Breast Invasive Carcinoma: 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 781 tumor samples used in this analysis: 24 significant arm-level results, 33 significant focal amplifications, and 54 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 - 33 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
--- | --- | --- | --- | ---
11q13.2 | 6.2398e-132 | 3.1548e-117 | chr11:69127320-69212109 | 2
17q12 | 1.6886e-146 | 1.9194e-106 | chr17:35058337-35130413 | 5
8p12 | 9.2976e-89 | 3.9629e-77 | chr8:37455229-37877695 | 7
20q13.2 | 1.4043e-38 | 1.4043e-38 | chr20:51589756-51792983 | 1
17q23.1 | 1.2708e-56 | 1.1605e-34 | chr17:55272646-55331439 | 5
8q24.21 | 2.1214e-35 | 6.7125e-33 | chr8:128726635-128869482 | 1
6q21 | 2.2287e-16 | 2.2287e-16 | chr6:107313549-107666415 | 5
15q26.3 | 1.6765e-15 | 1.6765e-15 | chr15:96894457-97400543 | 2
12q15 | 1.6821e-13 | 1.6821e-13 | chr12:67551866-68152707 | 6
1q21.2 | 6.9357e-14 | 3.371e-12 | chr1:148685787-149028520 | 9
11q14.1 | 5.8926e-58 | 6.1681e-11 | chr11:76646424-77502922 | 11
8p11.21 | 1.6609e-27 | 1.8698e-06 | chr8:41880241-42375760 | 7
19q12 | 1.2345e-06 | 4.9246e-06 | chr19:34570957-35203256 | 6
3q26.32 | 2.3188e-05 | 2.3188e-05 | chr3:178351201-181130649 | 13
10q22.3 | 5.4961e-05 | 0.0001827 | chr10:80104653-81674323 | 10
19q13.42 | 8.6369e-05 | 0.00030848 | chr19:60152124-61460026 | 49
12p13.33 | 0.0012872 | 0.0012872 | chr12:464787-1013573 | 6
4q13.3 | 0.0057875 | 0.0057875 | chr4:73912775-75015054 | 11
11p13 | 0.0085476 | 0.0085476 | chr11:32090025-33820836 | 15
17p11.2 | 0.0095479 | 0.0095479 | chr17:20742429-20860095 | 1
14q13.2 | 0.01066 | 0.01066 | chr14:29770634-37944832 | 41
6p23 | 0.03301 | 0.03301 | chr6:12384812-16735233 | 16
3p24.3 | 0.035871 | 0.035871 | chr3:14660339-15129148 | 6
7p11.2 | 0.055552 | 0.055552 | chr7:55030853-56361153 | 16
13q12.3 | 0.038591 | 0.07461 | chr13:29130478-30291992 | 6
16q12.1 | 0.07461 | 0.07461 | chr16:46203187-46614683 | 1
8q21.13 | 5.8727e-09 | 0.085404 | chr8:80664841-82079291 | 7
10p14 | 0.19159 | 0.19159 | chr10:11564033-14045623 | 19
13q33.3 | 0.072666 | 0.19796 | chr13:89983379-114142980 | 101
10q26.13 | 0.001336 | 0.19818 | chr10:123195348-123465521 | 1
1p12 | 0.026226 | 0.20438 | chr1:119536850-120886543 | 13
1q32.1 | 0.0010181 | 0.23006 | chr1:200587802-204675237 | 63
1p31.3 | 0.19818 | 0.24847 | chr1:59528811-63038969 | 13

Genes in Wide Peak

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

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

Genes
CCND1
ORAOV1

Genes in Wide Peak

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

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

Genes
ERBB2
PNMT
TCAP
STARD3
PGAP3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p12.

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

Genes
ERLIN2
PROSC
GPR124
BRF2
ZNF703
RAB11FIP1
LOC728024

Genes in Wide Peak

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

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

Genes
ZNF217

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
hsa-mir-21
RPS6KB1
TUBD1
TMEM49
MIR21

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
MYC

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

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

Genes
hsa-mir-587
C6orf203
PDSS2
BEND3
LOC553137

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
IGF1R
LOC145814

Genes in Wide Peak

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

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

Genes
hsa-mir-1279
CPM
LYZ
YEATS4
FRS2
CPSF6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
CTSS
ECM1
ENSA
MCL1
RPRD2
ADAMTSL4
GOLPH3L
TARS2
HORMAD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q14.1.

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

Genes
CLNS1A
NDUFC2
PAK1
THRSP
C11orf67
RSF1
KCTD14
ALG8
INTS4
GDPD4
AQP11

Genes in Wide Peak

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

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

Genes
IKBKB
PLAT
POLB
VDAC3
MYST3
AP3M2
DKK4

Genes in Wide Peak

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

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

Genes
CCNE1
C19orf2
POP4
PLEKHF1
C19orf12
VSTM2B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

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

Genes
PIK3CA
ACTL6A
NDUFB5
USP13
KCNMB2
KCNMB3
ZNF639
PEX5L
MFN1
MRPL47
GNB4
ZMAT3
TBL1XR1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.3.

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

Genes
MBL1P1
PPIF
ZMIZ1
EIF5AL1
ZCCHC24
LOC283050
LOC642361
LOC650623
SFTPA1
SFTPA2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.42.

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

Genes
IL11
PTPRH
RPL28
SYT5
TNNI3
TNNT1
U2AF2
SAPS1
HSPBP1
UBE2S
CCDC106
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
EPS8L1
ZNF444
NLRP2
NAT14
ZSCAN5A
ISOC2
BRSK1
SUV420H2
FIZ1
GALP
ZNF628
RDH13
COX6B2
NLRP13
NLRP8
NLRP5
ZNF787
TMEM190
ZNF524
ZNF784
NLRP4
ZNF579
NLRP11
TMEM86B
SSC5D
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
C19orf51
SBK2
SHISA7

Genes in Wide Peak

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

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

Genes
NINJ2
RAD52
ERC1
WNK1
B4GALNT3
HSN2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
AFM
AFP
ALB
CXCL1
IL8
PF4V1
CXCL6
ANKRD17
RASSF6
COX18
PPBPL1

Genes in Wide Peak

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

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

Genes
WT1
CD59
CSTF3
HIPK3
EIF3M
C11orf41
FBXO3
WIT1
TCP11L1
PRRG4
QSER1
DEPDC7
LOC283267
CCDC73
C11orf91

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p11.2.

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

Genes
USP22

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.2.

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

Genes
NKX2-1
hsa-mir-624
ARHGAP5
CFL2
COCH
FOXA1
NFKBIA
PAX9
PSMA6
SRP54
SSTR1
AKAP6
KIAA0391
AP4S1
BAZ1A
SCFD1
HECTD1
HEATR5A
NKX2-8
STRN3
MBIP
PPP2R3C
G2E3
EAPP
SNX6
NPAS3
NUBPL
BRMS1L
INSM2
C14orf128
SLC25A21
EGLN3
C14orf126
MIPOL1
CLEC14A
C14orf147
RALGAPA1
SFTA3
C14orf19
FAM177A1
MIR624

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p23.

