Uterine Corpus Endometrioid 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 2.0.15 (cga svn revision 34144).

Summary

There were 363 tumor samples used in this analysis: 27 significant arm-level results, 38 significant focal amplifications, and 43 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 - 38 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
--- | --- | --- | --- | ---
19q12 | 2.5092e-19 | 2.5092e-19 | chr19:34997290-35049911 | 1
17q12 | 2.5982e-20 | 1.0871e-17 | chr17:35058337-35157736 | 7
8q24.21 | 2.5937e-16 | 3.3524e-11 | chr8:129601853-129641730 | 0 [hsa-mir-1208]
20q11.21 | 2.1679e-08 | 5.6875e-08 | chr20:30195134-30290778 | 5
3q26.2 | 6.0097e-13 | 4.1137e-06 | chr3:170100105-170222858 | 0 [MECOM]
3p25.1 | 5.3631e-06 | 5.3631e-06 | chr3:13689840-13701840 | 1
12q13.2 | 1.2015e-05 | 1.2015e-05 | chr12:54670955-54725180 | 4
1q21.2 | 1.5651e-07 | 1.6758e-05 | chr1:148783386-149189526 | 9
8q24.21 | 1.6192e-14 | 3.1382e-05 | chr8:128808954-128850916 | 1
10q22.2 | 7.5965e-05 | 7.5965e-05 | chr10:76370609-76742313 | 6
1q22 | 6.351e-07 | 0.00037228 | chr1:154037570-154394960 | 15
2q13 | 0.00044049 | 0.00044049 | chr2:113610311-114040907 | 5
3q26.32 | 2.5622e-08 | 0.0005077 | chr3:180434350-180434885 | 1
16p11.2 | 0.00057375 | 0.00057375 | chr16:30762454-30917088 | 8
11q13.1 | 0.00014686 | 0.0011443 | chr11:66848329-66981414 | 12
19p13.2 | 0.0021536 | 0.0021536 | chr19:10723193-10811837 | 4
8p11.21 | 0.00085506 | 0.0023453 | chr8:41593387-42321723 | 10
3q26.2 | 1.7149e-08 | 0.0058316 | chr3:170739826-171011142 | 5
6p24.1 | 0.0047162 | 0.0067638 | chr6:11338029-11638950 | 1
4p16.3 | 0.011337 | 0.011337 | chr4:1401560-1851244 | 7
9p24.2 | 0.013383 | 0.013383 | chr9:3604171-3985326 | 2
17q21.32 | 0.001962 | 0.015138 | chr17:43818787-43994144 | 4
20q13.12 | 0.0073185 | 0.017859 | chr20:45340612-45513482 | 2
11q13.1 | 0.002325 | 0.019453 | chr11:64982969-65093536 | 3
14q24.3 | 0.027579 | 0.027579 | chr14:76375738-76480683 | 1
7q22.1 | 0.068961 | 0.068961 | chr7:99376636-99943378 | 31
4q12 | 0.086245 | 0.086245 | chr4:55270144-55278857 | 1
1p34.2 | 0.093083 | 0.093083 | chr1:42417358-45586527 | 63
8p11.23 | 0.006956 | 0.11756 | chr8:38111673-38518999 | 10
17q11.2 | 0.0082322 | 0.12015 | chr17:24038779-24137799 | 12
2p25.1 | 0.12825 | 0.12825 | chr2:1-29140695 | 168
6q21 | 0.10801 | 0.12825 | chr6:104962798-109213742 | 23
11p11.2 | 0.13194 | 0.13194 | chr11:46257218-46826669 | 12
6q25.1 | 0.17377 | 0.1931 | chr6:151967071-152084182 | 2
1q32.1 | 0.022076 | 0.19439 | chr1:202780483-202781625 | 1
17p11.2 | 0.18256 | 0.21033 | chr17:20103493-22326436 | 14
12p12.1 | 0.22347 | 0.22347 | chr12:24620551-25231137 | 6
6p22.3 | 0.08883 | 0.23781 | chr6:18577799-18628995 | 0 [RNF144B]

Genes in Wide Peak

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

Table S1. 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 17q12.

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

Genes
ERBB2
GRB7
PNMT
TCAP
STARD3
C17orf37
PGAP3

Genes in Wide Peak

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

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

Genes
hsa-mir-1825
PLAGL2
TM9SF4
POFUT1
TSPYL3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p25.1.

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

Genes
LOC285375

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.2.

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

Genes
RAB5B
RPS26
SUOX
IKZF4

Genes in Wide Peak

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

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

Genes
ARNT
CTSK
CTSS
ENSA
MCL1
SETDB1
ADAMTSL4
GOLPH3L
HORMAD1

Genes in Wide Peak

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

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

Genes
MYC

Genes in Wide Peak

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

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

Genes
MYST4
VDAC2
DUSP13
COMTD1
SAMD8
DUPD1

Genes in Wide Peak

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

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

Genes
LMNA
RIT1
SSR2
ARHGEF2
KIAA0907
SYT11
ROBLD3
GON4L
UBQLN4
RAB25
SEMA4A
MEX3A
RXFP4
SCARNA4
SNORA42

Genes in Wide Peak

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

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

Genes
PAX8
PSD4
CBWD2
FOXD4L1
LOC654433

Genes in Wide Peak

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

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

Genes
PIK3CA

Genes in Wide Peak

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

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

Genes
CTF1
BCL7C
SETD1A
FBXL19
HSD3B7
ORAI3
STX1B
NCRNA00095

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.1.

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

Genes
PPP1CA
PTPRCAP
RAD9A
RPS6KB2
CLCF1
CABP4
CORO1B
ATPGD1
POLD4
TBC1D10C
GPR152
LOC100130987

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.2.

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

Genes
hsa-mir-199a-1
DNM2
TMED1
MIR199A1

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
IKBKB
PLAT
POLB
MYST3
AP3M2
AGPAT6
NKX6-3
MIR486

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
MECOM
TERC
MYNN
ARPM1
LRRC34

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.1.

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

Genes
NEDD9

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
LETM1
SLBP
TACC3
TMEM129
FAM53A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.2.

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

Genes
C9orf70
GLIS3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q21.32.

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

Genes
HOXB1
HOXB2
HOXB3
SKAP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.12.

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

Genes
ZMYND8
LOC100131496

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.1.

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

Genes
LTBP3
SCYL1
MALAT1

Genes in Wide Peak

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

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

Genes
C14orf166B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
hsa-mir-106b
AZGP1
MCM7
PMS2L1
TAF6
ZNF3
ZKSCAN1
ZSCAN21
AP4M1
STAG3
COPS6
PILRB
PILRA
ZCWPW1
C7orf43
MEPCE
PVRIG
GAL3ST4
TSC22D4
C7orf47
GPC2
C7orf51
CNPY4
MBLAC1
GATS
C7orf59
C7orf61
MIR106B
MIR25
MIR93
SPDYE3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
KIT

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
MPL
MUTYH
ATP6V0B
CDC20
PLK3
DPH2
YBX1
PTPRF
RPS8
ST3GAL3
SLC2A1
SLC6A9
TIE1
UROD
PTCH2
B4GALT2
EIF2B3
ARTN
IPO13
KDM4A
TESK2
PPIH
EBNA1BP2
KIF2C
FOXJ3
KIAA0467
SNORD55
ZNF691
RNF220
DMAP1
ZSWIM5
LEPRE1
ELOVL1
ERI3
C1orf50
TMEM53
HECTD3
PPCS
HYI
ZMYND12
HPDL
SNORD46
SNORD38A
SNORD38B
MED8
TOE1
ERMAP
KLF17
TMEM125
CLDN19
WDR65
C1orf210
C1orf84
CCDC24
BTBD19
BEST4
RIMKLA
C1orf228
TCTEX1D4
CCDC23
LOC400752
FAM183A
CCDC30

Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
STAR
ASH2L
BAG4
DDHD2
LSM1
PPAPDC1B
LETM2
C8orf86

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q11.2.

