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: 17 significant arm-level results, 23 significant focal amplifications, and 36 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 | 1.133e-17 | 1.133e-17 | chr17:37836582-37906169 | 5
19q12 | 8.9269e-17 | 8.9269e-17 | chr19:30306758-30312349 | 1
12p12.1 | 6.2803e-11 | 6.2803e-11 | chr12:25348817-25514596 | 2
12q15 | 7.0108e-10 | 7.0108e-10 | chr12:68580570-69976199 | 16
7q21.2 | 6.2803e-11 | 1.2549e-09 | chr7:92155110-92557998 | 6
8q24.21 | 1.1695e-07 | 1.1695e-07 | chr8:128146051-128601201 | 2
8p23.1 | 1.6156e-07 | 1.6156e-07 | chr8:11547791-12562991 | 19
20q13.2 | 5.0915e-07 | 5.0915e-07 | chr20:51919706-52670389 | 4
10q26.13 | 2.3413e-06 | 2.3413e-06 | chr10:123240288-123399846 | 1
7p11.2 | 7.727e-06 | 7.727e-06 | chr7:55076540-55540131 | 3
6p21.1 | 0.00015869 | 0.00015869 | chr6:43593968-43657002 | 4
1q42.3 | 0.00027806 | 0.00027806 | chr1:234915448-235098068 | 0 [LOC100506810]
18q11.2 | 0.00030677 | 0.00030677 | chr18:19478025-19759102 | 1
11q13.3 | 0.0042809 | 0.0042809 | chr11:68597105-69807193 | 13
13q22.1 | 0.0030008 | 0.005493 | chr13:73664648-73917853 | 0 [KLF5]
15q26.1 | 0.016843 | 0.016843 | chr15:88693634-102531392 | 109
1p36.22 | 0.032908 | 0.032908 | chr1:10694126-11093740 | 4
3q26.2 | 0.047429 | 0.047429 | chr3:158545238-198022430 | 255
11p13 | 0.087861 | 0.087861 | chr11:34975068-35618590 | 4
9p24.1 | 0.088497 | 0.088497 | chr9:4764022-5566129 | 11
13q12.3 | 0.13592 | 0.17272 | chr13:29203205-53972588 | 169
6q12 | 0.22529 | 0.22529 | chr6:63775924-64332852 | 2
7q31.2 | 0.016456 | 0.24327 | chr7:116238641-117591387 | 11

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
MIEN1
PGAP3
MIR4728

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

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
MIR1279
SNORA70G
LOC100507250

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
RBM48
MGC16142
FAM133B
LOC728066

Genes in Wide Peak

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

Table S6. 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 8p23.1.

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

Genes
CTSB
FDFT1
GATA4
FAM86B1
DEFB109P1
DEFB130
NEIL2
USP17L2
FAM90A25P
LOC392196
DEFB135
DEFB136
DEFB134
FAM86B2
ZNF705D
FAM66D
FAM66A
LOC100133267
LOC100506990

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 11q13.3.

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

Genes
CCND1
hsa-mir-3164
CPT1A
FGF3
FGF4
IGHMBP2
FGF19
MYEOV
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
NTRK3
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
ACAN
ALDH1A3
ANPEP
CHD2
FES
IGF1R
ISG20
MAN2A2
MEF2A
MFGE8
FURIN
PCSK6
PLIN1
POLG
RLBP1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
ABHD2
CHSY1
SYNM
GABARAPL3
VPS33B
MRPL46
OR4F4
SLCO3A1
NGRN
RHCG
DET1
LINS
FANCI
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
AEN
TTC23
MRPS11
LRRK1
TM2D3
C15orf42
RCCD1
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
ADAMTS17
DNM1P46
CERS3
LOC254559
LOC283738
LOC283761
FAM169B
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
WASH3P
FLJ42289
C15orf58
OR4F6
OR4F15
FAM174B
LOC400456
MIR7-2
MIR9-3
TTLL13
ASB9P1
FAM138E
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1179
MIR1469
MIR3175
LOC100507217
LOC100507472
C15orf38-AP3S2
MIR3529
MIR4714

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
MASP2
TARDBP
CASZ1
C1orf127

Genes in Wide Peak

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

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
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
RFC4
SNORA63
RPL35A
TRA2B
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
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
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
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
EGFEM1P
CAMK2N2
TM4SF19
RPL39L
DNAJC19
OTOL1
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
PPM1L
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
SPTSSB
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
NAALADL2
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
TRIM59
CCDC39
LOC339926
LPP-AS2
LRRIQ4
SAMD7
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
TMEM212
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
MIR15B
MIR16-2
SNORD2
SNORA4
LOC646168
C3orf65
LOC647107
GMNC
LOC647323
IQCJ
SCARNA7
SNORA81
SNORD66
MIR551B
MIR569
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100128164
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
MIR3919
IQCJ-SCHIP1
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

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

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

Genes
CD44
SLC1A2
PDHX
PAMR1

Genes in Wide Peak

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

Table S18. 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 13q12.3.