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

Genes
EDN1
GMPR
JARID2
ATXN1
CD83
RANBP9
SIRT5
MYLIP
TBC1D7
NOL7
GFOD1
CCDC90A
DTNBP1
C6orf114
RNF182
PHACTR1

Genes in Wide Peak

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

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

Genes
NR2C2
C3orf19
ZFYVE20
MRPS25
C3orf20
FGD5

Genes in Wide Peak

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

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

Genes
EGFR
CCT6A
GBAS
PHKG1
PSPH
SUMF2
CHCHD2
MRPS17
LANCL2
VOPP1
SEPT14
ZNF713
FKBP9L
LOC389493
LOC442308
SNORA15

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.3.

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

Genes
ALOX5AP
HMGB1
UBL3
USPL1
KATNAL1
LOC100188949

Genes in Wide Peak

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

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

Genes
PHKB

Genes in Wide Peak

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

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

Genes
TPD52
STMN2
HEY1
MRPS28
PAG1
ZBTB10
ZNF704

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p14.

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

Genes
PHYH
PRPF18
CDC123
USP6NL
OPTN
NUDT5
SEPHS1
UPF2
SEC61A2
MCM10
DHTKD1
FRMD4A
CAMK1D
ECHDC3
CCDC3
UCMA
BEND7
C10orf47
LOC283070

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q33.3.

Table S29. 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
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
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
OXGR1
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
A2LD1
C13orf27
ADPRHL1
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
MIR623
FAM155A
FKSG29

Genes in Wide Peak

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

Table S30. 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 1p12.

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

Genes
NOTCH2
FCGR1B
HMGCS2
HSD3B1
HSD3B2
ADAM30
PHGDH
HAO2
REG4
ZNF697
HIST2H2BA
NBPF7
FAM72B

Genes in Wide Peak

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

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

Genes
ELK4
MDM4
SLC45A3
hsa-mir-135b
ADORA1
ATP2B4
AVPR1B
CHI3L1
CHIT1
CTSE
FMOD
KISS1
MYBPH
MYOG
PPP1R12B
PCTK3
PIK3C2B
PRELP
RABIF
RBBP5
REN
SNRPE
CNTN2
BTG2
PPFIA4
RAB7L1
SOX13
ZC3H11A
TMCC2
LRRN2
KDM5B
PLEKHA6
NFASC
SRGAP2
DSTYK
OPTC
ADIPOR1
CYB5R1
LAX1
KLHDC8A
ETNK2
KLHL12
NUCKS1
NUAK2
PPP1R15B
TMEM183A
LEMD1
SLC26A9
SYT2
LOC127841
GOLT1A
LOC148709
MFSD4
PM20D1
SLC41A1
C1orf157
LOC284578
TMEM81
C1orf186
MIR135B
TMEM183B
SNORA77
FAM72A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p31.3.

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

Genes
CYP2J2
NFIA
USP1
INADL
ANGPTL3
HOOK1
L1TD1
FGGY
TM2D1
ATG4C
DOCK7
C1orf87
KANK4

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 5.4308e-27 | 3.8191e-24 | chr9:21855498-21987722 | 2
1p36.13 | 1.3167e-24 | 5.2751e-24 | chr1:7751874-22911318 | 201
13q14.2 | 1.2161e-22 | 6.1724e-20 | chr13:47731768-47962808 | 2
6q27 | 9.5854e-20 | 1.7491e-17 | chr6:167402953-168450508 | 12
8p23.2 | 5.5498e-18 | 3.4158e-17 | chr8:2080589-6255647 | 1
10q23.31 | 8.9965e-17 | 7.2472e-16 | chr10:89607138-90024018 | 2
19p13.3 | 5.1687e-15 | 5.2967e-15 | chr19:1-3590971 | 125
17p12 | 6.1709e-16 | 2.6337e-13 | chr17:11837355-12512565 | 3
2q37.3 | 7.2567e-14 | 1.4852e-12 | chr2:234304973-242951149 | 74
11q25 | 6.8541e-21 | 2.8709e-11 | chr11:133637835-133772004 | 2
4q35.2 | 5.5015e-11 | 5.8992e-11 | chr4:187110625-191273063 | 19
11p15.5 | 4.6631e-10 | 4.831e-10 | chr11:1-1028970 | 49
3p21.31 | 2.2521e-18 | 3.6473e-09 | chr3:48907188-50694348 | 66
7q36.1 | 4.6541e-09 | 4.6182e-09 | chr7:151448348-151767007 | 1
14q24.3 | 2.2875e-08 | 2.2525e-08 | chr14:65202185-90651830 | 151
15q13.2 | 3.6436e-14 | 2.8409e-08 | chr15:1-30800105 | 146
16q24.3 | 2.0947e-12 | 5.4135e-07 | chr16:87821235-88104546 | 1
21q11.2 | 7.1718e-07 | 7.5154e-07 | chr21:1-21038973 | 28
3p14.1 | 1.0422e-14 | 1.7922e-06 | chr3:55083399-85095529 | 75
11q23.3 | 5.1687e-15 | 5.0215e-06 | chr11:104515402-127834492 | 226
6p25.2 | 3.6758e-05 | 3.6758e-05 | chr6:1-7488350 | 43
10q26.3 | 3.8575e-06 | 0.00019242 | chr10:129138633-135374737 | 46
20p13 | 0.00014126 | 0.00023248 | chr20:1-802133 | 19
6q15 | 6.6976e-07 | 0.00027621 | chr6:74594481-112089697 | 139
16p11.2 | 3.409e-05 | 0.0008517 | chr16:31679819-45256717 | 11
18q23 | 0.00089719 | 0.00089246 | chr18:72400113-76117153 | 15
5q13.3 | 2.3111e-06 | 0.0014419 | chr5:66498811-79652693 | 85
20p12.1 | 0.0014419 | 0.002149 | chr20:14250876-15984135 | 2
9p13.1 | 8.1224e-05 | 0.0023162 | chr9:38609152-70342057 | 46
5q21.3 | 0.00065155 | 0.0051318 | chr5:104437684-107222809 | 2
17q21.31 | 0.00021417 | 0.0054479 | chr17:37824299-41072667 | 96
9p24.1 | 7.5224e-06 | 0.0060336 | chr9:7786330-12683402 | 2
12p13.1 | 0.0077948 | 0.0078028 | chr12:10870038-19485837 | 69
12q23.1 | 0.0006834 | 0.0084302 | chr12:97648132-98955403 | 2
13q12.11 | 4.3657e-06 | 0.0084302 | chr13:1-24156843 | 35
7p22.3 | 0.011514 | 0.011361 | chr7:1-2370980 | 28
16q23.1 | 3.6195e-06 | 0.015007 | chr16:76614605-78185271 | 1
1p13.3 | 0.0016094 | 0.019522 | chr1:82229663-119715206 | 255
15q15.3 | 8.4754e-08 | 0.020373 | chr15:31935411-50837720 | 197
11q11 | 0.012555 | 0.02435 | chr11:51369237-56513463 | 50
12q13.13 | 0.006619 | 0.036962 | chr12:46677323-54887564 | 221
5q11.2 | 2.0672e-05 | 0.043102 | chr5:50724626-65930217 | 68
17p12 | 0.0016347 | 0.060675 | chr17:15405082-15555845 | 2
2p25.1 | 0.079864 | 0.079776 | chr2:1-27049802 | 118
22q11.1 | 0.080692 | 0.083086 | chr22:1-16425857 | 14
8p12 | 0.012834 | 0.091256 | chr8:21949765-37835996 | 103
17p13.3 | 0.0014814 | 0.093679 | chr17:1-589677 | 4
19q13.32 | 0.13814 | 0.13545 | chr19:51409314-53193111 | 60
2q22.1 | 0.0016853 | 0.20603 | chr2:115632787-158560069 | 135
17q12 | 0.005828 | 0.20603 | chr17:25671879-34089640 | 111
22q13.31 | 0.20611 | 0.20611 | chr22:42536653-49691432 | 84
12q24.31 | 0.0023485 | 0.213 | chr12:102679860-132349534 | 264
4p16.3 | 0.21974 | 0.22508 | chr4:1-6837356 | 86
2q21.1 | 9.8714e-05 | 0.4428 | chr2:109733438-137467837 | 141