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

Genes
RPL23A
SUPT6H
TRAF4
SNORD4B
SNORD4A
SNORD42B
SNORD42A
C17orf63
RAB34
TLCD1
PROCA1
NEK8

Genes in Wide Peak

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

Table S29. 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
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
FOSL2
FTHL3P
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
PPP1CB
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
MRPL33
BRE
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
GPN1
MAPRE3
SLC4A1AP
EFR3B
MYT1L
WDR43
LPIN1
PUM2
NTSR2
IFT172
SH3YL1
SNORD53
TRIB2
GRHL1
NRBP1
ITSN2
TTC15
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
TRMT61B
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
RBKS
HS1BP3
FNDC4
COLEC11
CENPO
CCDC121
SMC6
NOL10
C2orf44
FAM49A
C2orf16
ZNF512
ABHD1
SELI
RSAD2
C2orf39
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
LOC150622
TCF23
PLB1
FAM84A
GDF7
GPR113
FAM179A
UBXN2A
CYS1
KRTCAP3
SPDYA
ATP6V1C2
RNASEH1
FAM150B
DNAJC5G
IAH1
C2orf70
C2orf53
LOC339788
MSGN1
GEN1
C2orf48
PFN4
LOC375190
MFSD2B
C2orf71
C2orf90
C2orf79
LOC400940
FAM110C
C2orf84
SNORD92
RAD51AP2
LOC730811
LOC100128731
LOC100302650
SNORA80B

Genes in Wide Peak

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

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

Genes
PRDM1
hsa-mir-587
AIM1
FOXO3
PREP
NR2E1
SNX3
ATG5
BVES
SEC63
OSTM1
C6orf203
SOBP
QRSL1
PDSS2
HACE1
BEND3
POPDC3
RTN4IP1
LACE1
SCML4
LIN28B
LOC553137

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p11.2.

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

Genes
CREB3L1
ARHGAP1
CHRM4
F2
MDK
DGKZ
KIAA0652
CKAP5
AMBRA1
ZNF408
HARBI1
SNORD67

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q25.1.

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

Genes
ESR1
C6orf97

Genes in Wide Peak

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

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

Genes
MDM4

Genes in Wide Peak

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

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

Genes
KCNJ12
MAP2K3
TMEM11
USP22
DHRS7B
CYTSB
C17orf103
FAM27L
FLJ36000
LGALS9B
CCDC144NL
C17orf51
CCDC144C
MGC102966

Genes in Wide Peak

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

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

Genes
BCAT1
LRMP
CASC1
DAD1L
C12orf67
C12orf77

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 - 43 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
--- | --- | --- | --- | ---
19p13.3 | 2.7028e-33 | 2.7028e-33 | chr19:3412119-4202032 | 30
10q23.31 | 3.5024e-17 | 3.5024e-17 | chr10:89607138-90024018 | 2
2q22.1 | 4.2407e-11 | 1.1208e-10 | chr2:139248662-143354308 | 1
1p36.11 | 1.5012e-13 | 1.6981e-08 | chr1:26773226-27845422 | 22
22q13.31 | 9.3893e-09 | 1.6981e-08 | chr22:44619793-45401422 | 17
20p12.1 | 2.316e-08 | 2.316e-08 | chr20:14250876-15984135 | 2
6q26 | 2.666e-08 | 2.6766e-08 | chr6:161613089-163073197 | 1
16q23.1 | 2.6766e-08 | 7.0285e-08 | chr16:76686559-78185271 | 1
17q11.2 | 1.2149e-07 | 3.1368e-07 | chr17:26350862-26746744 | 4
5q11.2 | 4.882e-07 | 4.8714e-07 | chr5:58180924-59823742 | 3
1p36.31 | 3.059e-11 | 4.4803e-05 | chr1:1-24616189 | 357
7q31.1 | 3.1459e-05 | 9.6721e-05 | chr7:110512908-111163100 | 1
7p22.1 | 0.00039169 | 0.00039169 | chr7:1-16469584 | 96
11p15.5 | 0.00043284 | 0.00043284 | chr11:1-63090793 | 695
8p23.2 | 0.0010585 | 0.0012943 | chr8:1-6255647 | 14
11q25 | 0.00078924 | 0.0023079 | chr11:118566980-134452384 | 127
12q23.1 | 0.00079546 | 0.0028669 | chr12:97648132-98652008 | 2
13q14.2 | 0.00065346 | 0.0036081 | chr13:47731768-47962808 | 2
9p21.2 | 0.0046936 | 0.0047359 | chr9:27562512-28858209 | 3
18q23 | 0.0051607 | 0.0051607 | chr18:54039160-76117153 | 76
17p13.3 | 0.00018169 | 0.0092938 | chr17:1-1140309 | 13
4q35.2 | 0.0072324 | 0.0099711 | chr4:166515715-191273063 | 88
17p12 | 0.0019829 | 0.012284 | chr17:12856720-13915807 | 3
3p14.2 | 0.013526 | 0.014026 | chr3:48164594-73763253 | 224
8p21.2 | 0.012697 | 0.01927 | chr8:22268591-37835459 | 89
4q22.1 | 0.016502 | 0.020565 | chr4:91092757-93459528 | 2
16q21 | 0.0025643 | 0.028051 | chr16:31629916-67926375 | 208
2q37.3 | 0.0019055 | 0.030421 | chr2:207211570-242951149 | 279
20q13.12 | 0.030885 | 0.030421 | chr20:44797174-45272132 | 1
16p13.3 | 0.032354 | 0.033026 | chr16:3704794-3953467 | 1
13q12.11 | 0.008325 | 0.034707 | chr13:1-43355956 | 142
22q11.1 | 0.011381 | 0.034707 | chr22:1-16340585 | 13
17q21.31 | 0.013045 | 0.043392 | chr17:36159680-43569474 | 212
9q34.11 | 0.051641 | 0.051903 | chr9:100086923-140273252 | 446
4p16.3 | 0.080348 | 0.081396 | chr4:1-1333404 | 27
7q36.3 | 0.021307 | 0.081396 | chr7:117649647-158821424 | 308
14q13.1 | 0.081279 | 0.081396 | chr14:1-38573164 | 195
12q24.31 | 0.022309 | 0.095492 | chr12:103373158-132349534 | 254
11q14.1 | 0.089613 | 0.15447 | chr11:77817311-117175491 | 203
18q12.2 | 0.15286 | 0.15447 | chr18:19994877-44647031 | 83
15q21.1 | 0.12682 | 0.21558 | chr15:1-57214850 | 379
3p24.3 | 0.22584 | 0.22718 | chr3:1-33849454 | 160
15q23 | 0.099987 | 0.24935 | chr15:1-100338915 | 745

Genes in Wide Peak

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

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

Genes
hsa-mir-637
DAPK3
EEF2
MATK
MAP2K2
TBXA2R
APBA3
EBI3
HMG20B
ZFR2
PIP5K1C
SNORD37
TJP3
ITGB1BP3
ZBTB7A
FZR1
SIRT6
PIAS4
C19orf29
DOHH
CREB3L3
RAX2
ATCAY
MRPL54
C19orf28
GIPC3
ANKRD24
C19orf77
MIR637
C19orf71

Genes in Wide Peak

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

Table S37. 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 2q22.1.

