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 2.0.16a (cga svn revision 43808).

Summary

There were 443 tumor samples used in this analysis: 29 significant arm-level results, 47 significant focal amplifications, and 50 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 - 47 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
--- | --- | --- | --- | ---
3q26.2 | 5.9075e-37 | 5.9075e-37 | chr3:168674013-168760976 | 0 [MECOM]
8q24.21 | 4.4853e-36 | 4.1896e-22 | chr8:129543557-129554481 | 0 [MIR1208]
19q12 | 3.8395e-21 | 4.252e-21 | chr19:30304858-30358071 | 1
17q12 | 3.0363e-22 | 6.9507e-16 | chr17:37827871-37877201 | 2
1q22 | 2.7204e-19 | 5.6355e-12 | chr1:155817553-156103772 | 14
1p22.3 | 2.9238e-13 | 6.3618e-12 | chr1:85979933-86002734 | 1
8q24.21 | 5.8793e-32 | 2.7892e-10 | chr8:128739772-128781734 | 1
3p25.1 | 7.4629e-10 | 7.4629e-10 | chr3:13714839-13726839 | 1
2q13 | 2.4021e-09 | 2.4021e-09 | chr2:113953684-114236549 | 4
8p11.21 | 4.7012e-09 | 4.7012e-09 | chr8:41695855-42077182 | 4
10q22.2 | 4.2407e-08 | 4.2407e-08 | chr10:76700603-77071885 | 7
6p24.2 | 8.209e-08 | 8.209e-08 | chr6:11216701-11530964 | 1
19p13.2 | 7.4629e-10 | 4.0066e-07 | chr19:10848467-10927539 | 2
20q11.21 | 1.9744e-09 | 2.4597e-06 | chr20:30731473-30798667 | 4
1q21.3 | 1.7176e-18 | 3.0535e-06 | chr1:150493148-150919620 | 11
4p16.3 | 3.9871e-05 | 3.9871e-05 | chr4:1512439-1905088 | 7
11q13.2 | 4.9407e-06 | 0.0001289 | chr11:67093861-67231888 | 13
12q13.2 | 4.5786e-07 | 0.00024986 | chr12:56481350-56491606 | 1
5p15.33 | 0.00026981 | 0.00026981 | chr5:1-2037533 | 34
2p23.2 | 0.0002808 | 0.0002808 | chr2:28477194-28873211 | 4
16p11.2 | 0.000381 | 0.000381 | chr16:30854953-30989870 | 9
20q13.33 | 4.3572e-06 | 0.00046309 | chr20:60923133-61054962 | 5
9p24.2 | 0.0028394 | 0.0028394 | chr9:3631009-3996780 | 2
18q11.2 | 0.0039543 | 0.0039543 | chr18:23786856-24119078 | 2
17q11.2 | 1.6714e-05 | 0.0071057 | chr17:26941897-27113673 | 16
1q44 | 1.0278e-07 | 0.0078038 | chr1:225374027-249250621 | 216
17q25.3 | 2.425e-05 | 0.011659 | chr17:79923719-80022360 | 8
Xq28 | 0.016686 | 0.016686 | chrX:152805056-154883395 | 79
12q13.11 | 6.7927e-05 | 0.025077 | chr12:48199740-48265041 | 2
19p13.11 | 5.134e-05 | 0.034796 | chr19:15293986-19250144 | 118
9q34.3 | 0.053174 | 0.053174 | chr9:139812578-139898208 | 8
14q24.3 | 0.0064516 | 0.054562 | chr14:77305985-77565703 | 3
11q13.3 | 0.00011898 | 0.062451 | chr11:69351722-70132817 | 10
6q25.1 | 0.064184 | 0.064184 | chr6:151921400-152042501 | 2
12p12.1 | 0.073078 | 0.073078 | chr12:24643054-25683946 | 9
Xp11.22 | 0.082456 | 0.082456 | chrX:45447113-53005732 | 143
13q34 | 0.089513 | 0.089513 | chr13:109144777-114923884 | 39
20p13 | 0.097887 | 0.097887 | chr20:2576157-4359815 | 48
1p35.2 | 0.016686 | 0.1313 | chr1:31354381-31376674 | 1
11p11.2 | 0.1313 | 0.1313 | chr11:46300642-46481485 | 9
14q32.33 | 0.035873 | 0.13437 | chr14:103967300-104100604 | 6
17q21.32 | 4.9526e-05 | 0.14289 | chr17:46458792-46639145 | 4
1p34.3 | 0.050259 | 0.15992 | chr1:36519744-36611286 | 5
15q26.3 | 0.16384 | 0.16384 | chr15:98000287-102531392 | 35
7q32.2 | 0.17346 | 0.17346 | chr7:129494947-129721643 | 3
17p13.3 | 0.20406 | 0.20406 | chr17:1095274-1574341 | 12
22q12.2 | 0.21599 | 0.21599 | chr22:30270268-31334517 | 26

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
PGAP3

Genes in Wide Peak

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

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

Genes
LMNA
RIT1
SSR2
ARHGEF2
KIAA0907
SYT11
LAMTOR2
GON4L
UBQLN4
RAB25
MEX3A
RXFP4
SCARNA4
SNORA42

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p22.3.

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

Genes
DDAH1

Genes in Wide Peak

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

Table S5. 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 3p25.1.

Table S6. 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 2q13.

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

Genes
PAX8
PSD4
CBWD2
LOC654433

Genes in Wide Peak

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

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

Genes
ANK1
PLAT
KAT6A
AP3M2

Genes in Wide Peak

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

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

Genes
VDAC2
KAT6B
DUSP13
COMTD1
SAMD8
ZNF503-AS1
DUPD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.2.

Table S10. 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 19p13.2.

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

Genes
DNM2
MIR4748

Genes in Wide Peak

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

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

Genes
PLAGL2
TM9SF4
POFUT1
TSPY26P

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
ARNT
hsa-mir-4257
CTSK
CTSS
ENSA
MCL1
SETDB1
ADAMTSL4
GOLPH3L
HORMAD1
MIR4257

Genes in Wide Peak

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

Table S14. 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 11q13.2.

