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 2.0.15 (cga svn revision 32817).

Summary

There were 136 tumor samples used in this analysis: 20 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 | 8.1576e-18 | 8.1576e-18 | chr17:35058337-35159695 | 7
19q12 | 1.8283e-15 | 1.8283e-15 | chr19:34875012-35091997 | 2
12p12.1 | 2.0185e-11 | 2.0185e-11 | chr12:25240084-25405863 | 2
12q15 | 1.6137e-10 | 1.6137e-10 | chr12:66890102-68262466 | 13
7q21.2 | 2.0675e-10 | 7.5884e-10 | chr7:91993046-92395934 | 5
8p23.1 | 1.3349e-08 | 1.3349e-08 | chr8:11585200-11830754 | 4
8q24.21 | 4.7538e-08 | 1.2965e-06 | chr8:128215233-128670383 | 2
20q13.2 | 1.5586e-06 | 1.5586e-06 | chr20:51356899-52100291 | 4
10q26.13 | 3.1481e-06 | 3.1481e-06 | chr10:123230278-123389836 | 1
7p11.2 | 6.7937e-06 | 6.7937e-06 | chr7:55044034-55507625 | 3
6p21.1 | 0.00015773 | 0.00015773 | chr6:43701946-43788316 | 4
18q11.2 | 0.00038565 | 0.00038565 | chr18:17732023-18152003 | 1
1q42.3 | 0.00040793 | 0.00040793 | chr1:232974712-233190000 | 0 [TOMM20]
11q13.2 | 0.0015891 | 0.0015891 | chr11:68238807-70026660 | 19
13q22.1 | 0.0071403 | 0.0071403 | chr13:72562649-72815854 | 0 [KLF5]
15q26.1 | 0.023274 | 0.023274 | chr15:87481512-92176114 | 47
1p36.22 | 0.043673 | 0.043673 | chr1:10591686-11040730 | 6
11p13 | 0.075716 | 0.075716 | chr11:34391504-35616010 | 9
9p24.1 | 0.084594 | 0.098579 | chr9:4754022-5596715 | 11
3q26.2 | 0.10771 | 0.10771 | chr3:158738746-199501827 | 239
9p13.3 | 0.097233 | 0.14135 | chr9:32129737-37751043 | 98
7q31.2 | 0.014787 | 0.14222 | chr7:116025877-117087494 | 10
8q21.11 | 0.0083825 | 0.15373 | chr8:77316321-77670309 | 0 [LOC100192378]

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 12p12.1.

Table S3. 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 12q15.

Table S4. 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 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 8q24.21.

Table S7. 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 20q13.2.

Table S8. 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 S9. 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 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 9p13.3.

Table S19. 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

Genes in Wide Peak

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

Table S20. 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

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 | 1.9873e-86 | 1.9873e-86 | chr3:59009803-61522370 | 1
16q23.1 | 4.5261e-35 | 4.5261e-35 | chr16:76686559-78185271 | 1
20p12.1 | 1.1311e-14 | 1.1311e-14 | chr20:14250876-15984135 | 2
5q11.2 | 4.3117e-14 | 4.3117e-14 | chr5:58296055-59823742 | 3
9p21.3 | 2.4053e-18 | 8.9232e-13 | chr9:21855498-21987722 | 2
9p24.1 | 8.4437e-15 | 1.2081e-12 | chr9:7786330-12683402 | 2
6q26 | 6.395e-12 | 6.395e-12 | chr6:161613089-163073197 | 1
6p25.3 | 3.5248e-10 | 3.5248e-10 | chr6:1553836-2569051 | 2
4q22.1 | 1.3535e-10 | 1.4944e-09 | chr4:91367303-93459528 | 2
1p36.11 | 4.6608e-06 | 4.6608e-06 | chr1:26773226-27306046 | 11
7q31.1 | 3.8547e-06 | 6.16e-06 | chr7:110512908-111163100 | 1
3q26.31 | 2.9392e-05 | 2.9392e-05 | chr3:175482500-178221491 | 1
4q35.1 | 2.2379e-10 | 0.00029063 | chr4:179148868-186527695 | 24
22q13.31 | 0.0021564 | 0.0021734 | chr22:44619793-49691432 | 62
10q23.31 | 0.0021734 | 0.0058784 | chr10:89302988-90024018 | 5
15q21.3 | 0.012829 | 0.012663 | chr15:54995064-55370592 | 1
2q37.2 | 0.0043408 | 0.015023 | chr2:235626319-237660719 | 5
19p13.3 | 0.015214 | 0.015023 | chr19:1-9438458 | 283
21q22.3 | 0.018043 | 0.017235 | chr21:37560448-46944323 | 118
2q33.2 | 0.0021564 | 0.019611 | chr2:204534470-206266883 | 1
18q21.2 | 0.0093388 | 0.023213 | chr18:46604315-48124308 | 4
1q44 | 0.004423 | 0.025066 | chr1:243931413-244771113 | 1
2q32.1 | 0.0067918 | 0.025066 | chr2:185509151-187268840 | 2
7q36.3 | 0.010527 | 0.062016 | chr7:156902368-158821424 | 10
4q35.2 | 2.733e-08 | 0.090017 | chr4:169652719-191273063 | 80
14q21.3 | 0.059588 | 0.090017 | chr14:44648919-44677557 | 2
11p15.5 | 0.098416 | 0.098867 | chr11:1-11267794 | 261
13q33.1 | 0.15868 | 0.16627 | chr13:78339687-114142980 | 109
10q22.2 | 0.051225 | 0.19754 | chr10:75564411-78299547 | 11
14q32.32 | 0.1276 | 0.19754 | chr14:85064045-106368585 | 266
1q44 | 0.069049 | 0.20683 | chr1:243348890-243980330 | 1
18q12.2 | 0.044256 | 0.20683 | chr18:28340262-76117153 | 169
11q22.3 | 0.23316 | 0.23297 | chr11:95757487-134452384 | 291