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
ARID1A
FGR
SFN
GPR3
SLC9A1
NR0B2
FCN3
MAP3K6
WASF2
NUDC
WDTC1
AHDC1
GPN2
PIGV
GPATCH3
TMEM222
ZDHHC18
SYTL1
FAM46B
C1orf172
TRNP1
CD164L2

Genes in Wide Peak

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

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

Genes
hsa-let-7b
PPARA
WNT7B
CELSR1
PKDREJ
GTSE1
TTC38
C22orf26
TRMU
LOC150381
C22orf40
CN5H6.4
LOC400931
MIRLET7A3
MIRLET7B
LOC730668
LOC100271722

Genes in Wide Peak

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

Table S41. 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 6q26.

Table S42. 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 16q23.1.

Table S43. 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 17q11.2.

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

Genes
NF1
EVI2A
EVI2B
OMG

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
MDS2
hsa-mir-1256
hsa-mir-1290
hsa-mir-34a
hsa-mir-551a
hsa-mir-429
hsa-mir-1977
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
TNFRSF8
CDA
CDC2L1
CDC42
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
MTOR
FUCA1
GABRD
GALE
GNB1
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RPL11
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
LUZP1
PRDM2
MMP23B
MMP23A
KCNAB2
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
KIAA0562
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
ANGPTL7
HNRNPR
UBE4B
MAD2L2
PDPN
MASP2
SFRS13A
UTS2
RER1
MSTP2
MSTP9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLSTN1
AKR7A3
SPEN
KDM1A
KIAA0090
KIF1B
PLEKHM2
OTUD3
KIAA1026
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
CHD5
C1orf144
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
HSPC157
SSU72
UBIAD1
PADI1
PLA2G2E
WDR8
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
ARHGEF10L
VPS13D
ATAD3A
PANK4
CAMK2N1
ASAP3
PNRC2
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
AGTRAP
C1orf128
KIAA0495
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
PLA2G2F
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
EFHD2
MMEL1
C1orf89
OR4F5
MUL1
NOL9
AGMAT
NCRNA00115
MORN1
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
USP48
NBPF3
SLC25A33
DDI2
LZIC
C1orf170
CROCCL1
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf201
C1orf158
FBXO44
CROCCL2
FHAD1
LOC115110
RBP7
ACAP3
UBE2J2
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
C1orf93
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
TTLL10
TMCO4
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
C1orf70
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
C1orf151
LOC441869
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC649330
PRAMEF22
PRAMEF15
WASH5P
PRAMEF16
FAM138C
SNORA59B
SNORA59A
MIR551A
CDC2L2
LOC728661
PRAMEF14
FLJ37453
OR4F29
LOC100128003
LOC100128842
LOC100129534
FLJ39609
LOC100132062
LOC100132287
LOC100133331
LOC100133612
LOC100288778

Genes in Wide Peak

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

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

Genes
LRRN3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.1.

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

Genes
ETV1
PMS2
CARD11
hsa-mir-589
hsa-mir-339
ACTB
DGKB
GNA12
GPER
ICA1
LFNG
MEOX2
NUDT1
NDUFA4
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
PHF14
KIAA0415
ARL4A
KDELR2
ADAP1
IQCE
UNC84A
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
NXPH1
C7orf20
C7orf28A
MIOS
RNF216
TMEM106B
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
RADIL
PAPOLB
C1GALT1
FAM20C
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
C7orf70
SCIN
ZFAND2A
COX19
GLCCI1
KIAA1908
GPR146
AMZ1
PER4
TMEM184A
VWDE
C7orf27
SDK1
FOXK1
MMD2
DAGLB
C7orf28B
THSD7A
SLC29A4
RSPH10B
TFAMP1
UNCX
COL28A1
LOC389458
ELFN1
TMEM195
GRID2IP
ZNF815
RNF216L
PMS2CL
MIR339
OCM
MIR589
RSPH10B2
ISPD