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

Genes
BRCA2
LCP1
RB1
LHFP
TTL
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
ALOX5AP
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HMGB1
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
UBL3
RFC3
RFXAP
SLC7A1
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
KL
ITM2B
MTRF1
UTP14C
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
DLEU1
N4BP2L2
OLFM4
POSTN
HSPH1
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
INTS6
CKAP2
NUFIP1
NBEA
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
POMP
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
CDADC1
CAB39L
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
LOC440131
ALG11
TSC22D1-AS1
ZAR1L
SERPINE3
SNORA31
MIR621
CCDC169
LINC00426
TPT1-AS1
MIR548F5
MIR759
MIR320D1
MIR4305
MIR3613
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
PTP4A1
LGSN

Genes in Wide Peak

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

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

Genes
MET
CAPZA2
CFTR
WNT2
ST7
CTTNBP2
ST7-AS1
ST7-AS2
ST7-OT3
ASZ1
ST7-OT4

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 - 36 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
--- | --- | --- | --- | ---
16q23.1 | 6.056e-38 | 6.056e-38 | chr16:78129058-79627770 | 1
5q11.2 | 4.3629e-17 | 4.3629e-17 | chr5:58260298-59787985 | 3
9p24.1 | 4.3629e-17 | 1.4363e-15 | chr9:8310705-12693402 | 1
9p21.3 | 4.3629e-17 | 5.4009e-13 | chr9:21865498-21996995 | 2
3p14.2 | 1.7282e-12 | 2.727e-12 | chr3:59034763-61547330 | 1
4q22.1 | 2.3367e-12 | 2.367e-10 | chr4:91148280-93240505 | 1
20p12.1 | 8.0493e-10 | 8.0493e-10 | chr20:14302876-15179819 | 2
6p25.3 | 1.1844e-09 | 1.1844e-09 | chr6:1608837-2252425 | 2
1p36.11 | 5.4614e-07 | 5.4614e-07 | chr1:26900639-27433459 | 11
6q26 | 1.6636e-06 | 4.9889e-06 | chr6:161693099-163153207 | 1
7q31.1 | 2.7198e-06 | 1.2788e-05 | chr7:109599468-111366370 | 2
3q26.31 | 2.9653e-05 | 2.9653e-05 | chr3:173999806-175760559 | 2
4q34.3 | 1.7951e-07 | 0.00016918 | chr4:170312827-191154276 | 96
2q33.3 | 1.8749e-05 | 0.0010773 | chr2:204826225-206558638 | 1
10q23.31 | 0.0011933 | 0.0011838 | chr10:89506488-90034038 | 4
18q21.2 | 0.0015052 | 0.001643 | chr18:48351671-56118998 | 30
2q37.2 | 0.001315 | 0.0076357 | chr2:235913227-237079324 | 2
22q13.32 | 0.0049765 | 0.0076357 | chr22:45736500-51304566 | 75
15q21.3 | 0.011906 | 0.011906 | chr15:57207772-57583300 | 1
7q36.3 | 0.0040876 | 0.015473 | chr7:157210222-159138663 | 11
16p13.3 | 0.041698 | 0.041698 | chr16:5144019-7771745 | 1
1q44 | 0.043735 | 0.0431 | chr1:245282267-245913707 | 1
19p13.3 | 0.056235 | 0.054698 | chr19:2473582-4772399 | 72
14q32.33 | 0.058871 | 0.059417 | chr14:92629600-107349540 | 248
3p26.1 | 0.014498 | 0.064845 | chr3:1-8263567 | 17
14q21.2 | 0.06365 | 0.064845 | chr14:45424235-47120973 | 6
17q24.3 | 0.11409 | 0.11409 | chr17:68173089-71163787 | 4
21q22.3 | 0.11409 | 0.11409 | chr21:35985896-48129895 | 150
11q24.1 | 0.12274 | 0.12384 | chr11:101912572-128395332 | 274
18p11.23 | 0.15535 | 0.15535 | chr18:7231473-9108125 | 4
3p24.3 | 0.055517 | 0.17508 | chr3:15735039-40306561 | 113
11p15.5 | 0.17928 | 0.17508 | chr11:1-13033154 | 288
6q14.1 | 0.066576 | 0.18346 | chr6:53658212-134374203 | 322
22q12.1 | 0.14227 | 0.19763 | chr22:1-32077766 | 269
13q33.1 | 0.22627 | 0.23782 | chr13:75123902-115169878 | 146
20p12.1 | 8.0493e-10 | 1 | chr20:1-63025520 | 672

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 5q11.2.