Table S15. 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
CARNS1
POLD4
TMEM134
TBC1D10C
GPR152
LOC100130987

Genes in Wide Peak

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

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

Genes
ERBB3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

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

Genes
hsa-mir-4277
NDUFS6
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
IRX4
CEP72
AHRR
MRPL36
BRD9
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
SDHAP3
LOC728613
MIR4277
LOC100506688
MIR4457
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
FOSL2
BRE
PLB1
LOC100505716

Genes in Wide Peak

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

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

Genes
hsa-mir-762
CTF1
BCL7C
SETD1A
FBXL19
ORAI3
FBXL19-AS1
MIR762
MIR4519

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
LAMA5
RPS21
CABLES2
GATA5
C20orf151

Genes in Wide Peak

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

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

Genes
GLIS3-AS1
GLIS3

Genes in Wide Peak

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

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

Genes
TAF4B
KCTD1

Genes in Wide Peak

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

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

Genes
RPL23A
SDF2
SUPT6H
TRAF4
KIAA0100
SNORD4B
SNORD4A
SNORD42B
SNORD42A
C17orf63
RAB34
TLCD1
PROCA1
NEK8
SPAG5-AS1
RAB34

Genes in Wide Peak

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

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
CHML
LYST
CHRM3
EPHX1
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
LBR
LGALS8
MTR
NID1
PSEN2
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
LEFTY2
GPR137B
TSNAX
WNT9A
ZNF124
HIST3H3
GNPAT
CDC42BPA
KMO
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
AKT3
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
COG2
RBM34
ABCB10
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
TAF5L
DISC2
DISC1
PYCR2
PPPDE1
SCCPDH
TRIM17
ARID4B
EGLN1
KIAA1383
KIF26B
HEATR1
ZNF692
ENAH
NUP133
ERO1LB
FMN2
ADCK3
ZNF695
GJC2
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
ACBD3
SMYD3
ARV1
JMJD4
C1orf35
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
EFCAB2
KIAA1804
ZNF496
C1orf198
WNT3A
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
EXOC8
RNF187
C1orf55
CNST
PLD5
C1orf100
IBA57
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf95
FAM89A
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
DUSP5P
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
MIR3123
MIR3124
MIR3620
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

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

Genes
ASPSCR1
GPS1
RAC3
RFNG
DCXR
DUS1L
STRA13
LRRC45

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

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

Genes
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
OPN1MW
GDI1
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
TAZ
VBP1
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SRPK3
SNORA70
CTAG2
TMLHE
PLXNA3
PDZD4
FAM3A
FUNDC2
BRCC3
H2AFB3
FAM58A
RAB39B
GAB3
PNCK
CTAG1A
LINC00204B
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CXorf68
LINC00204A
MTCP1NB
MIR1184-1
MIR718
MIR3202-2
MIR1184-3
MIR1184-2
MIR3202-1
LOC100507404

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.11.

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

Genes
VDR
HDAC7

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.11.

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

Genes
JAK3
TPM4
ELL
BRD4
hsa-mir-3189
hsa-mir-3188
hsa-mir-1470
BST2
COMP
NR2F6
GDF1
IL12RB1
INSL3
JUND
KCNN1
CYP4F3
RAB8A
MYO9B
NOTCH3
PDE4C
PIK3R2
RAB3A
UPF1
RPL18A
SLC5A5
UBA52
CYP4F2
AP1M1
F2RL3
CRLF1
MED26
HOMER3
GDF15
SUGP2
AKAP8
B3GNT3
KLF2
IFI30
CHERP
CERS1
CYP4F8
COPE
UNC13A
MAST3
FCHO1
SIN3B
CRTC1
FKBP8
TMEM59L
PGLS
LSM4
FAM32A
OR10H3
OR10H2
OR10H1
SNORA68
AKAP8L
ARRDC2
CPAMD8
BABAM1
ISYNA1
DDX49
PGPEP1
TMEM161A
C19orf60
MAP1S
KLHL26
USE1
ANO8
CYP4F11
EPS15L1
WIZ
RASAL3
MRPL34
CYP4F12
DDA1
KXD1
TMEM38A
C19orf42
ABHD8
OCEL1
GLT25D1
EPHX3
SLC35E1
KIAA1683
PLVAP
USHBP1
C19orf44
GTPBP3
MPV17L2
HSH2D
HAUS8
FAM125A
ARMC6
PGLYRP2
CCDC124
NXNL1
CIB3
CALR3
LRRC25
CYP4F22
LOC126536
OR10H4
ANKLE1
FLJ25328
SSBP4
FAM129C
OR10H5
NWD1
SLC25A42
SLC27A1
CYP4F24P
UCA1
LOC729966
TMEM221
MIR1470
MIR3188
MIR3189

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
C8G
PTGDS
TRAF2
CLIC3
FBXW5
LCN12
C9orf142
LCNL1

Genes in Wide Peak

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

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

Genes
IRF2BPL
KIAA1737
C14orf166B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CCND1
hsa-mir-548k
FGF3
FGF4
PPFIA1
FADD
FGF19
ANO1
ORAOV1
MIR548K

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 12p12.1.

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

Genes
KRAS
BCAT1
LRMP
SOX5
CASC1
LINC00477
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.22.

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

Genes
GATA1
SSX1
SSX2
SSX4
TFE3
WAS
hsa-mir-502
hsa-mir-222
ARAF
CACNA1F
CLCN5
ELK1
GAGE1
GAGE2C
GAGE4
GAGE5
GAGE6
GAGE7
ERAS
KCND1
PRICKLE3
TBC1D25
CDK16
CFP
PLP2
RBM3
RP2
SSX5
SUV39H1
SYN1
SYP
TIMP1
UBA1
SLC35A2
ZNF182
ZNF41
ZNF157
USP11
RBM10
UXT
INE1
PAGE1
AKAP4
RGN
BMP15
MAGED1
XAGE2
XAGE1D
PAGE4
PHF16
HDAC6
PQBP1
SSX3
TIMM17B
EBP
PIM2
WDR45
PRAF2
GSPT2
FTSJ1
GAGE12I
GAGE2E
GPKOW
PCSK1N
CCDC22
FAM156A
FOXP3
NDUFB11
NUDT11
OTUD5
ZNF673
CHST7
GRIPAP1
ZNF630
SHROOM4
WDR13
PORCN
MAGIX
MAGED4B
SLC9A7
CCNB3
PPP1R3F
CCDC120
SLC38A5
DGKK
LOC158572
XAGE3
XAGE5
NUDT10
SSX6
SSX7
SSX8
ZNF81
SPACA5
USP27X
CENPVL1
CXXC1P1
GLOD5
LOC401588
MIR188
MIR221
MIR222
LOC441495
SPANXN5
SSX4B
MIR362
MIR500A
MIR501
MIR502
ZNF674
GAGE10
GAGE2B
GAGE13
GAGE12G
XAGE1C
XAGE1E
XAGE1A
XAGE1B
MIR532
MIR660
CXorf31
SSX2B
FAM156B
MAGED4
XAGE2B
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
GAGE12F
GAGE8
SNORA11C
SNORA11D
SNORA11E
GAGE12D
LOC100133957
MIR500B
LOC100509575
MIR4769

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q34.