Genes in Wide Peak

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

Table S34. 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 1p36.13.

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

Genes
PAX7
SDHB
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
TNFRSF8
CDA
CDC42
CLCN6
CLCNKA
CLCNKB
CORT
DDOST
DFFA
ECE1
EPHA2
ENO1
EPHA8
MTOR
HSPG2
HTR6
TNFRSF9
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
RAP1GAP
RSC1A1
SLC2A5
SRM
TNFRSF1B
ZBTB17
PRDM2
AKR7A2
ALDH4A1
EIF4G3
PER3
DHRS3
VAMP3
H6PD
CROCC
ZBTB40
MFN2
CELA3A
ANGPTL7
UBE4B
MAD2L2
PDPN
MASP2
UTS2
MSTP2
MSTP9
PADI2
PARK7
CTRC
CLSTN1
AKR7A3
SPEN
KIAA0090
KIF1B
PLEKHM2
OTUD3
KIAA1026
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
PADI4
C1orf144
FBXO2
FBXO6
PLA2G2D
HSPB7
HSPC157
UBIAD1
PADI1
PLA2G2E
SLC45A1
HP1BP3
CELA2B
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
FBLIM1
PQLC2
CASZ1
TMEM51
ARHGEF10L
VPS13D
CAMK2N1
NBPF1
NECAP2
RCC2
CTNNBIP1
AGTRAP
PTCHD2
KIF17
MIIP
CELA2A
PLA2G2F
NMNAT1
PINK1
PRAMEF1
PRAMEF2
EFHD2
C1orf89
MUL1
AGMAT
GPR157
SPSB1
TAS1R2
ACTL8
USP48
NBPF3
SLC25A33
DDI2
LZIC
CROCCL1
IGSF21
KIAA2013
C1orf158
FBXO44
CROCCL2
FHAD1
RBP7
AADACL3
IFFO2
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf127
C1orf64
SLC2A7
FAM43B
TMEM201
C1orf126
AKR7L
TMCO4
SLC25A34
ESPNP
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
APITD1
TMEM82
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
PRAMEF3
LDLRAD2
MIR34A
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
PRAMEF7
C1orf200
PRAMEF19
PRAMEF20
LOC649330
PRAMEF22
PRAMEF15
PRAMEF16
SNORA59B
SNORA59A
PRAMEF14
FLJ37453

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

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

Genes
MLLT4
CCR6
GPR31
KIF25
TCP10
C6orf123
UNC93A
FRMD1
TTLL2
TCP10L2
C6orf124
HGC6.3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
PTEN
KILLIN

Genes in Wide Peak

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

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

Genes
GNA11
STK11
TCF3
FSTL3
hsa-mir-1227
hsa-mir-1909
hsa-mir-1302-2
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
GADD45B
NFIC
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
SGTA
TBXA2R
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
MED16
APC2
ABCA7
HMG20B
UQCR
SBNO2
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
SLC39A3
THEG
FZR1
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
NCLN
SPPL2B
WDR18
REXO1
ZNF77
C19orf29
BRUNOL5
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
DOHH
KLF16
DOT1L
KISS1R
LMNB2
MUM1
MIDN
C19orf22
C19orf6
C19orf20
REEP6
C19orf36
SCAMP4
ADAT3
ZNF554
GRIN3B
ZNF57
JSRP1
MOBKL2A
C19orf28
GIPC3
C19orf21
PLK5P
C2CD4C
C19orf23
C19orf25
ATP8B3
DIRAS1
ZNF555
C19orf26
C19orf34
C19orf77
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
ONECUT3
MEX3D
FLJ45445
PRSSL1
FAM138F
LINGO3
FAM138A
FAM138C
C19orf71

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
MIR744

Genes in Wide Peak

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

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

Genes
hsa-mir-149
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
SPP2
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A1
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
AGAP1
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC151174
MSL3L2
C2orf85
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
MIR149
DNAJB3
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

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

Genes
GLB1L2
GLB1L3

Genes in Wide Peak

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

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

Genes
DUX4
F11
FAT1
FRG1
KLKB1
MTNR1A
TLR3
FAM149A
TUBB4Q
ZFP42
TRIML2
CYP4V2
TRIML1
FRG2
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

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

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

Genes
HRAS
hsa-mir-210
AP2A2
CD151
DRD4
IRF7
MUC6
POLR2L
PSMD13
RNH1
RPLP2
SCT
TALDO1
TSPAN4
RASSF7
IFITM1
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
BET1L
CEND1
MUPCDH
LRDD
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
ODF3
LRRC56
LOC143666
SCGB1C1
NLRP6
C11orf35
EFCAB4A
TMEM80
ANO9
B4GALNT4
PDDC1
IFITM5
MIR210
SNORA52
LOC100133161

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.31.

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

Genes
hsa-mir-566
hsa-mir-191
AMT
APEH
RHOA
CISH
DAG1
GNAI2
GNAT1
GPX1
HYAL1
IMPDH2
LAMB2
MST1
MST1R
QARS
SEMA3F
TCTA
UBA7
USP4
IFRD2
MAPKAPK3
SEMA3B
HYAL3
HYAL2
BSN
CACNA2D2
IP6K1
RBM6
RBM5
TRAIP
ARIH2
TUSC4
USP19
SLC38A3
CYB561D2
TMEM115
WDR6
RASSF1
TUSC2
LAMB2L
NAT6
NDUFAF3
GMPPB
C3orf18
ZMYND10
HEMK1
P4HTM
QRICH1
DALRD3
RNF123
CCDC71
CAMKV
NICN1
MON1A
C3orf45
KLHDC8B
CCDC36
C3orf62
AMIGO3
CDH29
C3orf54
MIR191
MIR425
C3orf71
LOC646498

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.1.