Table S23. 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 S24. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PTPRD

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 3p14.2.

Table S26. 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 4q22.1.

Table S27. 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 20p12.1.

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

Genes
FLRT3
MACROD2-AS1

Genes in Wide Peak

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

Table S29. 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 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 6q26.

Table S31. 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 7q31.1.

Table S32. 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 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 4q34.3.

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
SCRG1
FAM149A
FBXO8
DUX2
PDLIM3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
LOC100506085
LOC100506122
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q33.3.

Table S35. 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 10q23.31.

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

Genes
PTEN
ATAD1
CFL1P1
KLLN

Genes in Wide Peak

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

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

Genes
hsa-mir-122
DCC
FECH
SMAD4
ME2
NARS
ATP8B1
RAB27B
TCF4
MBD2
TXNL1
ONECUT2
POLI
NEDD4L
WDR7
ST8SIA3
MEX3C
ELAC1
CCDC68
STARD6
C18orf54
C18orf26
BOD1P
MIR122
SNORA37
LOC100287225
LOC100505474
LOC100505549
MIR4529
MIR3591

Genes in Wide Peak

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

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

Genes
GBX2
AGAP1

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
hsa-let-7b
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
TTC38
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR3201
MIR3619
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

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

Table S40. 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 7q36.3.

Table S41. 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
LOC100506585

Genes in Wide Peak

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

Table S42. 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 1q44.

Table S43. 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 19p13.3.

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

Genes
GNA11
SH3GL1
hsa-mir-7-3
hsa-mir-637
AES
DAPK3
EEF2
GNA15
GNG7
MATK
GADD45B
NFIC
MAP2K2
SGTA
TBXA2R
THOP1
TLE2
S1PR4
APBA3
CHAF1A
EBI3
HMG20B
SEMA6B
ZFR2
PIP5K1C
SNORD37
TJP3
ITGB1BP3
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
STAP2
CCDC94
C19orf10
NCLN
SHD
ZNF77
C19orf29
CELF5
FSD1
TLE6
ZNF556
UBXN6
DOHH
CREB3L3
HDGFRP2
RAX2
MPND
ATCAY
DPP9
ZNF554
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
MFSD12
GIPC3
DIRAS1
ZNF555
ANKRD24
C19orf77
C19orf29-AS1
MIR7-3
PLIN5
MIR637
PLIN4
C19orf71
LOC100131094
MIR4746

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.33.

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

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

Genes in Wide Peak

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

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

Genes
GRM7
IL5RA
ITPR1
SETMAR
BHLHE40
EDEM1
CHL1
CNTN6
TRNT1
CRBN
ARL8B
LRRN1
CNTN4
SUMF1
EGOT
LOC100507582
MIR4790

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.2.

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

Genes
FKBP3
FAM179B
PRPF39
MIS18BP1
FANCM
SNORD127

Genes in Wide Peak

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

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

Genes
SOX9
SLC39A11
LINC00511
LOC100499467

Genes in Wide Peak

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

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

Genes
RUNX1
ERG
TMPRSS2
hsa-mir-3197
hsa-mir-802
ADARB1
AIRE
PTTG1IP
C21orf2
CBR1
CBR3
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
DYRK1A
ETS2
HLCS
HMGN1
PRMT2
ITGB2
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SIM2
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
TTC3
U2AF1
UBE2G2
WRB
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DOPEY2
DSCR4
DSCR3
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
DNMT3L
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
PCBP3
C21orf58
YBEY
LINC00160
TSPEAR
LINC00112
LINC00111
SETD4
FAM3B
RIPK4
CLIC6
AGPAT3
PRDM15
TMPRSS3
RUNX1-IT1
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
FAM207A
RSPH1
UMODL1
LINC00313
C21orf88
C21orf90
MCM3AP-AS1
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00315
DSCR9
BRWD1-IT2
DSCR10
LINC00323
LINC00319
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
COL18A1-AS1
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
LINC00114
LOC642852
LINC00163
SSR4P1
MIR802
LOC100129027
LOC100133286
MIR3197
LOC100505746
LOC100506385
CBR3-AS1
DSCAM-AS1
MIR4760

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.1.