Genes in Wide Peak

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

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

Genes
CARS
DDB2
EXT2
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
CREB3L1
hsa-mir-1908
hsa-mir-130a
hsa-mir-129-2
hsa-mir-610
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-210
ACP2
ADM
AP2A2
APLNR
AMPD3
APBB1
RHOG
ARHGAP1
ARNTL
ART1
ASCL2
BDNF
SERPING1
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAT
CCKBR
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CHRM1
CHRM4
TPP1
CNGA4
CNTF
COPB1
CRY2
CSTF3
CTNND1
CTSD
DDB1
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
F2
MS4A2
FEN1
FOLH1
FSHB
FTH1
GAS2
GIF
GNG3
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INCENP
INS
IRF7
CD82
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
FADS1
FADS3
LRP4
LSP1
CAPRIN1
MDK
SCGB2A1
SCGB2A2
MUC2
MUC6
MYBPC3
MYOD1
NAP1L4
NDUFS3
NELL1
NUCB2
SLC22A18
SLC22A18AS
OSBP
P2RX3
PAX6
PDE3B
PGA5
PIK3C2A
POLR2G
POLR2L
PRG2
PSMA1
PSMC3
PSMD13
PTH
PTPRJ
RAB3IL1
RAG1
RAG2
RAPSN
RARRES3
RCN1
RNH1
ROM1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SLC1A2
SLC3A2
SMPD1
SPI1
TRIM21
SSRP1
ST5
STIM1
STX3
STX5
ABCC8
TAF10
TALDO1
TCN1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TSG101
PHLDA2
TUB
SCGB1A1
BEST1
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
BBOX1
PPFIBP2
SLC43A1
IFITM1
DGKZ
CHST1
API5
MADD
OR6A2
DCHS1
EIF3F
BRSK2
SYT7
SLC6A5
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
SLC22A6
SLC22A8
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
MICAL2
CTR9
KIAA0652
CKAP5
TRIM66
NR1H3
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
GLYAT
MRVI1
TRIM22
PRG3
IFITM3
SPON1
EIF3M
NXF1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
TAF6L
SCGB1D2
SCGB1D1
CUGBP1
OR5I1
LYVE1
C11orf58
CLP1
KCNQ1OT1
PKP3
HPS5
GPR44
RRAS2
ZP1
SWAP70
GANAB
DTX4
DENND5A
NUP160
FNBP4
RRP8
SIRT3
OR52A1
SNHG1
ARFIP2
MTCH2
FJX1
C11orf41
ABTB2
PAMR1
ZDHHC5
DAK
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
OR10A3
FXC1
TIMM10
BSCL2
ELP4
DKK3
RBMXL2
PGAP2
PRPF19
SLC43A3
COMMD9
C11orf21
PACSIN3
TRPM5
UBQLN3
RNF141
UBXN1
APIP
TMX2
HSD17B12
IGF2AS
TMEM216
BET1L
CEND1
SLC15A3
PHF21A
MS4A4A
WIT1
TMEM138
CYB5R2
TRIM34
MUPCDH
TOLLIP
ZDHHC13
WDR74
TRIM44
MS4A12
MRPL16
SDHAF2
TMEM132A
HRASLS2
USP47
VPS37C
TRIM68
NAT10
UEVLD
LIN7C
SLC35C1
TCP11L1
LGR4
LRDD
KCNQ1DN
SOX6
AMBRA1
KBTBD4
PARVA
TTC17
MMP26
C11orf17
C11orf16
TMEM9B
NRIP3
ASCL3
PRDM11
CHRNA10
SLC17A6
PNPLA2
SYT13
PHRF1
LRRC4C
SCUBE2
MS4A7
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
FAM111A
ANO3
MS4A6A
MS4A5
EPS8L2
TUT1
STK33
CHID1
AHNAK
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ZNF408
QSER1
AGBL2
ZBTB3
CPSF7
PRR5L
ASRGL1
ATHL1
INTS5
ZFP91
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
PTDSS2
HCCA2
SBF2
KIF18A
MS4A8B
FAM160A2
FAR1
BTBD10
ARFGAP2
ACCS
MS4A14
SPRYD5
PTPN5
MICALCL
LGALS12
TRIM5
TNKS1BP1
NAV2
SYT8
TSPAN18
CCDC34
SLC39A13
DEPDC7
GLYATL1
PRKCDBP
RPLP0P2
SAAL1
ODF3
SLC22A9
OSBPL5
C1QTNF4
PTPMT1
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIMP1
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
CYP2R1
DBX1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
C11orf94
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
METT5D1
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
C11orf66
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
OR51F1
SVIP
MRGPRX1
C11orf31
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
FLJ46111
CSNK2A1P
OR51V1
H19
OR9G4
C11orf64
EFCAB4A
TMEM80
TTC9C
SLC22A24
HARBI1
LOC283267
IGSF22
OR10A4
OLFML1
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
OR5F1
OR5AP2
B4GALNT4
OR52L1
OR2AG2
OR52B6
DCDC1
MS4A10
OR10A2
OVCH2
PDDC1
RTN4RL2
GALNTL4
DKFZp686O24166
DKFZp779M0652
FAM111B
TMEM179B
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
SLC22A25
IFITM5
FAM99A
OR56B1
GVIN1
INSC
FIBIN
LOC387763
SLC22A10
OR52K1
OR52I1
OR51D1
OR52A4
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
FAM180B
OR51T1
OR51A4
OR51A2
OR4A47
OR4C45
SCGB1D4
MIR129-2
MIR130A
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440040
LOC441601
OR5B3
TRIM6-TRIM34
CCDC73
LOC494141
BDNFOS
MS4A13
OR8U8
OR9G9
MIR483
SNORA3
SNORA52
BTBD18
PGA3
PGA4
RASSF10
LOC646813
LOC650368
SNORA23
SNORA45
SNORA54
SNORD67
SNORA57
SNORD97
MIR610
MIR611
INS-IGF2
MUC5B
LOC729799
METTL12
C11orf83
MIR675
LOC100126784
C11orf91
FAM99B
LOC100133161
LOC100133545

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
CBL
FLI1
ARHGEF12
hsa-mir-100
hsa-mir-125b-1
ACRV1
APLP2
CHEK1
ETS1
GRIK4
HSPA8
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NFRKB
NRGN
OPCML
PVRL1
SC5DL
ST3GAL4
SORL1
SRPR
ST14
TECTA
THY1
ZNF202
BARX2
USP2
EI24
FEZ1
RICS
ADAMTS8
IGSF9B
NCAPD3
VSIG2
TRIM29
POU2F3
OR8G2
OR8B8
OR8G1
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
CRTAM
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ROBO3
RNF26
FAM118B
C11orf61
ASAM
C11orf63
CCDC15
PUS3
MFRP
JAM3
KIRREL3
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
TMEM45B
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
OR8D1
OR8D2
OR8B4
LOC283174
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
LOC399959
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
NCRNA00167
HEPN1
LOC100128239
PATE3

Genes in Wide Peak

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

Table S52. 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 13q14.2.

Table S53. 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 9p21.2.

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

Genes
hsa-mir-876
LINGO2
MIR876

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
CYB5A
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NFATC1
SERPINB2
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
SERPINB3
SERPINB4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
NEDD4L
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
C18orf55
RAX
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
C18orf22
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
CCBE1
CBLN2
FBXO15
DOK6
RNF152
C18orf20
ZADH2
C18orf62
LOC284276
HMSD
CPLX4
ATP9B
LOC390858
LOC400657
MIR122
HSBP1L1
LOC100130522

Genes in Wide Peak

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

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

Genes
ABR
RPH3AL
TIMM22
GEMIN4
GLOD4
RNMTL1
VPS53
NXN
FAM57A
FAM101B
C17orf97
BHLHA9
ELP2P

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-1979
AGA
SLC25A4
CASP3
CLCN3
CPE
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
TLL1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
MORF4
ADAM29
ANXA10
SCRG1
PALLD
FAM149A
FBXO8
PDLIM3
SPOCK3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
TUBB4Q
STOX2
KIAA1430
SH3RF1
SPCS3
C4orf41
MLF1IP
NBLA00301
WWC2
KIAA1712
SNX25
CBR4
MGC45800
DDX60L
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
TRIML1
ANKRD37
HELT
FAM92A3
C4orf47
GALNTL6
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
MIR578
LOC728410

Genes in Wide Peak

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

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

Genes
hsa-mir-548h-3
HS3ST3A1
CDRT15P

Genes in Wide Peak

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

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

Genes
FHIT
MITF
BAP1
FOXP1
PBRM1
hsa-mir-1284
hsa-mir-135a-1
hsa-let-7g
hsa-mir-566
hsa-mir-191
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
MST1
MST1R
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTPRG
QARS
RPL29
ATXN7
SEMA3F
NEK4
TCTA
TKT
TMF1
TNNC1
UBA7
USP4
UQCRC1
WNT5A
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
BSN
UBA3
RRP9
MAGI1
CACNA2D2
VPRBP
IP6K1
PSMD6
PARP3
RBM6
RBM5
NME6
TRAIP
ARIH2
ARL6IP5
TUSC4
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
LAMB2L
PDZRN3
RAD54L2
FRMD4B
STAB1
C3orf63
RYBP
NAT6
ABHD14A
WDR51A
NDUFAF3
DNAH1
LRIG1
ERC2
APPL1
GNL3
SPCS1
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
P4HTM
IL17RD
QRICH1
PXK
FEZF2
FLJ10213
DALRD3
SHQ1
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
LMOD3
SEMA3G
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
SELK
PROK2
RNF123
CCDC71
NT5DC2
SLC26A6
CAMKV
CCDC51
THOC7
WDR82
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
UCN2
RFT1
ACTR8
SLC25A26
GPR62
FAM3D
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
KLHDC8B
DNAH12
PDE12
FAM116A
C3orf64
FBXW12
CCDC66
LOC285401
EIF4E3
CCDC36
SPATA12
C3orf62
TMEM110
AMIGO3
CDH29
C3orf54
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR191
FAM19A1
TMEM89
IQCF6
LOC440957
MIR425
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
GLT8D4
HESRG
SNORD19B
C3orf74

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

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

Genes in Wide Peak

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

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q21.