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

Genes
MLL3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.3.

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

Genes
RAD51L1
TSHR
GPHN
hsa-mir-1260
ACTN1
ACYP1
ARG2
BCYRN1
ZFP36L1
CALM1
ENTPD5
FOXN3
DIO2
DLST
EIF2S1
ERH
ESRRB
FOS
FUT8
GALC
GSTZ1
GTF2A1
LTBP2
MAP3K9
ALDH6A1
PGF
PIGH
PSEN1
PSMC1
ABCD4
SEL1L
SFRS5
SLC8A3
SLC10A1
TGFB3
DPF3
GPR65
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
RPS6KA5
NRXN3
SPTLC2
RGS6
KIAA0247
KIAA0317
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
PTPN21
C14orf1
VASH1
SNW1
PCNX
TTLL5
ANGEL1
ZFYVE26
TTC9
FLRT2
SIPA1L1
DCAF4
PLEK2
MLH3
PRO1768
POMT2
COQ6
FCF1
RDH11
COX16
ATP6V1D
ZFYVE1
KCNK10
C14orf102
EXD2
C14orf115
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
TDP1
SPATA7
YLPM1
KCNK13
C14orf162
ADCK1
TMEM63C
GALNTL1
PLEKHH1
ZNF410
NGB
RBM25
C14orf133
SMOC1
C14orf4
MPP5
FAM164C
C14orf169
ZC3H14
C14orf45
C14orf156
DNAL1
RPS6KL1
STON2
KIAA1737
PAPLN
C14orf143
C14orf43
LIN52
NEK9
C14orf179
C14orf148
JDP2
ISCA2
ACOT4
TTC8
RDH12
ADAM21P
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
C14orf145
TTC7B
FAM71D
TMEM229B
C14orf174
EML5
PROX2
ZDHHC22
TMED8
C14orf178
SNORD56B
VSX2
HEATR4
C14orf181
FLJ44817
C14orf53
ACOT1
ACOT6
TMEM90A
SNORA79
LOC100289511

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.2.

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

Genes
hsa-mir-211
hsa-mir-1268
APBA2
BCL8
CHRNA7
GABRA5
GABRB3
GABRG3
IPW
TRPM1
NDN
OCA2
SCG5
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
ARHGAP11A
MTMR15
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
KLF13
MAGEL2
MTMR10
NDNL2
ATP10A
NIPA2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
OTUD7A
OR4N4
GOLGA6L1
GOLGA8G
GOLGA9P
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMML1
POTEB
SNORD64
PAR4
PAR-SN
GOLGA8E
OR4M2
OR4N3P
HERC2P2
MIR211
NF1P1
WHAMML2
LOC646214
CXADRP2
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
HBII-52-24
HBII-52-27
HBII-52-28
HBII-52-45
HBII-52-46
GOLGA8F
GOLGA8D
FAM7A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

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

Genes
ANKRD11

Genes in Wide Peak

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

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

Genes
hsa-mir-125b-2
BAGE
CXADR
PRSS7
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
NCRNA00157
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
C21orf99
LIPI
ABCC13
POTED
C21orf34
C21orf81
MIRLET7C
MIR125B2
MIR99A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
FHIT
MITF
FOXP1
hsa-mir-1324
hsa-mir-1284
ARF4
C3orf51
DNASE1L3
FLNB
GBE1
GPR27
CNTN3
PDHB
PTPRG
ROBO1
ROBO2
ATXN7
TMF1
WNT5A
SLMAP
ACOX2
CADPS
SUCLG2
HESX1
UBA3
MAGI1
PSMD6
ARL6IP5
RPP14
FAM107A
PDZRN3
FRMD4B
C3orf63
RYBP
LRIG1
ERC2
APPL1
ARHGEF3
IL17RD
PXK
FEZF2
FLJ10213
SHQ1
LMOD3
ADAMTS9
ABHD6
C3orf14
PROK2
THOC7
ID2B
KBTBD8
SLC25A26
FAM3D
C3orf49
SNTN
SYNPR
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
DNAH12
PDE12
FAM116A
C3orf64
CCDC66
LOC285401
EIF4E3
SPATA12
FAM19A1
FAM86D
GLT8D4
ZNF717
FRG2C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.3.

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

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-100
hsa-mir-125b-1
hsa-mir-34c
ACAT1
ACRV1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
VWA5A
MCAM
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
C11orf60
DSCAML1
GRAMD1B
ARHGAP20
USP28
AASDHPPT
PKNOX2
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
C11orf61
ALG9
ASAM
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
C1QTNF5
PANX3
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
MPZL3
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
LOC399959
PATE2
PATE4
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
HEPN1
LOC643923
CLDN25
RPL23AP64
PATE3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.2.

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

Genes
IRF4
BPHL
SERPINB1
F13A1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TUBB2A
RIPK1
PRPF4B
CDYL
LY86
PECI
FARS2
RPP40
FAM50B
NRN1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
RIOK1
FOXQ1
HUS1B
C6orf195
C6orf145
C6orf146
LOC285768
LOC285780
CAGE1
MYLK4
TUBB2B
FAM136B
PSMG4
DKFZP686I15217
C6orf201
PPP1R3G

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
DUX4
hsa-mir-202
ADAM8
BNIP3
CYP2E1
ECHS1
INPP5A
MGMT
MKI67
PTPRE
UTF1
GLRX3
DPYSL4
TUBGCP2
VENTX
CALY
PPP2R2D
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
CLRN3
C10orf91
PWWP2B
PAOX
EBF3
C10orf93
TCERG1L
C10orf125
JAKMIP3
STK32C
FOXI2
FRG2B
SPRN
MIR202
NPS
LOC619207
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p13.

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

Genes
CSNK2A1
SOX12
TCF15
RBCK1
TRIB3
NRSN2
DEFB126
FAM110A
ZCCHC3
SCRT2
C20orf54
TBC1D20
C20orf96
SRXN1
DEFB127
DEFB129
DEFB125
DEFB128
DEFB132

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q15.

