0.000332 | 0.07 | -1.4 | 1
14q | 1144 | 0.03 | -2.01 | 1 | 0.05 | -1.09 | 1
15q | 1132 | 0.02 | -2.32 | 1 | 0.07 | -0.491 | 1
16p | 719 | 0.09 | -0.5 | 1 | 0.06 | -1.59 | 1
16q | 562 | 0.05 | -2.1 | 1 | 0.09 | -0.784 | 1
17p | 575 | 0.07 | -1.32 | 1 | 0.23 | 4.44 | 0.000173
17q | 1321 | 0.09 | 0.781 | 0.606 | 0.09 | 0.781 | 0.526
18p | 117 | 0.10 | -0.95 | 1 | 0.18 | 1.68 | 0.166
18q | 340 | 0.05 | -2.25 | 1 | 0.22 | 3.5 | 0.00308
19p | 870 | 0.14 | 1.61 | 0.19 | 0.14 | 1.61 | 0.166
19q | 1452 | 0.17 | 4.43 | 2.66e-05 | 0.11 | 1.74 | 0.161
20p | 295 | 0.42 | 10.3 | 0 | 0.09 | -0.905 | 1
20q | 627 | 0.52 | 15.4 | 0 | 0.02 | -2.35 | 1
21q | 422 | 0.00 | -3.74 | 1 | 0.19 | 2.64 | 0.0268
22q | 764 | 0.03 | -2.34 | 1 | 0.12 | 0.971 | 0.431

Methods & Data
Input

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/STAD/1216965/2.GDAC_MergeDataFiles.Finished/STAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

- Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

- CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt

- Amplification Threshold = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 132 Input Tumor Samples.

Tumor Sample Names
TCGA-B7-5816-01A-21D-1599-01
TCGA-B7-5818-01A-11D-1599-01
TCGA-BR-4183-01A-02D-1130-01
TCGA-BR-4184-01A-01D-1130-01
TCGA-BR-4187-01A-01D-1130-01
TCGA-BR-4188-01A-01D-1130-01
TCGA-BR-4190-01A-01D-1130-01
TCGA-BR-4191-01A-02D-1130-01
TCGA-BR-4194-01A-02D-1130-01
TCGA-BR-4195-01A-01D-1130-01

Figure 3. Segmented copy number profiles in the input data

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
Meta

- Maintainer = Dan DiCara

Copyright © 2011 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
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