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

Genes
CBFB
CDH1
CDH11
CYLD
HERPUD1
hsa-mir-328
hsa-mir-138-2
hsa-mir-1826
ADCY7
AGRP
AMFR
BBS2
CA7
CBLN1
CDH3
CDH5
CDH8
CDH16
CES1
CETP
CNGB1
CSNK2A2
CTRL
DYNC1LI2
E2F4
GNAO1
GOT2
HAS3
HSD11B2
HSF4
KIFC3
LCAT
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1M
MT1L
MT1X
MT2A
MT3
NFATC3
PHKB
POLR2C
PSKH1
PSMB10
RBL2
RRAD
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
TK2
TRADD
CES2
NAE1
NOL3
SLC7A6
ATP6V0D1
GPR56
N4BP1
NUP93
NUTF2
IRX5
DNAJA2
KATNB1
ZNF267
CTCF
NUDT21
CNOT1
ZNF423
RPGRIP1L
CES3
ARL2BP
ORC6L
EDC4
PLA2G15
TP53TG3
PLEKHG4
DKFZP434H168
LRRC29
VPS4A
TOX3
CCDC113
TMEM208
C16orf80
FHOD1
BRD7
ZDHHC1
PARD6A
PLLP
CKLF
FAM96B
TPPP3
CES4
PRMT7
DUS2L
CHTF8
LPCAT2
HEATR3
SLC38A7
OGFOD1
LRRC36
FBXL8
SMPD3
DOK4
VPS35
DDX28
TSNAXIP1
COQ9
CIAPIN1
THAP11
PDP2
ZNF319
RANBP10
NOD2
PDF
DPEP2
DPEP3
PAPD5
AKTIP
GINS3
NDRG4
ACD
FTO
IRX6
IRX3
FAM65A
TMCO7
C16orf57
ELMO3
SHCBP1
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
ITFG1
GFOD2
NETO2
LONP2
C16orf48
SLC7A6OS
NLRC5
CCDC135
CAPNS2
MT4
GPT2
B3GNT9
CIRH1A
ABCC11
NKD1
RSPRY1
MYLK3
CCDC102A
ABCC12
CMTM1
NRN1L
CMTM3
C16orf78
ANKRD26P1
ZNF720
SNX20
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN
LOC146481
CPNE2
GPR114
KLKBL4
CES7
GPR97
TMEM188
CCDC79
CES8
EXOC3L
LOC283856
LOC283867
LOC283914
MT1DP
TEPP
SLC6A10P
C16orf87
C16orf86
MIR138-2
HERC2P4
MIR328
UBE2MP1
MT1IP
LOC644649
KIAA0895L
SNORA46
SNORA50
TP53TG3B

Genes in Wide Peak

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

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

Genes
ATIC
CREB1
ACSL3
IDH1
PAX3
FEV
hsa-mir-149
hsa-mir-562
hsa-mir-1471
hsa-mir-1244
hsa-mir-153-1
hsa-mir-375
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
IL8RA
IL8RB
IL8RBP
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
FZD5
SCG2
CUL3
DGKD
STK16
KLF7
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
FASTKD2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
C2orf24
STK36
LOC29034
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
KIAA1486
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
C2orf67
LOC151174
FAM119A
CCNYL1
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
C2orf52
MSL3L2
WDR69
C2orf57
PIKFYVE
LOC200726
TIGD1
CCDC108
C2orf72
C2orf85
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
ASB18
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
PP14571

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20q13.12.

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

Genes
EYA2

Genes in Wide Peak

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

Table S65. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CREBBP

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
LHFP
hsa-mir-621
hsa-mir-320d-1
PARP4
ALOX5AP
ATP12A
CDK8
ELF1
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
GTF3A
HMGB1
PDX1
MAB21L1
SMAD9
MIPEP
PABPC3
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
CCNA1
MTMR6
DCLK1
ZMYM5
KL
MTRF1
NUPL1
FRY
SLC25A15
USPL1
MRPS31
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
WBP4
AKAP11
EXOSC8
PDS5B
KIAA0564
SPG20
MTUS2
SACS
LATS2
OR7E37P
SNORD102
NBEA
C13orf15
DNAJC15
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
PSPC1
TNFRSF19
FAM48A
CENPJ
RNF17
COG6
XPO4
MRP63
NARG1L
C13orf23
KATNAL1
KBTBD7
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
CG030
CSNK1A1L
RXFP2
C13orf26
C13orf30
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
ZDHHC20
PAN3
DKFZp686A1627
SUGT1L1
SLC46A3
LOC284232
C1QTNF9
FREM2
LOC348021
LOC374491
RASL11A
C1QTNF9B
SHISA2
NHLRC3
C13orf36
ATP5EP2
PCOTH
SNORA27
LOC646405
PRHOXNB
ZAR1L
LOC646982
MIR621
C13orf38
LOC100101938
RPL21P28
LOC100188949
LOC100288730

Genes in Wide Peak

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

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

Genes
IL17RA
POTEH
HSFYP1
CECR6
CECR5
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 17q21.31.

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

Genes
BRCA1
ETV4
hsa-mir-152
ACLY
AOC2
ARL4D
ATP6V0A1
FMNL1
CDC27
CNP
CRHR1
DHX8
DUSP3
EZH1
GAST
FZD2
G6PC
KAT2A
GFAP
CCR10
GRN
HCRT
HSD17B1
IFI35
ITGA2B
ITGB3
JUP
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
NAGLU
NFE2L1
NMT1
NSF
PPY
PYY
RAB5C
RPL27
SLC4A1
SP2
STAT3
STAT5A
STAT5B
MLX
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
RND2
CNTNAP1
AOC3
BECN1
KRT38
KRT37
KRT36
HAP1
MAP3K14
EFTUD2
NPEPPS
GOSR2
TBKBP1
PLEKHM1
LRRC37A
HDAC5
GJC1
PSME3
EIF1
NBR2
RAMP2
VAT1
SC65
HEXIM1
C1QL1
RUNDC3A
CBX1
GPATCH8
KCNH4
C17orf88
KRT23
TUBG2
NKIRAS2
CCDC56
PSMC3IP
SNX11
TBX21
SOST
COPZ2
ARL17P1
SLC25A39
HIGD1B
KRT20
LRRC37A4
PNPO
KLHL11
ATXN7L3
FKBP10
WNK4
C17orf53
TMUB2
DHX58
PRR15L
ACBD4
DCAKD
PLEKHH3
DBF4B
CDK5RAP3
SP6
COASY
AARSD1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP2-1
TTC25
KRTAP4-12
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
VPS25
TMEM101
GHDC
KRTAP4-4
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
LRRC46
SCRN2
LOC90586
G6PC3
ASB16
HSPB9
PLCD3
TMEM106A
OSBPL7
NT5C3L
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
C17orf57
MRPL10
KRT40
CD300LG
KIF18B
RUNDC1
C17orf69
TMEM99
NAGS
FAM134C
IMP5
KRT28
SH3D20
ARHGAP27
STH
KIAA1267
C17orf105
FAM171A2
C17orf104
PTRF
KLHL10
C17orf65
KRT27
KRT26
LOC388387
CCDC103
RPRML
KRT39
MGC57346
MIR152
LRRC37A2
ARL17
LOC644172
KRTAP4-11
KRTAP4-8
LOC100128977
LOC100130148
LOC100130581
KRTAP4-9
KRTAP4-7
LOC100133991
LOC100190938
LOC100272146

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.11.