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
BCKDHB
CCNC
CGA
CNR1
COL12A1
COX7A2
EPHA7
FOXO3
GABRR1
GABRR2
GPR6
GRIK2
HTR1B
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
REV3L
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDC2L6
MDN1
KIAA0776
ORC3L
SFRS18
IBTK
SENP6
FBXL4
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
CYB5R4
C6orf203
CDC40
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
NCRNA00120
FAM46A
TMEM30A
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
C6orf168
GJA10
RTN4IP1
USP45
SLC22A16
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
SLC16A10
RIPPLY2
IRAK1BP1
PM20D2
SFRS13B
C6orf165
PRSS35
LCA5
C6orf163
C6orf185
AKD1
LACE1
C6orf167
SCML4
C6orf182
PPIL6
GJB7
SNHG5
LIN28B
LOC442245
LOC553137
TSG1
SNORD50B
C6orf186

Genes in Wide Peak

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

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

Genes
hsa-mir-1826
ZNF267
TP53TG3
SHCBP1
ANKRD26P1
LOC146481
LOC283914
SLC6A10P
HERC2P4
UBE2MP1
TP53TG3B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
GALR1
MBP
NFATC1
ZNF236
CTDP1
TXNL4A
ADNP2
KCNG2
SALL3
C18orf22
PQLC1
PARD6G
ATP9B
HSBP1L1
LOC100130522

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.3.

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

Genes
PIK3R1
ARSB
BHMT
BTF3
CCNB1
CDK7
CRHBP
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
TNPO1
CD180
MAP1B
NAIP
OCLN
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
THBS4
SERF1A
ENC1
AP3B1
PDE8B
HOMER1
SCAMP1
CARTPT
COL4A3BP
LHFPL2
NSA2
IQGAP2
SV2C
MRPS27
OTP
BHMT2
FAM169A
DMGDH
GCNT4
POLK
AGGF1
WDR41
BDP1
ANKRA2
MCCC2
RGNEF
SLC30A5
CENPH
PTCD2
UTP15
ZBED3
GFM2
MRPS36
FCHO2
JMY
TMEM171
TMEM174
C5orf37
MARVELD2
PAPD4
ZNF366
S100Z
CCDC125
CMYA5
ANKRD31
SERINC5
MTX3
LOC644936
LOC647859
GUSBP3
GTF2H2B
LOC653391
SNORA47
GTF2H2C
SERF1B
LOC728723
GTF2H2D
LOC100170939
LOC100272216
NCRUPAR

Genes in Wide Peak

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

Table S61. 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 9p13.1.

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

Genes
hsa-mir-1299
PGM5
ZNF658
FAM75A7
CNTNAP3
ANKRD20A1
C9orf122
CBWD5
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
AQP7P2
FAM74A1
FAM74A4
ZNF658B
LOC440839
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
FAM75A2
LOC642929
CBWD6
FAM75A1
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
ANKRD20A4
CCDC29
FOXD4L2
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.3.

Table S63. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
EFNA5
RAB9P1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

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

Genes
BRCA1
ETV4
AOC2
ARL4D
ATP6V0A1
FMNL1
DHX8
DUSP3
EZH1
FZD2
G6PC
GFAP
CCR10
GRN
HSD17B1
IFI35
ITGA2B
NBR1
ADAM11
MEOX1
MPP2
MPP3
NAGLU
NMT1
PPY
PYY
RPL27
SLC4A1
MLX
TUBG1
UBTF
RND2
CNTNAP1
AOC3
BECN1
MAP3K14
EFTUD2
PLEKHM1
HDAC5
GJC1
PSME3
NBR2
RAMP2
VAT1
HEXIM1
C1QL1
RUNDC3A
GPATCH8
C17orf88
TUBG2
CCDC56
PSMC3IP
SOST
SLC25A39
HIGD1B
LRRC37A4
ATXN7L3
WNK4
C17orf53
TMUB2
ACBD4
DCAKD
PLEKHH3
DBF4B
COASY
AARSD1
VPS25
TMEM101
LOC90586
G6PC3
ASB16
PLCD3
TMEM106A
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
CD300LG
KIF18B
RUNDC1
NAGS
FAM134C
SH3D20
ARHGAP27
C17orf105
FAM171A2
C17orf104
C17orf65
LOC388387
CCDC103
MGC57346
LOC644172
LOC100130581
LOC100133991
LOC100190938

Genes in Wide Peak

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

Table S65. 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 12p13.1.

Table S66. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ETV6
hsa-mir-614
hsa-mir-613
hsa-mir-1244
ARHGDIB
ART4
CDKN1B
CREBL2
EMP1
EPS8
GPR19
GRIN2B
GUCY2C
LRP6
MGP
MGST1
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PRH2
PTPRO
GPRC5A
STRAP
PRR4
TAS2R13
TAS2R14
HEBP1
DERA
DDX47
WBP11
PLEKHA5
MANSC1
GPRC5D
ATF7IP
H2AFJ
LMO3
KIAA1467
BCL2L14
RERGL
PLBD1
DUSP16
APOLD1
GSG1
RERG
PLCZ1
HTR7P
CAPZA3
LOH12CR1
HIST4H4
ERP27
C12orf60
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
C12orf36
TAS2R42
RPL13AP20
C12orf69
LOH12CR2
PRB2
MIR613
MIR614

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

Table S67. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ANKS1B
FAM71C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

Table S68. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PARP4
FGF9
GJA3
GJB2
MIPEP
SGCG
TUBA3C
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
PSPC1
TNFRSF19
XPO4
MRP63
TPTE2
N6AMT2
SKA3
EFHA1
SPATA13
ZDHHC20
DKFZp686A1627
LOC284232
C1QTNF9
LOC348021
LOC374491
C1QTNF9B
PCOTH
LOC100101938

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.3.

Table S69. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-339
GPER
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
ADAP1
UNC84A
INTS1
SNX8
FTSJ2
C7orf20
CYP2W1
HEATR2
FAM20C
MICALL2
PSMG3
C7orf50
ZFAND2A
COX19
KIAA1908
GPR146
TMEM184A
TFAMP1
UNCX
ELFN1
MIR339

Genes in Wide Peak

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

Table S70. 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 1p13.3.

Table S71. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
PTPN22
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
C1orf103
CTTNBP2NL
C1orf183
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
SPATA1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
C1orf203
FAM40A
C1orf59
GBP4
GBP5
SSX2IP
OLFM3
WDR63
C1orf161
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
LOC149620
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AFARP1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
LOC400759
MIR137
MIR197
C1orf180
BCL2L15
LOC441897
LOC492303
RBMXL1
CYMP
LOC648740
NBPF6
SCARNA2
MIR553
MIR942
MIR760

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.3.

Table S72. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BUB1B
C15orf55
C15orf21
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
ACTC1
B2M
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
MYO5A
PLCB2
MAPK6
RAD51
SLC12A1
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
USP8
SLC28A2
COPS2
TGM5
HISPPD2A
AQR
SECISBP2L
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
CEP152
MAPKBP1
GOLGA8A
RTF1
MGA
DMXL2
VPS39
AP4E1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PLDN
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
TRPM7
PPP1R14D
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
MYO5C
KIAA1370
C15orf24
PAK6
DTWD1
CASC5
AVEN
GJD2
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
C15orf41
SPPL2A
ZFYVE19
FRMD5
DISP2
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
SLC24A5
FAM98B
PLA2G4D
GLDN
MRPL42P5
USP50
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
GOLGA8B
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
MIR548A3
MIR626
MIR627
LOC723972
LOC728758
LOC729082
MIR147B
LOC100129387
LOC100132724
JMJD7
PLA2G4B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q11.