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
BIRC2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
ZNF259
USP2
HTR3B
ZW10
MMP20
UBE4A
EI24
FEZ1
C2CD2L
RBM7
MPZL2
YAP1
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
MMP27
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
MPZL3
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
PATE3
LOC100288077
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.23.

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

Genes
PTPRM
CCDC165
RAB12
LOC100192426

Genes in Wide Peak

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

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

Genes
MLH1
MYD88
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
ACAA1
ACVR2B
CCR4
CCR8
CX3CR1
DAZL
GLB1
GOLGA4
ITGA9
RPSA
MOBP
PLCD1
RAB5A
RARB
SNORA62
RPL15
SATB1
SCN5A
SCN10A
STAC
TGFBR2
THRB
TOP2B
UBE2E1
UBE2E2
UBP1
EOMES
KAT2B
LRRFIP2
SLC22A14
SLC22A13
SLC4A7
TBC1D5
EPM2AIP1
TRANK1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
CTDSPL
CRTAP
ARPP21
SCN11A
CLASP2
GPD1L
RFTN1
PLCL2
FBXL2
CNOT10
MYRIP
SUSD5
RBMS3
NKIRAS1
VILL
DYNC1LI1
CMTM6
SLC25A38
OXSM
NGLY1
WDR48
AZI2
CSRNP1
GORASP1
ZNF385D
DCLK3
OXNAD1
CMTM7
OSBPL10
LRRC3B
GALNTL2
KCNH8
TRIM71
SGOL1
PP2D1
EFHB
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
XIRP1
TTC21A
STT3B
LOC285326
DPH3
LOC339862
C3orf35
GADL1
ZNF860
VENTXP7
MIR128-2
MIR26A1
SNORA6
TMPPE
LOC644990
LOC645206
MIR563
LOC100128640
MIR3714
MIR4791
MIR548AC
MIR4792
MIR4442

Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
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
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
MRVI1
TRIM22
IFITM3
DEAF1
IPO7
IFITM2
TRIM3
OR7E12P
LYVE1
KCNQ1OT1
PKP3
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
USP47
TRIM68
PIDD
KCNQ1DN
PARVA
MMP26
AKIP1
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
MOB2
SBF2
FAM160A2
MICALCL
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
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
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC644656
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
LOC729013
MIR675
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
MIR210HG
LOC100506305
MIR4686
MIR4485
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.1.

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

Genes
PRDM1
ROS1
STL
GOPC
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
AIM1
AMD1
ARG1
BAI3
BCKDHB
BMP5
DST
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
FABP7
FOXO3
FRK
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HCRTR2
HDAC2
HSF2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
ME1
MYO6
NT5E
ENPP1
ENPP3
PGM3
PLN
POU3F2
PREP
PRIM2
PKIB
PTPRK
REV3L
RNY4
RPS12
SIM1
SMPD2
ELOVL4
MAP3K7
TCF21
NR2E1
TPBG
TPD52L1
TSPYL1
TTK
PTP4A1
STX7
DDO
SNX3
RNGTT
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
TBX18
TAAR2
TAAR3
HMGN3
MED23
FHL5
AKAP7
ATG5
TBPL1
BAG2
KIAA0408
ZBTB24
SNAP91
FIG4
CASP8AP2
TRDN
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
SMPDL3A
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
PHF3
HEY2
ORC3
BRD7P3
MTO1
ASF1A
PNISR
IBTK
MOXD1
ZNF451
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
TINAG
OSTM1
NDUFAF4
DSE
HDDC2
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
LGSN
RAB23
COQ3
HMGCLL1
PHIP
SOBP
AKIRIN2
LRRC1
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
ECHDC1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
SERINC1
HACE1
FAM135A
BEND3
KIAA1586
RRAGD
PRDM13
BACH2
TRMT11
SMAP1
C6orf164
POPDC3
MICAL1
OR2A4
OGFRL1
FAM184A
MANEA
LINC00472
KHDC1
GPR63
COL21A1
SPACA1
RNF146
TAAR8
SH3BGRL2
ARMC2
RPF2
L3MBTL3
MCHR2
FAXC
GJA10
RTN4IP1
RSPO3
USP45
SLC22A16
C6orf7
UBE2CBP
MLIP
KIAA1919
ARHGAP18
GTF3C6
MRAP2
RWDD2A
KLHL32
TMEM200A
MB21D1
NUS1
C6orf192
SLC16A10
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
NCOA7
HINT3
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
SAMD3
MGC34034
SLC2A12
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
KHDRBS2
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
VGLL2
LACE1
C6orf191
MMS22L
FAM26E
MCM9
SCML4
LINC00326
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
TAAR6
DPPA5
RSPH4A
EYS
C6orf58
GUSBP4
GJB7
SNHG5
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
THEMIS
GFRAL
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
GSTM2P1
RFPL4B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
LOC100507203
LOC100507254
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.1.