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

Genes
ABL1
NOTCH1
RALGDS
SET
TAL2
TSC1
NR4A3
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-126
hsa-mir-219-2
hsa-mir-199b
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
BAAT
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CYLC2
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FPGS
NR5A1
FUT7
NR6A1
GGTA1
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
TMEFF1
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
GABBR2
RALGPS1
ADAMTSL2
KIAA0649
SEC16A
TNFSF15
ROD1
SH2D3C
RABEPK
LAMC3
TUBB2C
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
SEC61B
SLC27A4
CEP110
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
PTGR1
TRIM32
SETX
ERP44
ZBTB43
PMPCA
ASTN2
FKBP15
KIAA0368
EXOSC2
FREQ
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
LOC26102
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
RAB14
C9orf78
POLE3
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
BSPRY
C9orf167
TEX10
LPPR1
EXD3
C9orf6
STX17
TMEM38B
NIPSNAP3B
STRBP
C9orf86
CDK5RAP2
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
SLC46A2
C9orf27
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
C9orf45
URM1
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
C9orf125
NTNG2
BAT2L
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FAM125B
WDR34
C9orf140
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
C9orf98
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
C9orf96
OLFML2A
QSOX2
LOC169834
C9orf91
NAIF1
ANKS6
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
NCRNA00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
C9orf75
C9orf109
FAM78A
OR13C9
OR13D1
LOC286367
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf119
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
LOC402377
SOHLH1
ZBTB34
MIR126
MIR147
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR32
C9orf106
LCN10
C9orf173
NRARP
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
FAM163B
FLJ40292
TUBBP5
SNORA17
SNORA43
SNORD62B
SNORD90
MIR548D1
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
C9orf110
LOC100129034
LOC100131193
FAM157B
RNU6ATAC
LOC100272217
LOC100289341

Genes in Wide Peak

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

Table S70. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-571
ATP5I
CTBP1
DGKQ
GAK
IDUA
MYL5
PDE6B
ZNF141
MAEA
PCGF3
SPON2
CPLX1
SLC26A1
FGFRL1
PIGG
ABCA11P
MFSD7
TMEM175
C4orf42
ZNF595
ZNF721
ZNF718
RNF212
ZNF876P
ZNF732
LOC100130872

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
C7orf54
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
C7orf68
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
C7orf4
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CADPS2
CPA5
TSGA14
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
TRYX3
MOXD2
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF783
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5L3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FLJ40852
FAM115C
ZNF775
ATG9B
LOC286016
MESTIT1
TAS2R60
CTAGE6
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
LOC441294
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF5L
GIMAP6
WEE2
MIR490
ZNF862
PL-5283
ACTR3C
MIR592
MIR593
MIR595
LOC728743
TMEM229A
LUZP6
MIR671
LOC100124692
LOC100128542
CTAGE4
LOC100128822
LOC100132707
LOC100134229
LOC100134713

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q13.1.

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

Genes
NKX2-1
CCNB1IP1
hsa-mir-624
hsa-mir-208b
hsa-mir-208a
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GZMH
GZMB
FOXA1
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
NP
NRL
OXA1L
PAX9
PCK2
PRKD1
PSMA6
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
SRP54
SSTR1
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
AKAP6
KIAA0391
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
FAM12A
DHRS4
RIPK3
AP4S1
BAZ1A
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
NKX2-8
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
MBIP
HAUS4
PPP2R3C
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
FLJ10357
EAPP
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
SNX6
C14orf93
ABHD4
NPAS3
FAM12B
CDH24
METT11D1
IL25
THTPA
OR4K5
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
BRMS1L
JPH4
RNASE7
INSM2
C14orf128
RAB2B
JUB
RPPH1
SLC25A21
LRRC16B
PPP1R3E
TMEM55B
TTC5
EGLN3
C14orf126
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MIPOL1
MDP1
CLEC14A
FITM1
REM2
C14orf21
C14orf147
ADCY4
RALGAPA1
SFTA3
C14orf19
TSSK4
FAM177A1
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
P704P
C14orf176
CBLN3
SNORD9
MIR624
DHRS4L1
SNORD126
MIR208B

Genes in Wide Peak

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

Table S73. 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
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
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
CHST11
GALNT9
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
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
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
LRRC43
TCP11L2
GPR133
MORN3
MYO1H
C12orf51
KSR2
NME2P1
GATC
C12orf27
DDX51
MMAB
GPR109A
TMEM119
LOC338799
EP400NL
RILPL1
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MAP1LC3B2
SNORA49
MIR620
LOC100128554
LOC100130238
LOC100190940
NCRNA00173
ZNF605

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
DDX10
PAFAH1B2
POU2AF1
SDHD
PICALM
PCSK7
MAML2
hsa-mir-34c
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-708
ACAT1
BIRC2
APOA1
APOA4
APOC3
CASP1
CASP4
CASP5
CTSC
CRYAB
DLAT
DLG2
DRD2
FDX1
FUT4
GRIA4
GRM5
GUCY1A2
HSPB2
HTR3A
IL18
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
NCAM1
NNMT
NPAT
PGR
PPP2R1B
PRCP
PTS
RDX
SLN
TAGLN
TRPC6
TYR
ZBTB16
CUL5
FZD4
JRKL
EED
ZNF259
MTMR2
HTR3B
ZW10
MMP20
MED17
CEP57
NAALAD2
RBM7
YAP1
ME3
GPR83
SFRS2B
PRSS23
CEP164
ENDOD1
EXPH5
SIK2
SIK3
BACE1
RAB38
CADM1
PANX1
REXO2
ODZ4
TIMM8B
CHORDC1
RAB30
C11orf54
NOX4
SIDT2
C11orf73
CWC15
PCF11
CNTN5
C11orf71
SLC35F2
RAB39
BTG4
FAM55D
SYTL2
ANKRD49
TTC12
C11orf57
ELMOD1
KDM4D
TMEM126B
TEX12
C11orf75
TRIM49
DSCAML1
KIAA1377
ARHGAP20
USP28
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
MMP27
C11orf1
TMEM135
TAF1D
DYNC2H1
NARS2
CCDC82
ALG9
PDGFD
TMPRSS5
BCO2
TMEM133
TMEM126A
DCUN1D5
KIAA1826
BUD13
C11orf70
DIXDC1
KIAA1731
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
TMEM123
APOA5
SLC36A4
FAT3
TRIM64
CASP12
C11orf93
PIH1D2
FAM55A
FAM55B
FAM76B
SESN3
PIWIL4
FLJ32810
KBTBD3
CWF19L2
KDELC2
LAYN
AMOTL1
CCDC67
C11orf65
FOLH1B
C11orf82
CCDC83
FAM181B
CCDC89
ANGPTL5
ANKK1
RNF214
ANKRD42
C11orf53
HEPHL1
C11orf34
C11orf90
TRIM77
FOLR4
KDM4DL
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
DDI1
CARD17
SCARNA9
TRIM64B
TRIM53
UBTFL1
LOC643923
CLDN25
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
LOC729384