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

Genes
ATP4B
COL4A1
COL4A2
F7
F10
GAS6
ING1
LAMP1
GRK1
SOX1
TFDP1
CUL4A
IRS2
PROZ
ARHGEF7
TUBGCP3
RASA3
MYO16
ATP11A
MCF2L
TMCO3
DCUN1D2
ANKRD10
RAB20
CARKD
PCID2
CARS2
GRTP1
ADPRHL1
TEX29
SPACA7
LINC00346
FAM70B
C13orf35
FLJ44054
FLJ41484
LINC00552
MCF2L-AS1
LOC100506394

Genes in Wide Peak

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

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

Genes
hsa-mir-103-2-as
hsa-mir-1292
ADRA1D
AVP
CDC25B
CENPB
GNRH2
IDH3B
ITPA
OXT
PTPRA
SIGLEC1
ATRN
ProSAPiP1
NOP56
RNF24
UBOX5
SPEF1
C20orf194
SNORD57
SNORD56
SMOX
C20orf27
C20orf29
CPXM1
MAVS
EBF4
FASTKD5
GFRA4
VPS16
FAM113A
MRPS26
DDRGK1
PANK2
ADAM33
SLC4A11
HSPA12B
TMC2
C20orf141
MIR103A2
SNORA51
SNORD86
SNORD110
LOC728228
LOC100134015
TMEM239
MIR1292
MIR103B2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p35.2.

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

Genes
SDC3

Genes in Wide Peak

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

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

Genes
CREB3L1
hsa-mir-3160-2
CHRM4
MDK
DGKZ
AMBRA1
MIR3160-2
MIR3160-1
MIR4688

Genes in Wide Peak

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

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

Genes
CKB
KLC1
MARK3
BAG5
APOPT1
TRMT61A

Genes in Wide Peak

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

Table S40. 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 1p34.3.

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

Genes
COL8A2
TRAPPC3
TEKT2
ADPRHL2
EIF2C3

Genes in Wide Peak

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

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

Genes
hsa-mir-1302-10
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
LINS
SELS
TTC23
LRRK1
TM2D3
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
ADAMTS17
DNM1P46
CERS3
FAM169B
WASH3P
FLJ42289
OR4F6
OR4F15
FAM138E
GPCRLTM7
DDX11L1
DDX11L9
LOC100507472
MIR4714

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q32.2.

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

Genes
UBE2H
KLHDC10
ZC3HC1

Genes in Wide Peak

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

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

Genes
CRK
MYO1C
PITPNA
YWHAE
SCARF1
PRPF8
INPP5K
RILP
SLC43A2
TUSC5
BHLHA9
LOC100306951

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q12.2.

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

Genes
hsa-mir-3200
LIF
OSM
TCN2
MTMR3
GAL3ST1
SF3A1
MORC2
PES1
SEC14L2
OSBP2
MTFP1
TBC1D10A
KIAA1656
HORMAD2
DUSP18
MORC2-AS1
RNF215
SEC14L3
SEC14L4
SLC35E4
SDC4P
CCDC157
GATSL3
SEC14L6
MIR3200