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

Genes
BCR
EWSR1
MN1
NF2
SMARCB1
CLTCL1
CHEK2
hsa-mir-3200
hsa-mir-3199-2
hsa-mir-548j
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ADORA2A
ADRBK2
AP1B1
ARVCF
ATP6V1E1
BID
COMT
CRKL
CRYBA4
CRYBB1
CRYBB2
CRYBB2P1
CRYBB3
DDT
GGT1
GGT3P
GGT5
GNAZ
GP1BB
GSC2
GSTT1
GSTT2
SERPIND1
IGLL1
LIF
LIMK2
MIF
MMP11
DRG1
NEFH
OSM
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
RFPL1
SMTN
SLC7A4
SLC25A1
SNRPD3
TBX1
TCN2
CLDN5
TOP1P2
HIRA
UBE2L3
UFD1L
VPREB1
XBP1
ZNF70
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
TPST2
NIPSNAP1
THOC5
MTMR3
TOP3B
P2RX6
SNAP29
GAL3ST1
RAB36
PPM1F
SFI1
DGCR2
SF3A1
TXNRD2
RASL10A
GAS2L1
RFPL1-AS1
USP18
MORC2
HIC2
TTC28
SPECC1L
PES1
CABIN1
PRAME
SEC14L2
SEZ6L
PATZ1
TSSK2
SDF2L1
PPIL2
PITPNB
PISD
OSBP2
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
TFIP11
C22orf31
GSTTP1
DGCR11
DGCR9
RHBDD3
POM121L1P
DGCR5
DGCR10
FBXW4P1
TRMT2A
INPP5J
RTDR1
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L9P
UQCR10
POM121L8P
YPEL1
ZDHHC8
VPREB3
PLA2G3
C22orf43
MTFP1
MED15
UPB1
TUBA8
CECR1
DGCR8
GNB1L
TUG1
PEX26
ZMAT5
SUSD2
EIF4ENIF1
ASPHD2
MICAL3
MRPL40
RTN4R
SLC2A11
C22orf29
THAP7
OR11H1
C22orf13
SLC25A18
TBC1D10A
KREMEN1
ZNRF3
ASCC2
TMEM191A
MYO18B
KLHL22
DGCR6L
KIAA1656
RIMBP3
KIAA1671
HPS4
SCARF2
GGTLC2
GUSBP11
DERL3
IGLL3P
LRP5L
RNF185
LOC96610
MGC16703
PIK3IP1
GAB4
C22orf39
C22orf25
ZNF280A
SGSM1
EMID1
SELM
ZNF280B
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
C22orf15
HSCB
CCDC117
HORMAD2
DUSP18
MORC2-AS1
CCDC116
CABP7
RNF215
TMEM211
SEC14L3
POM121L4P
RGL4
LOC284865
LOC284889
TTC28-AS1
SEC14L4
SLC35E4
PI4KAP2
SDC4P
TPTEP1
LOC388849
FAM211B
LOC391322
LOC400891
BCRP2
CHCHD10
SRRD
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
PIWIL3
MIAT
CCDC157
BCRP3
TMEM191C
C22orf45
POM121L10P
LOC648691
CES5AP1
GATSL3
GSTTP2
GSTT2B
MIR648
MIR650
TMEM191B
PI4KAP1
LOC729444
SEC14L6
DDTL
SNORD125
MIR301B
LOC100128531
CECR7
CECR5-AS1
FLJ41941
MIR1286
MIR1306
MIR548J
MIR3200
MIR3199-2
MIR3198-1
MIR3199-1
IGLL5
MIR3653
MIR3618
MIR3928
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