Table S73. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
OR5I1
OR5L2
TRIM48
OR8J3
OR4P4
OR4C15
OR4A16
OR4A15
SPRYD5
OR4C46
OR8I2
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR10AG1
OR5J2
OR9G4
OR5F1
OR5AP2
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR8U8
OR9G9

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q13.13.

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ATF1
HOXC11
HOXC13
MLL2
hsa-mir-148b
hsa-mir-615
hsa-mir-196a-2
hsa-mir-1293
hsa-mir-1291
ACCN2
ACVR1B
ACVRL1
ADCY6
AMHR2
AQP2
AQP5
AQP6
ARF3
ATP5G2
CACNB3
CCNT1
CD63
CDK2
DGKA
EIF4B
CELA1
ERBB3
BLOC1S1
GPD1
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC8
HOXC9
HOXC10
HOXC12
IGFBP6
ITGA5
ITGA7
ITGB7
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
MMP19
MYL6
NFE2
SLC11A2
PA2G4
PCBP2
PDE1B
PFDN5
PFKM
POU6F1
PPP1R1A
PRKAG1
PRPH
RAB5B
RARG
RDH5
RPL41
RPS26
SCN8A
SILV
SMARCC2
SMARCD1
SP1
SUOX
TARBP2
TMBIM6
TFCP2
WNT1
WNT10B
MAP3K12
TUBA1A
AAAS
SOAT2
NPFF
KRT75
DDX23
SLC4A8
ESPL1
DAZAP2
KIAA0748
TROAP
GDF11
TUBA1B
MCRS1
ATF7
GALNT6
COPZ1
FAIM2
DDN
ESYT1
TENC1
KCNH3
CBX5
ANP32D
SMUG1
PRPF40B
METTL7A
LETMD1
ZNF385A
RND1
ORMDL2
RACGAP1
SENP1
DHH
FKBP11
KRT76
CSAD
BIN2
LIMA1
GPR84
PRR13
C12orf41
LMBR1L
SMAGP
DIP2B
CALCOCO1
NCKAP5L
NEUROD4
C12orf10
C12orf44
IKZF4
SPATS2
DNAJC22
CSRNP2
FAM186B
WIBG
SARNP
TUBA1C
ZC3H10
SPRYD3
MFSD5
C12orf62
DNAJC14
CCDC65
LACRT
FMNL3
LASS5
KRT71
LARP4
DCD
MUCL1
FAM186A
OR10P1
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
GTSF1
OR10A7
KRT74
ASB8
MYL6B
KRT72
BCDIN3D
LOC144438
KRT80
GRASP
KRT78
METTL7B
OR6C74
OR6C3
LOC255411
LOC283332
ZNF740
OR6C6
LOC283404
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
ANKRD33
OR6C2
OR6C4
H1FNT
OR8S1
KRT77
C12orf68
OR6C1
OR6C75
OR6C76
OR6C70
LOC400043
FIGNL2
OR6C65
OR6C68
MIR196A2
FLJ12825
OR9K2
MIR148B
HIGD1C
GLYCAM1
HNRPA1L-2
SNORA2A
SNORA2B
SNORA34
HOTAIR
LOC100240734
LOC100240735
LOC100286844

Genes in Wide Peak

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

Table S75. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IL6ST
hsa-mir-582
hsa-mir-449b
hsa-mir-581
TRIM23
ERCC8
GZMA
GZMK
HTR1A
ITGA1
ITGA2
KIF2A
MAP3K1
MOCS2
NDUFS4
PDE4D
PPAP2A
HSPB3
SDCCAG10
CCNO
FST
PLK2
ESM1
ADAMTS6
PPWD1
SKIV2L2
PART1
DIMT1L
IPO11
PELO
DHX29
DDX4
SGTB
ARL15
DEPDC1B
ERBB2IP
NLN
ZSWIM6
CENPK
GPBP1
ANKRD55
ELOVL7
C5orf44
NDUFAF2
SNX18
RAB3C
C5orf35
IL31RA
SFRS12
SLC38A9
MIER3
CDC20B
GAPT
FLJ37543
RNF180
SFRS12IP1
ACTBL2
RNF138P1
ISCA1L
RGS7BP
GPX8
MIR449A
C5orf43
MIR449B
MIR581
LRRC70
FAM159B
LOC100303749

Genes in Wide Peak

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

Table S76. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TRIM16
CDRT1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.1.

Table S77. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-1301
ACP1
ADCY3
APOB
RHOB
CENPA
DDX1
DTNB
E2F6
FKBP1B
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KIF3C
MATN3
ODC1
POMC
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
PDIA6
MYCNOS
RAB10
YWHAQ
EFR3B
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
ITSN2
TTC15
DNAJC27
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
C2orf18
ASXL2
ADI1
ALLC
DPYSL5
KIDINS220
WDR35
RDH14
C2orf43
HS1BP3
COLEC11
CENPO
SMC6
NOL10
C2orf44
FAM49A
SELI
RSAD2
C2orf39
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
C2orf50
PQLC3
LOC150622
FAM84A
GDF7
GPR113
UBXN2A
CYS1
ATP6V1C2
RNASEH1
FAM150B
IAH1
C2orf70
LOC339788
MSGN1
GEN1
C2orf48
PFN4
LOC375190
MFSD2B
C2orf90
C2orf79
LOC400940
FAM110C
C2orf84
RAD51AP2
LOC730811
SNORA80B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.1.

Table S78. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IL17RA
POTEH
HSFYP1
CECR6
CECR5
CECR2
CECR1
OR11H1
GAB4
CCT8L2
XKR3
psiTPTE22
CECR7
CECR4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p12.

Table S79. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
WRN
hsa-mir-548h-4
hsa-mir-320a
ADRA1A
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
EXTL3
PTK2B
GNRH1
GSR
GTF2E2
NRG1
LOXL2
NEFM
NEFL
NKX3-1
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
STC1
FZD3
UBXN8
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
ENTPD4
PHYHIP
SORBS3
DCTN6
PNMA2
ADAM28
RBPMS
ERLIN2
PROSC
TRIM35
RHOBTB2
KIF13B
LEPROTL1
SLC39A14
GPR124
ADAMDEC1
PURG
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
CCDC25
BRF2
INTS9
HR
PBK
ZNF395
BIN3
TEX15
KIAA1967
PDLIM2
EBF2
FAM160B2
DUSP26
HMBOX1
RNF122
NUDT18
DOCK5
FLJ14107
ZNF703
C8orf41
REEP4
STMN4
MAK16
FUT10
CHMP7
NKX2-6
UNC5D
PEBP4
CDCA2
ESCO2
FBXO16
KCNU1
R3HCC1
LGI3
SCARA5
LOC286135
C8orf80
MIR320A
C8orf58
C8orf75
MBOAT4
LOC728024

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.3.