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 - 50 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 | 1.7616e-34 | 4.2269e-34 | chr19:2734192-3143282 | 12
5q11.2 | 2.2705e-19 | 2.2705e-19 | chr5:58260298-59787985 | 3
4q34.3 | 3.1457e-24 | 1.3587e-17 | chr4:178911874-183060693 | 1
10q23.31 | 6.053e-15 | 2.439e-14 | chr10:89617158-90034038 | 2
22q13.31 | 2.8766e-14 | 6.2297e-13 | chr22:47571204-48018269 | 1
2q22.1 | 1.9576e-13 | 1.2299e-12 | chr2:139655617-143637838 | 1
Xp21.2 | 6.2508e-11 | 6.2508e-11 | chrX:30870233-34644819 | 4
16q23.1 | 2.1811e-13 | 3.1542e-10 | chr16:78129058-79627770 | 1
17q11.2 | 1.0014e-08 | 5.0513e-08 | chr17:29326736-29722618 | 5
3p14.2 | 1.0503e-07 | 1.0354e-07 | chr3:59034763-61547330 | 1
6q26 | 1.1535e-07 | 1.1017e-07 | chr6:161693099-163153207 | 1
11p15.5 | 8.5568e-06 | 8.9045e-06 | chr11:1-3679657 | 114
1p36.11 | 1.6243e-12 | 1.7884e-05 | chr1:26900639-27670158 | 15
7p22.3 | 3.7332e-05 | 3.79e-05 | chr7:1-5515694 | 57
12q23.1 | 2.5299e-06 | 4.1644e-05 | chr12:99124001-100107912 | 2
8p23.2 | 1.5046e-07 | 4.5109e-05 | chr8:1-6262191 | 15
18q23 | 4.4448e-05 | 4.5109e-05 | chr18:62012003-78077248 | 46
1p36.21 | 3.9995e-10 | 6.7445e-05 | chr1:1-22963470 | 348
11q25 | 3.1757e-06 | 0.00015629 | chr11:133400280-135006516 | 14
15q15.1 | 3.9984e-06 | 0.00039066 | chr15:1-47478056 | 339
20p12.1 | 0.00076779 | 0.00076853 | chr20:14302876-16252980 | 3
4q22.1 | 1.4699e-05 | 0.00096067 | chr4:90844993-93240505 | 1
7q31.1 | 2.7116e-05 | 0.0013155 | chr7:109599468-111366370 | 2
4p16.3 | 0.0014305 | 0.0013967 | chr4:1-1511830 | 31
17p11.2 | 0.0006617 | 0.0027999 | chr17:9693062-19556178 | 120
19q13.43 | 0.0042981 | 0.0042665 | chr19:56934523-59128983 | 83
8p21.2 | 2.5745e-08 | 0.0088257 | chr8:18079280-36642339 | 126
11q14.1 | 0.0027712 | 0.009559 | chr11:82995735-85348794 | 2
12q24.33 | 0.00052697 | 0.0097158 | chr12:121855762-133851895 | 110
9q34.11 | 0.010152 | 0.013832 | chr9:116359544-141213431 | 381
13q14.2 | 0.017319 | 0.01673 | chr13:1-58211590 | 250
14q13.1 | 0.018737 | 0.018708 | chr14:33301849-34394000 | 1
16q21 | 0.00026698 | 0.03294 | chr16:31772318-69350160 | 224
16p13.3 | 0.055067 | 0.056367 | chr16:3764793-4013466 | 1
17p13.3 | 0.0051657 | 0.056367 | chr17:1-1201203 | 17
7q36.3 | 0.00091175 | 0.06517 | chr7:117882615-159138663 | 336
9p24.1 | 0.07495 | 0.075452 | chr9:7799607-12693402 | 1
15q23 | 0.0010336 | 0.081313 | chr15:71406546-72105142 | 1
2q37.3 | 0.0035405 | 0.10357 | chr2:210440283-243199373 | 297
16q22.2 | 2.1673e-09 | 0.10757 | chr16:72204963-73126458 | 1
22q12.1 | 0.031094 | 0.1475 | chr22:29192671-29455701 | 1
1q43 | 0.15706 | 0.15316 | chr1:236767073-236961354 | 1
19p12 | 0.0026475 | 0.15316 | chr19:23939307-28240493 | 4
2p25.3 | 0.18078 | 0.18078 | chr2:1-27588658 | 163
9q21.2 | 0.15024 | 0.18078 | chr9:37783143-87284261 | 122
17q21.31 | 0.0096169 | 0.18507 | chr17:37899689-46607558 | 257
20q13.12 | 0.18382 | 0.18507 | chr20:45363767-45838725 | 2
10q21.1 | 0.036065 | 0.19784 | chr10:38987241-68686446 | 139
22q11.21 | 0.048726 | 0.23603 | chr22:1-22274744 | 117
10p12.31 | 0.24975 | 0.25377 | chr10:1-31607360 | 190

Genes in Wide Peak

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

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

Genes
GNA11
AES
SGTA
THOP1
TLE2
SLC39A3
ZNF77
TLE6
ZNF556
ZNF554
ZNF57
ZNF555

Genes in Wide Peak

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

Table S47. 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 4q34.3.

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

Genes
LINC00290

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

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

Table S51. 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 Xp21.2.

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

Genes
hsa-mir-548f-5
DMD
FTHL17
FAM47A

Genes in Wide Peak

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

Table S53. 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 S54. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

Table S56. 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 11p15.5.

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

Genes
CARS
HRAS
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
SCT
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
OR7E12P
KCNQ1OT1
PKP3
SIRT3
C11orf21
TRPM5
IGF2-AS1
BET1L
CEND1
CDHR5
TOLLIP
PIDD
KCNQ1DN
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
MOB2
SYT8
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
LOC143666
SCGB1C1
NLRP6
NS3BP
LOC255512
C11orf35
H19
EFCAB4A
TMEM80
C11orf36
ANO9
LOC338651
B4GALNT4
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
MIR483
SNORA52
LOC650368
LOC653486
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686

Genes in Wide Peak

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

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

Genes
ARID1A
SFN
SLC9A1
NR0B2
NUDC
WDTC1
GPN2
PIGV
GPATCH3
TMEM222
ZDHHC18
FAM46B
C1orf172
TRNP1
LOC644961

Genes in Wide Peak

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

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

Genes
CARD11
hsa-mir-339
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
EIF3B
KIAA0415
ADAP1
IQCE
SUN1
WIPI2
INTS1
SNX8
FTSJ2
GET4
CYP2W1
HEATR2
CHST12
RADIL
PAPOLB
FAM20C
RBAK
MICALL2
TTYH3
PSMG3
C7orf50
TNRC18
ZFAND2A
COX19
KIAA1908
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
SLC29A4
TFAMP1
UNCX
LOC389458
ELFN1
RNF216P1
FLJ44511
LOC442497
MIR339
ZNF890P
LOC100288524
RBAK-LOC389458
MIR4648
MIR4655
MIR4656

Genes in Wide Peak

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

Table S60. 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 8p23.2.

Table S61. 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
LOC286083
OR4F21
RPL23AP53
MIR596

Genes in Wide Peak

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

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

Genes
CDH7
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
SOCS6
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
SALL3
CDH19
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
RBFA
PQLC1
NETO1
PARD6G
CNDP1
DSEL
FAM69C
CBLN2
FBXO15
DOK6
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.21.

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
CA6
CAPZB
CASP9
TNFRSF8
CDA
CDK11B
CDC42
CLCN6
CLCNKA
CLCNKB
CORT
DDOST
DFFA
DFFB
DVL1
ECE1
MEGF6
EPHA2
ENO1
EPHA8
MTOR
GABRD
GNB1
ZBTB48
HSPG2
HTR6
TNFRSF9
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TNFRSF1B
TP73
TNFRSF4
ZBTB17
PRDM2
MMP23B
MMP23A
KCNAB2
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
ANGPTL7
UBE4B
MAD2L2
PDPN
MASP2
UTS2
RER1
MST1P2
MST1P9
PADI2
PARK7
CTRC
ACOT7
CLSTN1
AKR7A3
SPEN
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
CHD5
C1orf144
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
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
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
AGTRAP
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
MIIP
CELA2A
PLA2G2F
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
AGMAT
LINC00115
MORN1
GPR157
SPSB1
GLTPD1
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
USP48
NBPF3
SLC25A33
DDI2
LZIC
C1orf170
CROCCP2
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf158
FBXO44
CROCCP3
FHAD1
LOC115110
RBP7
ACAP3
UBE2J2
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf64
SLC2A7
CALML6
FAM43B
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
NPHP4
FAM41C
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
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
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC649330
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
NPPA-AS1
MIR4251
MIR4252
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4689
MIR4632
MIR4417

Genes in Wide Peak

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

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

Genes
IGSF9B
NCAPD3
ACAD8
B3GAT1
THYN1
JAM3
GLB1L2
VPS26B
GLB1L3
SPATA19
LOC283174
LOC283177
LOC100128239
MIR4697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.1.