Genes in Wide Peak

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

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

Genes
SS18
ZNF521
hsa-mir-924
hsa-mir-187
hsa-mir-302f
hsa-mir-320c-2
AQP4
ATP5A1
CDH2
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
GALNT1
SMAD2
MEP1B
PIK3C3
RIT2
SLC14A1
SYT4
TAF4B
TTR
ZNF24
SLC14A2
NOL4
PSTPIP2
PIAS2
B4GALT6
KIAA0427
ZNF271
MAPRE2
KIAA1012
SLC39A6
C18orf10
SETBP1
ST8SIA5
IER3IP1
TCEB3B
RNF138
RNF125
MOCOS
RPRD1A
ELP2
IMPACT
BRUNOL4
KIAA1328
KLHL14
KIAA1632
HRH4
FAM59A
FHOD3
ASXL3
KATNAL2
CHST9
C18orf21
HDHD2
ZNF397
OSBPL1A
HAUS1
LOXHD1
INO80C
PSMA8
C18orf25
MCART2
DSG4
C18orf16
TCEB3C
ZBTB7C
ZNF396
KCTD1
SIGLEC15
C18orf34
MIR187
WBP11P1
RNF165
KC6
LOC647946
LOC728606
TCEB3CL
ZNF397OS

Genes in Wide Peak

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

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

Genes
BUB1B
TCF12
C15orf55
C15orf21
hsa-mir-628
hsa-mir-1300
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
hsa-mir-211
hsa-mir-1268
ACTC1
ADAM10
APBA2
AQP9
B2M
BCL8
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
SNURF
USP8
CCNB2
SLC28A2
CCPG1
COPS2
TGM5
PIGB
HISPPD2A
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
MTMR15
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
KIAA1370
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
C15orf29
SLTM
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
GRINL1A
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SLC24A5
PRTG
LOC283663
OR4N4
FAM98B
PLA2G4D
GOLGA6L1
GOLGA8G
GOLGA9P
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMML1
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P1
WHAMML2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC646214
CXADRP2
HSP90AB4P
MIR548A3
MIR626
MIR627
MIR628
LOC723972
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
LOC729082
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
MIR147B
LOC100129387
GOLGA8F
LOC100132724
GOLGA8D
JMJD7
PLA2G4B
FAM7A2

Genes in Wide Peak

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

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

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-563
hsa-mir-885
ATP2B2
BTD
CAV3
CCR4
DAZL
FBLN2
GLB1
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RARB
RPL15
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
TGFBR2
THRB
TIMP4
TOP2B
NR2C2
UBE2E1
UBE2E2
UBP1
WNT7A
BRPF1
COLQ
EOMES
CAMK1
BHLHE40
KAT2B
SH3BP5
SLC4A7
VGLL4
EDEM1
TBC1D5
TATDN2
IQSEC1
NR1D2
PDCD6IP
ARPC4
TADA3
CRTAP
ATG7
CHL1
CAND2
CLASP2
GPD1L
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
FBXL2
CNOT10
THUMPD3
SUSD5
HACL1
TTLL3
CNTN6
LSM3
RBMS3
NKIRAS1
LOH3CR2A
LMCD1
C3orf32
TRNT1
DYNC1LI1
CRBN
C3orf19
GHRL
CMTM6
OXSM
ARL8B
SETD5
TMEM40
NGLY1
TMEM111
C3orf10
RAD18
LRRN1
CIDEC
ZFYVE20
AZI2
MTMR14
MRPS25
CRELD1
TMEM43
ZNF385D
HDAC11
TSEN2
GRIP2
C3orf20
JAGN1
C3orf42
IL17RC
EAF1
OXNAD1
CMTM7
OSBPL10
C3orf24
LRRC3B
GALNTL2
KCNH8
TRIM71
CHCHD4
METTL6
C3orf31
IL17RE
SGOL1
C3orf48
EFHB
CPNE9
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
FGD5
CIDECP
CNTN4
STT3B
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
GADL1
ZNF860
DVWA
TPRXL
LHFPL4
VENTXP7
LOC401052
LOC440944
SNORA7A
TMPPE
MIR563
MIR885
EGOT
GHRLOS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q23.

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

Genes
BLM
BUB1B
IDH2
NTRK3
PML
TCF12
CRTC3
C15orf55
C15orf21
hsa-mir-1302-2
hsa-mir-1469
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-628
hsa-mir-1300
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-626
hsa-mir-1233
hsa-mir-1233
hsa-mir-211
hsa-mir-1268
ACTC1
ADAM10
ACAN
ALDH1A3
ANPEP
ANXA2
APBA2
AQP9
B2M
BBS4
BCL2A1
BCL8
BNC1
BNIP2
CA12
CAPN3
CHD2
CHRM5
CHRNA3
CHRNA5
CHRNA7
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FES
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IDH3A
IGF1R
IL16
IPW
IREB2
ISG20
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2A2
MAN2C1
MAP1A
MEF2A
MEIS2
MFAP1
MFGE8
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
NMB
OAZ2
OCA2
FURIN
PCSK6
PDE8A
PKM2
PLCB2
PLIN1
POLG
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SH3GL3
SLC12A1
SNRPA1
SNRPN
SNX1
SORD
SPINT1
SRP14
NR2F2
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
UBE3A
MKRN3
SLC30A4
AP3B2
PAR5
ANP32A
ST8SIA2
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
PEX11A
IQGAP1
ALDH1A2
HERC2
HERC1
SNURF
PSTPIP1
PRC1
USP8
CCNB2
SLC28A2
SLC28A1
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
HISPPD2A
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
SV2B
ARNT2
USP3
SLC12A6
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
RASGRP1
SERF2
AP3S2
DENND4A
SNAPC5
HMG20A
CORO2B
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
SLC27A2
ABHD2
ADAMTS7
AKAP13
GPR176
CHP
OIP5
ITGA11
CHSY1
BAHD1
MTMR15
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
CYFIP1
ACSBG1
KIAA1024
MGA
DMXL2
SYNM
VPS39
FAM189A1
TMED3
AP4E1
SEC11A
CCNDBP1
DAPK2
EID1
C15orf2
GABARAPL3
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
VPS33B
GREM1
MRPL46
OR4F4
NPTN
FOXB1
RPUSD2
TUBGCP4
SLCO3A1
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
HDGFRP3
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
RASL12
SPG21
SPTBN5
NGRN
RHCG
PTPLAD1
CTDSPL2
KLF13
RAB8B
BTBD1
TM6SF1
DUOX1
CSNK1G1
ZFAND6
MAGEL2
DLL4
SCAND2
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZNF770
ZSCAN2
ZWILCH
FLJ10038
DET1
UACA
HAUS2
FAM82A2
LINS1
DNAJC17
FANCI
IMP3
LARP6
MNS1
DNAJA4
NOP10
MCTP2
SELS
GOLGA6B
MESP1
UNC45A
MYO5C
NDNL2
KIAA1370
C15orf24
C15orf39
THAP10
PAK6
RGMA
WDR93
PARP6
DTWD1
CASC5
AVEN
C15orf17
ADAMTSL3
ATP10A
KIAA1199
GJD2
ALPK3
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
MESDC1
PPCDC
BRUNOL6
STRA6
ZFP106
KLHL25
CPEB1
AEN
IQCH
ISL2
RFX7
TTC23
MRPS11
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
LRRK1
AAGAB
LMAN1L
C15orf29
SLTM
SGK269
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
C15orf28
C15orf34
PIF1
CCDC33
EDC3
LOC80154
SPG11
TM2D3
ELL3
PLEKHO2
WDR61
CD276
STARD5
GRINL1A
C15orf44
NIPA2
C15orf5
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
WDR73
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
FAM7A3
FAM7A1
ARHGAP11B
ATPBD4
C15orf42
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
RCCD1
LOC91450
CALML4
ARRDC4
LOC91948
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
C15orf40
SENP8
MTFMT
OSTbeta
TARSL2
HIGD2B
LRRC28
C15orf27
NIPA1
AGBL1
AGPHD1
WHAMM
FSD2
PLA2G4E
ASB7
TRIM69
PAR1
C15orf43
C2CD4A
LYSMD4
FAM81A
GCOM1
LOC145783
LOC145814
LOC145820
LOC145837
LOC145845
C15orf61
C15orf32
HAPLN3
MESP2
TMCO5A
SPATA8
NRG4
NCRNA00052
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
CSNK1A1P
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
ADAMTS17
RHOV
SCAMP5
C15orf33
C15orf51
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
LASS3
SPESP1
LPCAT4
LOC254559
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
SLC24A5
PRTG
LOC283663
TMEM84
C15orf60
C15orf37
OR4N4
FAM154B
LOC283731
FAM98B
PLA2G4D
LOC283761
GOLGA6L1
GOLGA8G
FAM169B
GOLGA9P
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
TMEM202
WHAMML1
POTEB
GLDN
GOLGA6A
TMC3
ZNF774
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
C15orf38
MRPL42P5
USP50
TEX9
GOLGA6L5
KIF7
ZNF710
HDDC3
WASH3P
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
LOC388152
UBE2QP1
FLJ42289
GOLGA8E
OR4M2
OR4N3P
LOC390594
LOC390595
LBXCOR1
ANKRD34C
C15orf58
OR4F6
OR4F15
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
ST20
FAM174B
DUOXA2
MIR184
MIR190
MIR211
MIR7-2
MIR9-3
C15orf50
NF1P1
WHAMML2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
GOLGA6L9
TTLL13
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645752
LOC646214
CXADRP2
SH2D7
GOLGA6L10
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA15
SCARNA14
FBXO22OS
MIR548A3
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
LOC723972
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
LOC729082
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
FAM138E
MIR147B
DNM1P35
LOC100129387
GOLGA8F
LOC100132724
GOLGA8D
LOC100133144
UBE2QP2
JMJD7
PLA2G4B
LOC100144604
FAM7A2
LOC100288778