Table S80. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RPH3AL
VPS53
FAM101B
C17orf97

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

Table S81. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
C5AR1
CALM3
AP2S1
CRX
GRLF1
NPAS1
PPP5C
PTGIR
SEPW1
SLC1A5
SLC8A2
SULT2A1
NAPA
DHX34
SAE1
KPTN
ZC3H4
PRKD2
CCDC9
BBC3
GPR77
STRN4
GLTSCR2
GLTSCR1
EHD2
TMEM160
PNMAL1
MEIS3
PNMAL2
HIF3A
FKRP
CCDC8
ZNF541
GNG8
DACT3
PRR24
TPRX1
IGFL1
SNORD23
SNAR-A1
SNAR-A2
SNAR-A12
BSPH1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-C1
SNAR-C3
SNAR-A14

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

Table S82. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERCC3
hsa-mir-1978
hsa-mir-128-1
hsa-mir-663b
ACVR1
ACVR2A
BIN1
RND3
CACNB4
CCNT2
DARS
DBI
EN1
GLI2
GPD2
GPR17
GPR39
GYPC
HNMT
INHBB
KCNJ3
KIF5C
LCT
MCM6
MGAT5
MYO7B
NEB
NR4A2
ORC4L
POLR2D
PROC
PTPN4
RALB
SCTR
TNFAIP6
TSN
CXCR4
MARCO
DDX18
KYNU
NMI
HS6ST1
CYTIP
ZEB2
STAM2
MAP3K2
GALNT5
NXPH2
RAB3GAP1
UBXN4
CLASP1
R3HDM1
EPC2
ARL5A
PTPN18
MMADHC
C2orf27A
TFCP2L1
ARHGEF4
INSIG2
LRP1B
CCDC93
PLEKHB2
RIF1
STEAP3
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
CFC1
RPRM
UGGT1
ERMN
DPP10
EPB41L5
TMEM185B
SAP130
GTDC1
FAM128B
YSK4
THSD7B
TMEM177
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
MKI67IP
SFT2D3
LOC84931
CCDC74A
CCDC74B
IMP4
TUBA3E
TUBA3D
FMNL2
GALNT13
LYPD1
CNTNAP5
ACMSD
FAM168B
C2orf76
ACVR1C
LYPD6
LYPD6B
TMEM37
LOC150527
LOC150776
LOC150786
LOC151162
ARL6IP6
C1QL2
PCDP1
FAM123C
SPOPL
CYP27C1
NCKAP5
GPR148
RBM43
LOC389033
LOC401010
MIR128-1
C2orf27B
LOC440905
POTEE
NCRNA00164
CFC1B
FAM128A
POTEF
PABPCP2
C2orf14
RNU4ATAC

Genes in Wide Peak

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

Table S83. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NF1
TAF15
SUZ12
hsa-mir-632
hsa-mir-365-2
ACACA
ACCN1
AP2B1
CPD
EVI2A
EVI2B
LHX1
LIG3
MYO1D
OMG
PEX12
PSMD11
RAD51L3
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
TADA2A
HNF1B
ZNF207
CDK5R1
ZNHIT3
GOSR1
CCL4L1
CCT6B
DDX52
DUSP14
SYNRG
TMEM98
TBC1D29
AATF
SOCS7
CRLF3
NLE1
FNDC8
SLFN12
RHOT1
C17orf79
ADAP2
UTP6
LYZL6
ARHGAP23
C17orf75
MMP28
DHRS11
C17orf42
GGNBP2
ATAD5
MRM1
MYO19
SNIP
TBC1D3F
RNF135
MRPL45
RAB11FIP4
ZNF830
SLFN11
RASL10B
LRRC37B
RFFL
TMEM132E
SPACA3
C17orf50
SLFN13
AMAC1
UNC45B
LRRC37B2
SLFN5
RHBDL3
RDM1
GAS2L2
C17orf66
PIGW
C17orf78
LOC284100
SLFN12L
SLFN14
CCL14-CCL15
CCL4L2
C17orf102
MIR193A
TBC1D3B
TBC1D3C
CCL3L3
SUZ12P
GPR179
ARGFXP2
DPRXP4
TBC1D3G
SNORD7
MIR632
TBC1D3
TBC1D3H
MIR365-2
C17orf96

Genes in Wide Peak

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

Table S84. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
C22orf9
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
ALG12
CRELD2
ADM2
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
PNPLA5
LOC150381
C22orf40
CN5H6.4
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
NCRNA00207
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.31.

Table S85. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ALDH2
BCL7A
PTPN11
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
ACACB
ACADS
ATP2A2
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DTX1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
MVK
MYL2
NFYB
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PLA2G1B
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFRS8
TBX5
TBX3
HNF1A
TDG
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
BRAP
ULK1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SFRS9
HRK
GPR109B
HIP1R
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
SH2B3
ARPC3
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
SDS
RAB35
SNRNP35
PRDM4
CIT
PWP1
FICD
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
FBXW8
HSPB8
GPR81
IFT81
C12orf24
HCFC2
CHST11
GALNT9
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
RIC8B
APPL2
SBNO1
SVOP
ZCCHC8
POLR3B
CHFR
WSB2
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
TRPV4
LHX5
SUDS3
C12orf43
VPS33A
RSRC2
AACS
DDX54
NOC4L
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
C12orf30
SLC24A6
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
SLC41A2
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf65
TMEM132C
CCDC64
SDSL
MGC16384
TMEM132B
IQCD
LOC116437
C12orf45
TMEM132D
SLC15A4
ASCL4
BTBD11
ALKBH2
FOXN4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
RAD9B
FAM109A
LOC144742
ALDH1L2
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
LOC253724
LRRC43
TCP11L2
GPR133
MORN3
MYO1H
C12orf51
KSR2
NME2P1
GATC
C12orf27
DDX51
MMAB
GPR109A
TMEM119
LOC338799
EP400NL
RILPL1
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
EID3
MAP1LC3B2
SNORA49
MIR620
C12orf73
LOC100128554
LOC100130238
LOC100190940
NCRNA00173
ZNF605

Genes in Wide Peak

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

Table S86. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FGFR3
WHSC1
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
EVC
GAK
GRK4
HTT
HGFAC
IDUA
LETM1
LRPAP1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
S100P
SH3BP2
WFS1
WHSC2
ZNF141
SLBP
NOP14
FAM193A
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
D4S234E
STX18
FGFRL1
CYTL1
PIGG
CNO
STK32B
LYAR
KIAA1530
ZFYVE28
TNIP2
HAUS3
ABCA11P
MFSD7
TMEM175
TMEM128
C4orf42
TMEM129
MRFAP1
LOC93622
MRFAP1L1
EVC2
OTOP1
ZNF595
JAKMIP1
FAM53A
ZNF509
ZNF721
ZNF718
CRIPAK
DOK7
RNF212
C4orf10
NAT8L
C4orf44
LOC348926
POLN
C4orf50
C4orf48
ZNF876P
ZNF732
SCARNA22
MIR943
LOC100130872

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q21.1.