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

Genes
BUB1B
C15orf55
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
EPB42
GABRA5
GABRB3
GABRG3
GANC
GATM
GCHFR
PDIA3
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
SLC28A2
TGM5
PPIP5K1
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
WDR76
TMEM62
SPG11
ELL3
NIPA2
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
HMGN2P46
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
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
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1282
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
LRRN3
IMMP2L

Genes in Wide Peak

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

Table S69. 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
KIAA1530
ABCA11P
MFSD7
TMEM175
C4orf42
ZNF595
ZNF721
ZNF718
CRIPAK
RNF212
ZNF876P
ZNF732
LOC100129917
LOC100130872
TMED11P

Genes in Wide Peak

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

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

Genes
MAP2K4
GAS7
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
COX10
DNAH9
DRG2
FOXO3B
FLII
LLGL1
MEIS3P1
MFAP4
MYH1
MYH2
MYH3
MYH4
MYH8
PMP22
MAPK7
PRPSAP2
RCVRN
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
MYH13
GLP2R
PIGL
NCOR1
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
GRAP
EPN2
MPRIP
TNFRSF13B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
C17orf48
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
FAM106A
LRRC48
MGC12916
ATPAF2
MYOCD
CDRT7
CDRT15P1
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
CDRT15
TRIM16L
USP32P1
FAM18B2
CENPV
FLCN
PLD6
USP32P2
TBC1D28
FLJ34690
CDRT4
CCDC144B
LOC339240
TBC1D26
CDRT1
TMEM220
SHISA6
FAM211A
KRT16P2
GRAPL
PIRT
CDRT15P2
FAM83G
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
MIR744
FAM106CP
LOC100289255
MIR1288
MIR1180
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.43.

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

Genes
hsa-mir-1274b
A1BG
FKBP1AP1
PEG3
RPS5
AURKC
ZNF8
ZNF17
MZF1
ZNF132
ZNF134
ZNF135
ZNF154
UBE2M
ZNF264
TRIM28
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
SLC27A5
ZIM2
ZNF324
CHMP2A
ZNF544
ZNF586
ZNF416
ZNF446
VN1R1
ZNF304
ZNF471
USP29
ZNF71
ZNF667
ZSCAN18
MGC2752
ZNF329
ZNF419
ZNF552
ZNF671
ZNF606
ZBTB45
ZNF587
ZNF551
ZNF835
ZIM3
ZNF837
ZNF543
ZFP28
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
ZNF497
ZNF550
ZNF584
ZSCAN4
ZNF549
ZNF547
ZIK1
ZNF776
ZSCAN1
ZSCAN22
ZNF530
ZNF773
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF772
A1BG-AS1
DUXA
LOC646862
ZNF814
MIMT1
LOC100128252
LOC100128398
LOC100131691
PEG3-AS1
ZNF587B
MIR4754

Genes in Wide Peak

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

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

Genes
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
hsa-mir-320a
NAT2
ADRA1A
ATP6V1B2
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
DPYSL2
DUSP4
EGR3
EPB49
EPHX2
EXTL3
PTK2B
GFRA2
GNRH1
GSR
GTF2E2
NRG1
LOXL2
LPL
NEFM
NEFL
NKX3-1
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC18A1
STC1
FZD3
UBXN8
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
ADAMDEC1
PURG
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
DUSP26
HMBOX1
RNF122
NUDT18
DOCK5
FLJ14107
TTI2
REEP4
STMN4
MAK16
FUT10
CHMP7
NKX2-6
UNC5D
PEBP4
CDCA2
ESCO2
FBXO16
R3HCC1
LGI3
LOC254896
LOC286059
LOC286114
SCARA5
LOC286135
LOC389641
C8orf80
MIR320A
C8orf58
C8orf75
MBOAT4
LOC100128750
LOC100128993
MIR4287
MIR3148
MIR4288
MIR3622A
MIR3622B
LOC100507156
LOC100507341
MIR548O2

Genes in Wide Peak

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

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

Genes
DLG2
TMEM126B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.33.

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

Genes
BCL7A
hsa-mir-4304
SCARB1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
POLE
PSMD9
PXMP2
RAN
CLIP1
SFSWAP
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
ULK1
DENR
HCAR3
HIP1R
PIWIL1
NCOR2
KNTC1
MPHOSPH9
ZNF268
TMED2
SNRNP35
FZD10
MLXIP
P2RX2
SETD1B
ANKLE2
ABCB9
RIMBP2
ATP6V0A2
HCAR1
GALNT9
ARL6IP4
RHOF
SBNO1
ZCCHC8
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
CCDC92
PUS1
CCDC62
KDM2B
ORAI1
C12orf65
TMEM132C
TMEM132B
LOC116437
TMEM132D
SLC15A4
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
MORN3
DDX51
HCAR2
LOC338799
EP400NL
RILPL1
IL31
SETD8
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
LOC647589
SNORA49
LOC100128554
LOC100130238
LOC100190940
ZNF605
MIR4304
MIR3612
MIR3908
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A