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 9p21.3.

Table S25. 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 9p24.1.

Table S26. 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 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 1p36.11.

Table S30. 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 7q31.1.

Table S31. 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 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
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
ODZ3
STOX2
KIAA1430
C4orf41
MLF1IP
WWC2
SNX25
MGC45800
ENPP6
C4orf38
RWDD4A
CCDC111
HELT
FAM92A3
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 21q22.3.

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

Genes
ERG
TMPRSS2
ADARB1
AIRE
PTTG1IP
C21orf2
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
DYRK1A
ETS2
HMGN1
PRMT2
ITGB2
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
U2AF1
UBE2G2
WRB
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DSCR4
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
BACE2
C2CD2
DNMT3L
ZNF295
UBASH3A
BRWD1
SLC37A1
PCBP3
C21orf58
C21orf57
C21orf29
NCRNA00112
NCRNA00111
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
C21orf70
RSPH1
UMODL1
C21orf84
C21orf88
C21orf90
MCM3APAS
LCA5L
IGSF5
SIK1
C21orf129
C21orf121
C21orf128
PLAC4
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

Genes in Wide Peak

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

Table S40. 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 18q21.2.

Table S41. 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 1q44.

Table S42. 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 S43. 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 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 4q35.2.

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

Genes
DUX4
hsa-mir-1305
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
MORF4
ADAM29
SCRG1
PALLD
FAM149A
FBXO8
PDLIM3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
TUBB4Q
STOX2
KIAA1430
SH3RF1
SPCS3
C4orf41
MLF1IP
NBLA00301
WWC2
KIAA1712
SNX25
CBR4
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
TRIML1
ANKRD37
HELT
FAM92A3
C4orf47
GALNTL6
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

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

Table S46. 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 S47. 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 13q33.1.

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-623
hsa-mir-92a-1
hsa-mir-622
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
FGF14
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
RAP2A
GRK1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
SPRY2
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
OXGR1
NDFIP2
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
RBM26
UPF3A
KDELC1
CARS2
GRTP1
SLITRK6
TMTC4
ABHD13
ZIC5
A2LD1
C13orf27
ADPRHL1
SLITRK1
C13orf16
LOC121952
C13orf28
RNF113B
LOC144776
GPR180
CLYBL
C13orf39
NALCN
HS6ST3
DAOA
C13orf29
ZNF828
UBAC2
FAM70B
C13orf35
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
FLJ44054
LOC643677
MIR548A2
MIR623
FAM155A
FKSG29

Genes in Wide Peak

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

Table S49. 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 S50. 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 S51. 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 S52. 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 11q22.3.