Table S87. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERCC3
PAX8
TTL
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
BIN1
BUB1
CCNT2
DARS
DBI
EN1
GLI2
GPR17
GPR39
GYPC
IL1A
IL1B
IL1RN
INHBB
LCT
MCM6
MGAT5
MYO7B
NPHP1
POLR2D
PROC
PTPN4
RALB
SCTR
SLC20A1
TSN
MALL
CXCR4
MARCO
DDX18
HS6ST1
BCL2L11
ACTR3
MERTK
MAP3K2
RABL2A
RAB3GAP1
UBXN4
CLASP1
R3HDM1
PSD4
PTPN18
IL1F5
IL1F8
IL1F7
IL1F6
C2orf27A
TFCP2L1
ARHGEF4
INSIG2
CCDC93
PLEKHB2
STEAP3
ACOXL
WDR33
SMPD4
IWS1
LIMS2
CFC1
IL1F9
UGGT1
DPP10
EPB41L5
ANAPC1
TMEM185B
SAP130
FAM128B
YSK4
SLC35F5
TMEM177
TMEM163
AMMECR1L
ZRANB3
RAB6C
POLR1B
RGPD5
CHCHD5
CCDC115
MKI67IP
ZC3H8
IL1F10
MGC13005
SFT2D3
TMEM87B
LOC84931
CCDC74A
CCDC74B
IMP4
LIMS3
TUBA3E
TUBA3D
LYPD1
RPL23AP7
CNTNAP5
FBLN7
ACMSD
FAM168B
C2orf76
TMEM37
CKAP2L
CBWD2
LOC150527
LOC150776
LOC150786
LOC151009
LOC151162
C1QL2
FOXD4L1
PCDP1
FAM123C
NCRNA00116
CYP27C1
NCKAP5
GPR148
WASH2P
ZC3H6
LOC389033
LOC401010
MIR128-1
C2orf27B
LOC440895
LOC440905
POTEE
LOC541471
NCRNA00164
CFC1B
FAM128A
FAM138B
LOC654433
RGPD8
POTEF
RGPD6
C2orf14
RNU4ATAC
LIMS3-LOC440895

Arm-level results

Table 3. Get Full Table Arm-level significance table - 24 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.16 | 1.48 | 0.304 | 0.19 | 3.74 | 0.000254
1q | 1572 | 0.61 | 36.4 | 0 | 0.11 | -1.55 | 1
2p | 753 | 0.07 | -7.01 | 1 | 0.08 | -6.05 | 1
2q | 1235 | 0.05 | -7.84 | 1 | 0.11 | -3.38 | 1
3p | 853 | 0.07 | -6.35 | 1 | 0.16 | -0.235 | 0.963
3q | 917 | 0.15 | -1.27 | 1 | 0.07 | -6.9 | 1
4p | 366 | 0.04 | -8.64 | 1 | 0.24 | 4.16 | 4.85e-05
4q | 865 | 0.05 | -7.92 | 1 | 0.19 | 2.06 | 0.0388
5p | 207 | 0.21 | 1.89 | 0.162 | 0.15 | -2.61 | 1
5q | 1246 | 0.15 | -0.232 | 1 | 0.20 | 3.36 | 0.000949
6p | 937 | 0.17 | 0.413 | 1 | 0.16 | -0.198 | 0.963
6q | 692 | 0.11 | -3.72 | 1 | 0.25 | 5.33 | 2.15e-07
7p | 508 | 0.20 | 1.39 | 0.319 | 0.10 | -4.76 | 1
7q | 1071 | 0.17 | 0.645 | 0.92 | 0.11 | -3.44 | 1
8p | 495 | 0.21 | 1.6 | 0.269 | 0.51 | 23.1 | 0
8q | 697 | 0.49 | 22.6 | 0 | 0.22 | 2.61 | 0.0093
9p | 343 | 0.11 | -4.72 | 1 | 0.25 | 5.05 | 8.65e-07
9q | 916 | 0.08 | -5.72 | 1 | 0.21 | 3.22 | 0.00141
10p | 312 | 0.15 | -2.14 | 1 | 0.13 | -3.22 | 1
10q | 1050 | 0.06 | -6.76 | 1 | 0.16 | 0.188 | 0.754
11p | 731 | 0.09 | -5.16 | 1 | 0.22 | 3.69 | 0.000287
11q | 1279 | 0.08 | -4.72 | 1 | 0.36 | 15.8 | 0
12p | 484 | 0.14 | -2.64 | 1 | 0.12 | -3.91 | 1
12q | 1162 | 0.13 | -2.25 | 1 | 0.11 | -3.69 | 1
13q | 554 | 0.08 | -6.07 | 1 | 0.32 | 10.7 | 0
14q | 1144 | 0.10 | -4.23 | 1 | 0.17 | 0.968 | 0.309
15q | 1132 | 0.06 | -6.92 | 1 | 0.20 | 3.3 | 0.00113
16p | 719 | 0.33 | 10.4 | 0 | 0.35 | 11.4 | 0
16q | 562 | 0.15 | -1.36 | 1 | 0.53 | 25.3 | 0
17p | 575 | 0.07 | -5.79 | 1 | 0.48 | 22.2 | 0
17q | 1321 | 0.21 | 4.05 | 0.000169 | 0.26 | 8.07 | 1.62e-15
18p | 117 | 0.11 | -5.13 | 1 | 0.26 | 4.87 | 1.97e-06
18q | 340 | 0.10 | -5 | 1 | 0.25 | 4.61 | 6.46e-06
19p | 870 | 0.12 | -3.56 | 1 | 0.10 | -4.43 | 1
19q | 1452 | 0.12 | -1.79 | 1 | 0.08 | -4.94 | 1
20p | 295 | 0.30 | 8.31 | 0 | 0.13 | -3 | 1
20q | 627 | 0.34 | 11.9 | 0 | 0.09 | -4.81 | 1
21q | 422 | 0.12 | -3.9 | 1 | 0.12 | -3.9 | 1
22q | 764 | 0.07 | -5.75 | 1 | 0.37 | 14.6 | 0

Methods & Data
Input

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1216786/2.GDAC_MergeDataFiles.Finished/BRCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

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

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

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

- Amplification Threshold = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 781 Input Tumor Samples.

Tumor Sample Names
TCGA-A1-A0SB-01A-11D-A141-01
TCGA-A1-A0SD-01A-11D-A111-01
TCGA-A1-A0SE-01A-11D-A087-01
TCGA-A1-A0SF-01A-11D-A141-01
TCGA-A1-A0SG-01A-11D-A141-01
TCGA-A1-A0SH-01A-11D-A087-01
TCGA-A1-A0SI-01A-11D-A141-01
TCGA-A1-A0SJ-01A-11D-A087-01
TCGA-A1-A0SK-01A-12D-A087-01
TCGA-A1-A0SM-01A-11D-A087-01

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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