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

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
ATP4B
BTF3P11
CLN5
COL4A1
COL4A2
DCT
GPR183
EDNRB
EFNB2
F7
F10
FGF14
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
LMO7
PCCA
POU4F1
DNAJC3
RAP2A
GRK1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
UCHL3
ZIC2
STK24
CUL4A
IRS2
SCEL
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
TBC1D4
GPC6
MBNL2
FARP1
SPRY2
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
MYCBP2
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
FBXL3
OXGR1
NDFIP2
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
RBM26
UPF3A
KDELC1
CARS2
RNF219
GRTP1
SLITRK6
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
SLITRK1
KCTD12
TEX29
METTL21CP1
SLAIN1
SPACA7
RNF113B
LINC00410
GPR180
COMMD6
CLYBL
METTL21C
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
LINC00347
FAM70B
C13orf35
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
MIR4500HG
FLJ44054
CCDC168
CTAGE11P
FLJ41484
MIR622
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
MIR3170
MIR3665
RBM26-AS1
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705

Genes in Wide Peak

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

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

Genes
GNAS
TOP1
MAFB
SS18L1
ASXL1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-1289-1
hsa-mir-499
hsa-mir-644
hsa-mir-1825
hsa-mir-3193
hsa-mir-663
hsa-mir-3192
hsa-mir-103-2-as
hsa-mir-1292
hsa-mir-3194
ADA
ADRA1D
JAG1
AHCY
ASIP
ATP5E
AVP
BCL2L1
BFSP1
BMP2
BMP7
BPI
ENTPD6
CD40
CDC25B
CDH4
CEBPB
CENPB
CHGB
CHRNA4
COL9A3
CSE1L
CSNK2A1
CST1
CST2
CST3
CST4
CST5
CSTF1
CTSZ
CYP24A1
DNMT3B
E2F1
EDN3
EEF1A2
EPB41L1
EYA2
FKBP1A
FOXS1
GGT7
GHRH
GNRH2
NPBWR2
GSS
HCK
FOXA2
HNF4A
ID1
IDH3B
INSM1
EIF6
ITPA
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
LBP
MC3R
MMP9
MYBL2
MYT1
NFATC2
NKX2-2
NNAT
NTSR1
OPRL1
OXT
PAX1
PCK1
PCNA
PCSK2
PDYN
PFDN4
PI3
PLAGL2
PLCB4
PLCG1
PLTP
CTSA
PPP1R3D
PRNP
PSMA7
PTGIS
PTK6
PTPN1
PTPRA
PYGB
RBL1
RPN2
RPS21
RRBP1
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SIGLEC1
SNAI1
SNAP25
SNRPB
SNRPB2
SNTA1
SOX12
SPAG4
SRC
SRMS
SSTR4
STAU1
STK4
AURKA
TAF4
TCEA2
TCF15
TFAP2C
TGM2
TGM3
THBD
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF133
ZNF217
MKKS
GDF5
NCOA3
ATRN
RAE1
CST7
BCAS1
STX16
CDS2
TNFRSF6B
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
VAPB
B4GALT5
KIF3B
PSMF1
RBM39
TTI1
SNPH
ProSAPiP1
RASSF2
TM9SF4
SPATA2
GINS1
OSBPL2
SLC23A2
ACOT8
CST8
ATP9A
SGK2
RBM12
ARFRP1
RGS19
SIRPB1
SYCP2
MYL9
WFDC2
SEC23B
NOP56
PROCR
ARFGEF2
RBCK1
POLR3F
TCFL5
RBBP9
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
DSTN
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
CEP250
RNF24
HRH3
PXMP4
RBPJL
XRN2
DLGAP4
UBOX5
BTBD3
RALY
CD93
MAPRE1
TPX2
NINL
ZHX3
NCOA6
PLCB1
SLC9A8
ADNP
POFUT1
ZMYND8
SPO11
PRND
FLRT3
LAMP5
PRPF6
SPEF1
SAMHD1
C20orf194
C20orf4
L3MBTL1
PPP1R16B
C20orf26
ABHD12
TRPC4AP
ZNF337
GTPBP5
GMEB2
SNORD12C
SNORA71B
SNORA71A
SNORD57
SNORD56
SDCBP2
SNX5
TP53TG5
MOCS3
SLCO4A1
REM1
C20orf30
HSPC072
NXT1
VSX1
STMN3
SLC35C2
SLMO2
IFT52
NAA20
PHF20
SCAND1
BPIFA1
CRNKL1