Genes in Wide Peak

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

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

Genes
ABL1
NOTCH1
RALGDS
SET
TSC1
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
ABCA2
ABO
AK1
AMBP
ASS1
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
CRAT
DBC1
DBH
SARDH
DNM1
TOR1A
MEGF9
ENDOG
ENG
STOM
FCN1
FCN2
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSPA5
TNC
LCN1
LCN2
LMX1B
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP6C
PSMB7
PSMD5
PTGDS
PTGS1
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TLR4
TRAF1
TRAF2
TTF1
VAV2
ZNF79
LHX3
GFI1B
SSNA1
EDF1
DPM2
FUBP3
CLIC3
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
RALGPS1
ADAMTSL2
PPP1R26
SEC16A
TNFSF15
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
SLC27A4
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
RPL35
MAN1B1
DOLK
TRIM32
SETX
ZBTB43
PMPCA
ASTN2
EXOSC2
NCS1
ANGPTL2
NUP188
RABGAP1
CIZ1
DFNB31
COBRA1
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
RAB14
C9orf78
FBXW5
RC3H2
TBC1D13
C9orf167
EXD3
STRBP
C9orf86
CDK5RAP2
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
LINC00474
PRDM12
CARD9
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
EHMT1
PTGES2
AKNA
MIR600HG
URM1
ARPC5L
AIF1L
UCK1
GARNL3
NTNG2
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
SLC25A25
ZNF618
ZMYND19
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
C9orf96
OLFML2A
QSOX2
C9orf91
NAIF1
LOC253039
PHYHD1
MORN5
OR1L4
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
FAM78A
GPR144
QRFP
OR1J1
OR1B1
GLT6D1
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
C9orf106
LCN10
C9orf173
NRARP
MIR455
NRON
FAM163B
FLJ40292
TUBBP5
RNF224
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
LOC100128505
LOC100128593
LOC100129034
LOC100129722
LOC100130954
LOC100131193
FAM157B
RNU6ATAC
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR181A2HG
MIR4292
MIR3154
MIR2861
MIR3621
MIR3689A
MIR3911
MIR3689B
LOC100505478
LOC100506100
LOC100506190
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4672
MIR3689E
MIR4479

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP7B
CDK8
RCBTB2
CPB2
ELF1
ESD
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCDH8
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
ITM2B
MTRF1
UTP14C
NUPL1
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SAP18
DLEU1
N4BP2L2
OLFM4
POSTN
GJB6
HSPH1
WASF3
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
XPO4
MRP63
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
CDADC1
CAB39L
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
C1QTNF9
FREM2
NEK5
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4305
MIR3613
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
NPAS3

Genes in Wide Peak

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

Table S78. 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-3181
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
MT1JP
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
ORC6
EDC4
PLA2G15
TP53TG3
PLEKHG4
DKFZP434H168
LRRC29
TOX3
CCDC113
TMEM208
C16orf80
FHOD1
BRD7
ZDHHC1
PARD6A
PLLP
CKLF
FAM96B
TPPP3
CES1P1
PRMT7
DUS2L
CHTF8
LPCAT2
HEATR3
SLC38A7
OGFOD1
LRRC36
FBXL8
SMPD3
DOK4
VPS35
DDX28
TSNAXIP1
COQ9
CIAPIN1
THAP11
PDP2
ZNF319
RANBP10
NOD2
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
SNX20
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
LOC146481
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
CCDC79
CES4A
EXOC3L1
LOC283856
LOC283867
LOC283914
MT1DP
TEPP
SLC6A10P
C16orf87
LOC388276
C16orf86
LOC390705
CES1P2
FLJ26245
MIR138-2
HERC2P4
MIR328
UBE2MP1
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
LINC00273
KIAA0895L
TP53TG3C
SNORA46
SNORA50
LOC729264
TP53TG3B
LOC100130700
MIR3935
LOC100505619
LOC100505865
LOC100507577
CKLF-CMTM1
MIR548AE2

Genes in Wide Peak

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

Table S79. 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 17p13.3.

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

Genes
hsa-mir-3183
ABR
DOC2B
RPH3AL
TIMM22
GEMIN4
GLOD4
RNMTL1
VPS53
NXN
FAM57A
FAM101B
C17orf97
BHLHA9
DBIL5P
MIR3183
LOC100506388

Genes in Wide Peak

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

Table S81. 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
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
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
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CADPS2
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
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
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

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

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
THSD4

Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
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
NYAP2
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
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.2.

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

Genes
ZFHX3

Genes in Wide Peak

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

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

Genes
ZNRF3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

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

Genes
ACTN2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p12.

Table S88. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZNF254
RPSAP58
ZNF726
LOC100101266

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.3.

Table S89. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ADCY3
APOB
RHOB
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
MAPRE3
EFR3B
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
ITSN2
TRAPPC12
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
HS1BP3
COLEC11
CENPO
SMC6
NOL10
C2orf44
FAM49A
ABHD1
EPT1
RSAD2
CCDC164
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
FAM84A
GDF7
GPR113
UBXN2A
CYS1
ATP6V1C2
RNASEH1
FAM150B
DNAJC5G
IAH1
FLJ33534
C2orf70
C2orf53
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
PFN4
LOC375190
LOC386597
MFSD2B
PTRHD1
LOC400940
LINC00487
FLJ12334
FAM110C
LOC645949
C2orf84
LOC727982
RAD51AP2
DNAJC27-AS1
LOC730811
OST4
MIR1301
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505624
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.2.

Table S90. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GNAQ
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
ALDH1A1
ALDH1B1
ANXA1
APBA1
KLF9
FXN
GCNT1
HNRNPK
PCSK5
PGM5
PRKACG
RORB
SHB
TLE1
TLE4
ZFAND5
PIP5K1B
FAM189A2
TJP2
GDA
GNA14
SMC5
VPS13A
TMEM2
ZNF658
FAM75A7
OSTF1
PSAT1
UBQLN1
PCA3
FAM108B1
C9orf95
C9orf40
RFK
KIF27
SLC28A3
DCAF10
CNTNAP3
RMI1
TRPM3
GKAP1
CEP78
ANKRD20A1
C9orf64
MCART1
FAM122A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
TRPM6
RASEF
FAM201A
PRUNE2
C9orf71
CBWD5
ANKRD18A
MAMDC2
FRMD3
LOC286297
FOXD4L3
FAM75D5
IGFBPL1
FOXD4L4
AQP7P1
PTAR1
KGFLP1
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
FAM74A1
FAM74A4
ZNF658B
MIR204
MIR7-1
C9orf103
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
FOXB2
CBWD3
LOC494558
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920
LOC100286938
MIR548H3
LOC100507244
LOC100507299