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-100
hsa-mir-125b-1
hsa-mir-34c
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
TRPC6
UPK2
ZBTB16
ZNF202
CUL5
BARX2
JRKL
ZNF259
USP2
HTR3B
ZW10
MMP20
UBE4A
EI24
FEZ1
RICS
C2CD2L
RBM7
MPZL2
YAP1
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
C11orf60
PRDM10
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
ASAM
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
TMEM45B
CASP12
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
FLJ32810
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANGPTL5
ANKK1
RNF214
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
LOC283174
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
LOC399959
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
NCRNA00167
HEPN1
LOC643923
CLDN25
RPL23AP64
LOC100128239
PATE3

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.04 | -0.668 | 1 | 0.08 | 1.19 | 0.332
1q | 1572 | 0.14 | 3.93 | 0.00018 | 0.01 | -2.35 | 1
2p | 753 | 0.05 | -1.78 | 1 | 0.01 | -3.43 | 1
2q | 1235 | 0.04 | -1.67 | 1 | 0.02 | -2.61 | 1
3p | 853 | 0.05 | -1.74 | 1 | 0.08 | -0.62 | 1
3q | 917 | 0.11 | 0.684 | 0.642 | 0.04 | -1.89 | 1
4p | 366 | 0.01 | -3.55 | 1 | 0.16 | 1.76 | 0.182
4q | 865 | 0.00 | -3.45 | 1 | 0.14 | 1.92 | 0.154
5p | 207 | 0.18 | 1.85 | 0.114 | 0.10 | -0.829 | 1
5q | 1246 | 0.03 | -2.04 | 1 | 0.14 | 2.65 | 0.0264
6p | 937 | 0.07 | -0.638 | 1 | 0.09 | 0.222 | 0.846
6q | 692 | 0.07 | -1.12 | 1 | 0.06 | -1.39 | 1
7p | 508 | 0.30 | 7.09 | 4.46e-12 | 0.02 | -2.76 | 1
7q | 1071 | 0.27 | 7.77 | 3.12e-14 | 0.07 | -0.493 | 1
8p | 495 | 0.35 | 8.3 | 0 | 0.23 | 3.78 | 0.00105
8q | 697 | 0.46 | 13.4 | 0 | 0.12 | 0.461 | 0.698
9p | 343 | 0.09 | -0.845 | 1 | 0.20 | 2.9 | 0.0145
9q | 916 | 0.09 | 0.0412 | 1 | 0.12 | 1.18 | 0.332
10p | 312 | 0.15 | 1.14 | 0.415 | 0.08 | -1.35 | 1
10q | 1050 | 0.06 | -0.869 | 1 | 0.06 | -0.869 | 1
11p | 731 | 0.07 | -0.88 | 1 | 0.12 | 0.754 | 0.525
11q | 1279 | 0.07 | -0.333 | 1 | 0.11 | 1.56 | 0.193
12p | 484 | 0.12 | 0.284 | 0.946 | 0.07 | -1.52 | 1
12q | 1162 | 0.10 | 0.96 | 0.47 | 0.07 | -0.563 | 1
13q | 554 | 0.22 | 4.04 | 0.00013 | 0.06 | -1.71 | 1
14q | 1144 | 0.03 | -2.04 | 1 | 0.05 | -1.13 | 1
15q | 1132 | 0.02 | -2.34 | 1 | 0.07 | -0.527 | 1
16p | 719 | 0.09 | -0.189 | 1 | 0.06 | -1.28 | 1
16q | 562 | 0.06 | -1.81 | 1 | 0.09 | -0.759 | 1
17p | 575 | 0.07 | -1.34 | 1 | 0.22 | 4.43 | 0.000188
17q | 1321 | 0.10 | 1.06 | 0.433 | 0.09 | 0.742 | 0.525
18p | 117 | 0.11 | -0.666 | 1 | 0.18 | 1.73 | 0.182
18q | 340 | 0.05 | -2.23 | 1 | 0.22 | 3.77 | 0.00105
19p | 870 | 0.14 | 1.89 | 0.114 | 0.13 | 1.61 | 0.192
19q | 1452 | 0.16 | 4.3 | 4.7e-05 | 0.10 | 1.65 | 0.192
20p | 295 | 0.43 | 10.9 | 0 | 0.09 | -0.879 | 1
20q | 627 | 0.53 | 16.5 | 0 | 0.02 | -2.3 | 1
21q | 422 | 0.00 | -3.73 | 1 | 0.19 | 2.92 | 0.0145
22q | 764 | 0.03 | -2.35 | 1 | 0.12 | 0.953 | 0.443

Methods & Data
Input

Table 4. Get Full Table First 10 out of 136 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-4186-01A-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

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

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