ANGPT4
TH1L
C20orf43
C20orf111
ESF1
PIGT
TRMT6
ERGIC3
CDK5RAP1
RTEL1
SOX18
HAO1
RIN2
SMOX
CRLS1
YTHDF1
LIME1
UCKL1
C20orf27
C20orf11
DZANK1
UQCC
PCMTD2
C20orf20
SPTLC3
C20orf29
TMEM74B
PPP4R1L
SIRPG
RBM38
FERMT1
KIF16B
TASP1
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
EDEM2
DOK5
PLK1S1
DBNDD2
ACSS2
RNF114
SULF2
NSFL1C
C20orf24
TMX4
CTNNBL1
GPCPD1
CPXM1
SLC2A4RG
OTOR
PMEPA1
CASS4
SPINLW1
C20orf3
PAK7
RALGAPB
JPH2
SALL4
ZNFX1
RALGAPA2
CSRP2BP
RAB22A
SLC24A3
NDRG3
SLC12A5
ZNF512B
MAVS
PREX1
EBF4
COL20A1
MYH7B
NCOA5
TRIB3
TP53INP2
RPRD1B
OVOL2
TGIF2
CDH26
FASTKD5
KCNK15
DHX35
MANBAL
NAPB
SLC17A9
ELMO2
ZNF335
ANKRD5
LOC63930
PCIF1
FAM217B
NECAB3
GFRA4
CDH22
GZF1
VPS16
FAM113A
SLC13A3
LPIN3
MRPS26
DDRGK1
GDAP1L1
LOC79015
C20orf195
C20orf7
PPDPF
ZNF343
TTPAL
BIRC7
NPEPL1
ACTR5
SYNDIG1
DSN1
NRSN2
PANK2
FER1L4
DNAJC5
ADAM33
PABPC1L
BPIFB2
SEL1L2
TUBB1
ZBP1
SLC2A10
HM13
PDRG1
FAM83D
DEFB126
CABLES2
FAM110A
DYNLRB1
ITCH
SLC4A11
SLA2
CHD6
MCM8
ACSS1
MAP1LC3A
PARD6B
ZGPAT
COX4I2
ZNF341
TOX2
ZCCHC3
MYLK2
PRIC285
KIAA1755
SCRT2
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
GGTLC1
C20orf72
DTD1
BPIFB1
TP53RK
C20orf54
DNTTIP1
FAM210B
PHACTR3
HSPA12B
DEFB118
TMC2
BHLHE23
NKAIN4
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
TBC1D20
SIRPD
C20orf141
PROKR2
C20orf94
CSTL1
CST9L
CST9
C20orf166
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
GATA5
MLLT10P1
SLC32A1
C20orf96
BPIFA2
ZBTB46
WFDC3
GCNT7
C20orf112
CBLN4
CTCFL
C20orf132
SAMD10
ABHD16B
C20orf160
KIAA0889
C20orf118
RIMS4
SUN5
MACROD2
SRXN1
ROMO1
NEURL2
LINC00261
ZSWIM3
WFDC10A
BANF2
NANP
LINC00266-1
DEFB127
C20orf79
ISM1
WFDC6
C20orf173
LINC00028
FAM65C
CST11
DEFB129
SIRPA
C20orf151
C20orf152
STK35
R3HDML
ADIG
GTSF1L
WFDC5
LOC149773
GNAS-AS1
PRNT
LOC149837
C20orf196
NCOR1P1
LOC149950
COMMD7
BPIFB4
LSM14B
WFDC13
APCDD1L
LRRN4
CSTT
TTLL9
ACTL10
C20orf201
FAM209A
LOC200261
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
DEFB125
DEFB128
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
SIRPB2
LOC284788
LOC284798
FAM182A
LOC284801
FRG1B
C20orf203
BPIFA4P
LOC339568
LOC339593
ARHGAP40
RSPO4
TGM6
XKR7
BPIFB3
TMEM189
TMEM189-UBE2V1
LINC00493
LOC388796
FAM209B
SPINT4
SUMO1P1
DEFB132
C20orf202
FLJ33581
MIR103A2
MIR1-1
MIR124-3
MIR133A2
MIR296
DZANK1-AS1
ZNFX1-AS1
MIR499A
RAD21L1
LOC643406
NKX2-4
LOC647979
SNORA39
SNORA51
SNORA60
SNORA71C
SNORA71D
SNORD12
SNORD17
SNORD86
SNORD110
MIR644A
MIR645
MIR647
MIR663A
LOC728228
FAM182B
SYS1-DBNDD2
HAR1A
HAR1B
PSIMCT-1
SNORD119
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
LOC100128496
LOC100130264
ZNF663
LOC100131208
LOC100131496
DPH3P1
LOC100134015
LOC100134868
LINC00029
LOC100144597
FLJ16779
LOC100270679
LOC100270804
LOC100287792
TMEM239
LOC100289473
MIR1914
MIR1292
MIR1257
MIR103B2
PCNA-AS1
PET117
MACROD2-AS1
MIR3192
MIR4325
MIR3194
MIR3193
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505536
LOC100505783
LOC100505815
LOC100505826
LOC100506384
LOC100507495
LOC100507629
SPINLW1-WFDC6
TGIF2-C20ORF24
FKBP1A-SDCBP2
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR499B
MIR4756
MIR4758
MIR4532
MIR4533
MIR4755
MIR5095
LOC100652730