Genes in Wide Peak

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

Table S91. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BRCA1
ETV4
RARA
hsa-mir-1203
hsa-mir-152
hsa-mir-4315-1
hsa-mir-2117
ACLY
AOC2
ARL4D
ATP6V0A1
FMNL1
CDC6
CDC27
CCR7
CNP
CRHR1
CSF3
DHX8
DUSP3
EZH1
GAST
FZD2
G6PC
KAT2A
GFAP
CCR10
GRN
HCRT
HSD17B1
IFI35
IGFBP4
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
PSMD3
RAB5C
RPL27
SLC4A1
SMARCE1
SP2
STAT3
STAT5A
STAT5B
MLX
THRA
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
RND2
CNTNAP1
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
HAP1
MAP3K14
EFTUD2
NPEPPS
GOSR2
NR1D1
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
GJC1
PSME3
EIF1
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
C1QL1
RUNDC3A
CBX1
CASC3
IKZF3
GPATCH8
KCNH4
FAM215A
KRT23
TUBG2
NKIRAS2
CCDC56
PSMC3IP
SNX11
TBX21
SOST
RAPGEFL1
COPZ2
ARL17A
SLC25A39
HIGD1B
KRT20
LRRC37A4
PNPO
KLHL11
GSDMB
ATXN7L3
FKBP10
WNK4
C17orf53
TMUB2
DHX58
PRR15L
ACBD4
DCAKD
PLEKHH3
DBF4B
CDK5RAP3
SP6
COASY
AARSD1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
TTC25
KRTAP4-12
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
VPS25
TMEM101
GHDC
KRTAP4-4
TNS4
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
LRRC46
SCRN2
AOC4
G6PC3
ASB16
HSPB9
ORMDL3
PLCD3
TMEM106A
OSBPL7
NT5C3L
ZPBP2
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
C17orf57
MRPL10
GJD3
KRT222
KRT40
CD300LG
KIF18B
RUNDC1
C17orf69
LOC147093
WIPF2
KRT25
TMEM99
NAGS
FAM134C
IMP5
KRT28
KRT24
ARHGAP27
ZNF385C
STH
KIAA1267
C17orf105
FAM171A2
C17orf104
GSDMA
KRT42P
PTRF
KLHL10
C17orf65
MSL1
KRT27
KRT26
LOC388387
CCDC103
RPRML
KRT39
MGC57346
MIR152
LRRC37A2
LOC644172
LOC644246
KRTAP4-11
MRPL45P2
KRTAP4-8
KRTAP2-2
KRTAP9-1
NSFP1
LOC730755
SNORD124
LOC100128977
LOC100130148
LOC100130581
KRTAP4-9
KRTAP4-7
LOC100133991
LOC100190938
MIR1203
MIR2117
MIR4315-2
MIR4315-1
LRRC3C
KRTAP16-1
LOC100505782
ARL17B

Genes in Wide Peak

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

Table S92. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
EYA2
MIR3616

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.1.

Table S93. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RET
NCOA4
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
hsa-mir-4294
hsa-mir-3156-1
ALOX5
ANXA8L2
ANK3
ANXA2P3
CDK1
CHAT
CTSL1P2
EGR2
ERCC6
GDF2
GDF10
HNRNPF
MBL2
MSMB
PPYR1
PRKG1
MAPK8
RBP3
CXCL12
SLC18A3
TFAM
UBE2D1
ZNF22
ZNF32
ZNF33B
CCDC6
ZNF239
PARG
GPRIN2
BMS1
RHOBTB1
HNRNPA3P1
C10orf10
ZWINT
ZNF365
DKK1
CSTF2T
PTPN20B
A1CF
NRBF2
FXYD4
CSGALNACT2
FAM21B
OGDHL
CISD1
ASAH2
WDFY4
ARHGAP22
PCDH15
OR13A1
BICC1
SYT15
RASSF4
ARID5B
PHYHIPL
LOC84856
ADO
LOC84989
ZFAND4
C10orf71
ZNF488
AGAP4
FRMPD2
FAM170B
C10orf128
ANTXRL
VSTM4
C10orf107
TMEM26
RTKN2
SLC16A9
FAM13C
MARCH8
C10orf25
TMEM72-AS1
ZNF485
RASGEF1A
REEP3
JMJD1C
IPMK
FAM21C
SGMS1
PGBD3
C10orf53
C10orf40
LOC283033
FLJ31813
LOC338579
FAM21A
ACTR3BP5
LOC399753
BMS1P5
AGAP6
ZNF32-AS3
FAM35B
C10orf136
FAM35B2
LOC441666
LRRC18
AGAP9
ZNF487P
LOC642826
TMEM72
LOC643650
FAM25C
DRGX
PTPN20A
ANXA8
AGAP7
ASAH2B
MIR605
BMS1P1
ANXA8L1
AGAP8
LOC728407
LOC728640
LOC728643
FRMPD2P1
ZNF37BP
FAM25B
FAM25G
LOC100133308
TIMM23
MIR1296
MIR4294
MIR3156-1
MTRNR2L5
MIR3924
LOC100506733
LOC100506835
LOC100506939
M1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.21.

Table S94. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CLTCL1
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ARVCF
ATP6V1E1
BID
COMT
CRKL
GGT3P
GP1BB
GSC2
SERPIND1
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
P2RX6
SNAP29
DGCR2
TXNRD2
USP18
HIC2
TSSK2
SDF2L1
PPIL2
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
DGCR11
DGCR9
DGCR5
DGCR10
TRMT2A
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L8P
YPEL1
ZDHHC8
MED15
TUBA8
CECR1
DGCR8
GNB1L
PEX26
MICAL3
MRPL40
RTN4R
C22orf29
THAP7
OR11H1
SLC25A18
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
MGC16703
GAB4
C22orf39
C22orf25
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
CCDC116
POM121L4P
LOC284865
PI4KAP2
TPTEP1
LOC388849
LOC400891
BCRP2
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
TMEM191C
MIR648
TMEM191B
PI4KAP1
LOC729444
MIR301B
CECR7
CECR5-AS1
FLJ41941
MIR1286
MIR1306
MIR3198-1
MIR3618
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p12.31.