Arm-level results

Table 3. Get Full Table Arm-level significance table - 27 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.04 | -1.22 | 1 | 0.03 | -1.67 | 1
1q | 1572 | 0.35 | 24.1 | 0 | 0.01 | -2.95 | 1
2p | 753 | 0.13 | 4.38 | 3.36e-05 | 0.03 | -3.13 | 1
2q | 1235 | 0.09 | 1.89 | 0.127 | 0.02 | -3.35 | 1
3p | 853 | 0.07 | 0.187 | 1 | 0.08 | 0.586 | 0.604
3q | 917 | 0.13 | 4.94 | 2.48e-06 | 0.04 | -2.1 | 1
4p | 366 | 0.01 | -4.81 | 1 | 0.09 | 1.08 | 0.322
4q | 865 | 0.00 | -4.93 | 1 | 0.09 | 1.49 | 0.206
5p | 207 | 0.07 | -0.767 | 1 | 0.07 | -0.767 | 1
5q | 1246 | 0.02 | -2.91 | 1 | 0.08 | 1.5 | 0.206
6p | 937 | 0.09 | 1.68 | 0.159 | 0.02 | -3.57 | 1
6q | 692 | 0.06 | -0.675 | 1 | 0.02 | -3.43 | 1
7p | 508 | 0.09 | 1.41 | 0.238 | 0.07 | -0.32 | 1
7q | 1071 | 0.09 | 1.65 | 0.159 | 0.06 | -0.601 | 1
8p | 495 | 0.18 | 6.84 | 3.07e-11 | 0.16 | 5.89 | 1.25e-08
8q | 697 | 0.22 | 11.1 | 0 | 0.06 | -0.983 | 1
9p | 343 | 0.02 | -3.65 | 1 | 0.13 | 3.72 | 0.000428
9q | 916 | 0.01 | -4.01 | 1 | 0.16 | 7.27 | 2.32e-12
10p | 312 | 0.21 | 9.52 | 0 | 0.06 | -1.17 | 1
10q | 1050 | 0.21 | 11.1 | 0 | 0.06 | -0.698 | 1
11p | 731 | 0.02 | -3.93 | 1 | 0.09 | 1.6 | 0.206
11q | 1279 | 0.02 | -3.11 | 1 | 0.08 | 1.31 | 0.247
12p | 484 | 0.08 | 0.645 | 0.723 | 0.05 | -1.85 | 1
12q | 1162 | 0.07 | 0.326 | 0.968 | 0.03 | -2.58 | 1
13q | 554 | 0.05 | -1.73 | 1 | 0.10 | 1.55 | 0.206
14q | 1144 | 0.03 | -2.78 | 1 | 0.08 | 1.16 | 0.301
15q | 1132 | 0.02 | -3.44 | 1 | 0.15 | 6.9 | 2.54e-11
16p | 719 | 0.03 | -2.69 | 1 | 0.14 | 4.99 | 1.72e-06
16q | 562 | 0.01 | -3.83 | 1 | 0.22 | 10.7 | 0
17p | 575 | 0.02 | -3.49 | 1 | 0.19 | 8.32 | 0
17q | 1321 | 0.04 | -1.47 | 1 | 0.14 | 6.15 | 3.11e-09
18p | 117 | 0.07 | -0.984 | 1 | 0.08 | 0.124 | 0.903
18q | 340 | 0.03 | -2.95 | 1 | 0.10 | 1.4 | 0.226
19p | 870 | 0.07 | -0.0531 | 1 | 0.07 | -0.0531 | 0.968
19q | 1452 | 0.04 | -1.2 | 1 | 0.06 | 0.0933 | 0.903
20p | 295 | 0.10 | 1.74 | 0.159 | 0.03 | -2.96 | 1
20q | 627 | 0.13 | 3.97 | 0.000175 | 0.03 | -3.24 | 1
21q | 422 | 0.04 | -2.63 | 1 | 0.06 | -1.3 | 1
22q | 764 | 0.03 | -2.45 | 1 | 0.13 | 4.67 | 7.5e-06

Methods & Data
Input

Table 4. Get Full Table First 10 out of 363 Input Tumor Samples.

Tumor Sample Names
TCGA-A5-A0G1-01A-11D-A120-01
TCGA-A5-A0G2-01A-11D-A042-01
TCGA-A5-A0G5-01A-11D-A042-01
TCGA-A5-A0G9-01A-11D-A042-01
TCGA-A5-A0GA-01A-11D-A042-01
TCGA-A5-A0GB-01A-11D-A042-01
TCGA-A5-A0GE-01A-11D-A042-01
TCGA-A5-A0GG-01A-11D-A120-01
TCGA-A5-A0GH-01A-21D-A042-01
TCGA-A5-A0GI-01A-11D-A042-01

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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