Arm-level results

Table 3. Get Full Table Arm-level significance table - 17 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.04 | -0.145 | 1 | 0.09 | 2.34 | 0.0471
1q | 1955 | 0.10 | 2.61 | 0.0196 | 0.06 | 0.33 | 0.891
2p | 924 | 0.06 | -1.58 | 1 | 0.00 | -3.76 | 1
2q | 1556 | 0.06 | -0.464 | 1 | 0.01 | -2.74 | 1
3p | 1062 | 0.05 | -1.76 | 1 | 0.07 | -0.921 | 1
3q | 1139 | 0.10 | 0.383 | 1 | 0.03 | -2.2 | 1
4p | 489 | 0.02 | -3.38 | 1 | 0.16 | 1.32 | 0.279
4q | 1049 | 0.00 | -3.48 | 1 | 0.14 | 1.57 | 0.254
5p | 270 | 0.21 | 2.34 | 0.0374 | 0.10 | -0.949 | 1
5q | 1427 | 0.04 | -1.68 | 1 | 0.15 | 2.98 | 0.0111
6p | 1173 | 0.07 | -0.947 | 1 | 0.08 | -0.369 | 1
6q | 839 | 0.05 | -2.09 | 1 | 0.06 | -1.56 | 1
7p | 641 | 0.31 | 6.88 | 2.29e-11 | 0.03 | -2.5 | 1
7q | 1277 | 0.24 | 6.21 | 1.74e-09 | 0.07 | -0.596 | 1
8p | 580 | 0.34 | 7.04 | 9.25e-12 | 0.23 | 3.39 | 0.00682
8q | 859 | 0.41 | 11.2 | 0 | 0.11 | 0.167 | 0.891
9p | 422 | 0.10 | -0.968 | 1 | 0.22 | 3.14 | 0.00815
9q | 1113 | 0.08 | -0.574 | 1 | 0.13 | 1.41 | 0.279
10p | 409 | 0.13 | 0.198 | 1 | 0.10 | -0.771 | 1
10q | 1268 | 0.06 | -1.11 | 1 | 0.08 | -0.221 | 1
11p | 862 | 0.06 | -1.55 | 1 | 0.14 | 1.12 | 0.366
11q | 1515 | 0.07 | -0.262 | 1 | 0.10 | 1.34 | 0.279
12p | 575 | 0.12 | -0.0865 | 1 | 0.10 | -0.588 | 1
12q | 1447 | 0.07 | -0.202 | 1 | 0.06 | -0.829 | 1
13q | 654 | 0.21 | 3.47 | 0.00142 | 0.06 | -1.87 | 1
14q | 1341 | 0.03 | -2 | 1 | 0.07 | -0.481 | 1
15q | 1355 | 0.02 | -2.27 | 1 | 0.09 | 0.166 | 0.891
16p | 872 | 0.08 | -0.85 | 1 | 0.07 | -1.12 | 1
16q | 702 | 0.04 | -2.45 | 1 | 0.10 | -0.38 | 1
17p | 683 | 0.05 | -2.14 | 1 | 0.21 | 3.5 | 0.00682
17q | 1592 | 0.08 | 0.503 | 1 | 0.07 | 0.174 | 0.891
18p | 143 | 0.15 | 0.158 | 1 | 0.13 | -0.303 | 1
18q | 446 | 0.09 | -1.23 | 1 | 0.22 | 3.15 | 0.00815
19p | 995 | 0.09 | -0.307 | 1 | 0.17 | 2.71 | 0.0216
19q | 1709 | 0.14 | 3.4 | 0.00167 | 0.09 | 1 | 0.411
20p | 355 | 0.38 | 8.45 | 0 | 0.08 | -1.27 | 1
20q | 753 | 0.49 | 13.8 | 0 | 0.01 | -2.52 | 1
21q | 509 | 0.01 | -3.57 | 1 | 0.19 | 2.39 | 0.0471
22q | 921 | 0.03 | -2.68 | 1 | 0.14 | 1.39 | 0.279

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.

- 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/STAD/1445460/2.GDAC_MergeDataFiles.Finished/STAD.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 = 0.30

- 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

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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