Table S95. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
GATA3
MLLT10
hsa-mir-938
hsa-mir-604
hsa-mir-603
hsa-mir-1915
hsa-mir-511-2
hsa-mir-511-1
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
BMI1
CACNB2
CALML3
AKR1C4
KLF6
MAP3K8
AKR1C1
AKR1C2
TRDMT1
GAD2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PIP4K2A
PRKCQ
RSU1
SVIL
VIM
STAM
CUBN
ITGA8
PRPF18
AKR1C3
CDC123
PTPLA
PTER
NMT2
SPAG6
USP6NL
ABI1
OPTN
NET1
NEBL
PITRM1
RPP38
CELF2
YME1L1
ZMYND11
NUDT5
ANKRD26
WDR37
MSRB2
SEPHS1
RAB18
KIN
DIP2C
LARP4B
COMMD3
GTPBP4
PDSS1
BAMBI
UPF2
HSPA14
WAC
CALML5
MYO3A
APBB1IP
ANKRD16
FAM208B
ARMC4
MTPAP
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
KIAA1217
PRTFDC1
CAMK1D
GPR158
ARHGAP21
KIAA1462
SFMBT2
DNAJC1
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
THNSL1
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
LYZL1
FBXO18
PLXDC2
MASTL
RBM17
ACBD5
IDI2
UCN3
LYZL2
MPP7
SFTA1P
ENKUR
ARMC3
LOC219731
OTUD1
LOC220906
ZNF438
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
LOC254312
C10orf47
PTF1A
C10orf67
LOC282980
LOC283070
MKX
LOC338588
ST8SIA6
AKR1CL1
EBLN1
TUBB8
PTCHD3
C10orf113
C10orf140
LINC00202
LOC387646
LOC387647
tAKR
C1QL3
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf114
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
MIR511-1
MIR511-2
ADARB2-AS1
MEIG1
LINC00264
TMEM236
MIR603
MIR604
LOC729668
LOC731789
MIR938
LOC100128098
LOC100128511
LOC100128811
LOC100129213
LOC100130992
PRINS
LOC100192204
LOC100216001
MIR1265
MIR1915
MIR3155A
LOC100499489
LOC100507034
LOC100507127
LOC100507605
COMMD3-BMI1
MIR4480
MIR4675
MIR3155B

Arm-level results

Table 3. Get Full Table Arm-level significance table - 29 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.06 | -1.65 | 1 | 0.05 | -2.33 | 1
1q | 1955 | 0.32 | 18.2 | 0 | 0.06 | -1.44 | 1
2p | 924 | 0.16 | 4.24 | 5.55e-05 | 0.02 | -5.05 | 1
2q | 1556 | 0.13 | 2.84 | 0.00899 | 0.03 | -4.17 | 1
3p | 1062 | 0.09 | -0.716 | 1 | 0.10 | 0.0414 | 0.879
3q | 1139 | 0.14 | 3.02 | 0.00556 | 0.07 | -1.55 | 1
4p | 489 | 0.02 | -5.2 | 1 | 0.16 | 3.75 | 0.000297
4q | 1049 | 0.02 | -5.13 | 1 | 0.16 | 4.42 | 2.43e-05
5p | 270 | 0.09 | -1.29 | 1 | 0.10 | -1 | 1
5q | 1427 | 0.04 | -3.77 | 1 | 0.12 | 2.36 | 0.0262
6p | 1173 | 0.12 | 2.09 | 0.0607 | 0.03 | -4.51 | 1
6q | 839 | 0.11 | 0.285 | 0.862 | 0.04 | -3.88 | 1
7p | 641 | 0.11 | 0.56 | 0.719 | 0.10 | -0.606 | 1
7q | 1277 | 0.11 | 1.48 | 0.197 | 0.09 | -0.525 | 1
8p | 580 | 0.22 | 7.44 | 4.09e-13 | 0.18 | 4.29 | 3.99e-05
8q | 859 | 0.28 | 12.1 | 0 | 0.04 | -3.46 | 1
9p | 422 | 0.04 | -4.49 | 1 | 0.18 | 4.97 | 2.22e-06
9q | 1113 | 0.01 | -5.21 | 1 | 0.21 | 8.21 | 2.22e-15
10p | 409 | 0.24 | 8.73 | 0 | 0.08 | -1.8 | 1
10q | 1268 | 0.23 | 9.54 | 0 | 0.07 | -1.38 | 1
11p | 862 | 0.04 | -4.26 | 1 | 0.13 | 1.71 | 0.117
11q | 1515 | 0.04 | -3.75 | 1 | 0.11 | 1.65 | 0.125
12p | 575 | 0.13 | 1.49 | 0.197 | 0.08 | -1.55 | 1
12q | 1447 | 0.10 | 0.389 | 0.821 | 0.06 | -1.82 | 1
13q | 654 | 0.06 | -2.82 | 1 | 0.15 | 3.02 | 0.00385
14q | 1341 | 0.07 | -1.84 | 1 | 0.11 | 1.43 | 0.178
15q | 1355 | 0.02 | -4.65 | 1 | 0.18 | 6.12 | 3.71e-09
16p | 872 | 0.04 | -3.73 | 1 | 0.16 | 4.17 | 5.62e-05
16q | 702 | 0.02 | -4.89 | 1 | 0.23 | 8.61 | 0
17p | 683 | 0.03 | -4.84 | 1 | 0.21 | 7.03 | 1.41e-11
17q | 1592 | 0.05 | -2.59 | 1 | 0.15 | 4.59 | 1.26e-05
18p | 143 | 0.09 | -1.27 | 1 | 0.12 | 0.264 | 0.754
18q | 446 | 0.06 | -2.82 | 1 | 0.13 | 1.2 | 0.257
19p | 995 | 0.10 | -0.0767 | 1 | 0.11 | 0.525 | 0.599
19q | 1709 | 0.09 | 0.583 | 0.719 | 0.09 | 0.583 | 0.59
20p | 355 | 0.18 | 4.65 | 9.57e-06 | 0.05 | -3.9 | 1
20q | 753 | 0.21 | 7.02 | 7.52e-12 | 0.03 | -4.63 | 1
21q | 509 | 0.06 | -3.23 | 1 | 0.10 | -0.335 | 1
22q | 921 | 0.07 | -2.15 | 1 | 0.19 | 6.21 | 2.72e-09
Xq | 1312 | 0.13 | 2.2 | 0.0499 | 0.15 | 4.21 | 5.06e-05

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/UCEC/1709094/2.GDAC_MergeDataFiles.Finished/UCEC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 443 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-A0GD-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

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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