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 492 tumor samples used in this analysis: 30 significant arm-level results, 48 significant focal amplifications, and 49 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 - 48 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 | 8.0191e-32 | 1.0442e-31 | chr19:30304858-30358071 | 1
3q26.2 | 8.5334e-49 | 2.997e-31 | chr3:168605367-168677467 | 0 [EGFEM1P]
8q24.21 | 3.7044e-45 | 6.3226e-26 | chr8:129543557-129554481 | 0 [MIR1208]
17q12 | 1.0336e-29 | 6.3556e-17 | chr17:37827871-37955801 | 6
8q24.21 | 9.5556e-38 | 1.8694e-13 | chr8:128739772-128781734 | 1
10q22.2 | 2.9294e-13 | 2.9294e-13 | chr10:77001334-77071885 | 1
1p22.3 | 3.9947e-13 | 1.9564e-11 | chr1:85979933-86002734 | 1
2q13 | 2.429e-11 | 2.429e-11 | chr2:114050324-114109976 | 0 [PAX8]
8p11.21 | 2.2151e-10 | 2.2151e-10 | chr8:41710601-42077182 | 4
6p24.2 | 1.4636e-09 | 1.4636e-09 | chr6:11230043-11466767 | 1
1q21.3 | 2.1066e-22 | 9.7686e-09 | chr1:150516762-150919620 | 11
3p25.1 | 3.273e-09 | 3.0272e-08 | chr3:13714839-13726839 | 1
1q22 | 1.2569e-21 | 9.9439e-08 | chr1:155817553-156146725 | 15
19p13.2 | 1.6805e-12 | 9.9439e-08 | chr19:10841050-10927539 | 2
3q26.2 | 1.1195e-35 | 5.2966e-07 | chr3:169257885-169521059 | 5
12q13.2 | 1.8279e-09 | 6.1143e-07 | chr12:56481350-56491606 | 1
17q25.1 | 2.6859e-10 | 2.353e-06 | chr17:73568926-73774242 | 9
11q13.2 | 9.072e-06 | 9.072e-06 | chr11:67093861-67213517 | 10
4p16.3 | 1.8445e-05 | 1.8445e-05 | chr4:1629690-1881446 | 7
20q11.21 | 1.5813e-08 | 2.6493e-05 | chr20:30731473-30921695 | 6
5p15.33 | 0.0001119 | 0.0001119 | chr5:1-1425066 | 26
16p11.2 | 0.00051802 | 0.00051802 | chr16:30854953-30989870 | 9
1q42.3 | 2.5138e-07 | 0.00055826 | chr1:234313543-249250621 | 132
2p23.2 | 0.0006367 | 0.0006367 | chr2:28477194-28894453 | 4
19p13.11 | 9.9439e-08 | 0.0010908 | chr19:15293986-18125987 | 78
9p24.2 | 0.0017269 | 0.0017269 | chr9:3631009-3867341 | 1
18q11.2 | 0.0022979 | 0.0022979 | chr18:23844490-24110158 | 2
20q13.12 | 8.7741e-07 | 0.0043011 | chr20:45921681-46076395 | 2
Xp11.23 | 0.0093574 | 0.0093574 | chrX:46547716-47356397 | 14
6q25.1 | 0.012565 | 0.012565 | chr6:151944419-152042501 | 1
Xq28 | 0.015341 | 0.015341 | chrX:153029080-153392575 | 18
1p34.2 | 0.00095606 | 0.016264 | chr1:41317021-41507861 | 5
12p12.1 | 0.018689 | 0.020979 | chr12:24643054-25683946 | 9
17q11.2 | 8.4341e-06 | 0.050215 | chr17:26704253-27113673 | 25
1p35.2 | 0.002664 | 0.058684 | chr1:31354381-31376674 | 1
11p11.2 | 0.0618 | 0.0618 | chr11:46300642-46711489 | 12
14q24.3 | 0.0078772 | 0.069885 | chr14:77305985-77553968 | 2
22q12.2 | 0.071546 | 0.071546 | chr22:30270268-31676489 | 34
20q13.33 | 0.00016402 | 0.086538 | chr20:62147281-63025520 | 41
13q34 | 0.088568 | 0.088568 | chr13:109144777-114923884 | 39
18p11.31 | 0.088568 | 0.088568 | chr18:3171389-3753688 | 6
20p13 | 0.14096 | 0.14096 | chr20:2661659-4372445 | 38
12q13.11 | 0.00044047 | 0.1468 | chr12:48135609-48272274 | 4
3p14.1 | 0.011453 | 0.16405 | chr3:66724129-66740563 | 0 [LRIG1]
5q35.3 | 0.16405 | 0.16405 | chr5:176740997-176957671 | 13
7q22.1 | 0.18192 | 0.18192 | chr7:99526111-99827234 | 24
9q34.3 | 0.20233 | 0.20233 | chr9:139812578-139898208 | 8
14q32.33 | 0.076936 | 0.24258 | chr14:103958644-104127342 | 6

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
IKZF3
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

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

Table S3. 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 S4. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZNF503-AS1

Genes in Wide Peak

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

Table S5. 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 8p11.21.

Table S6. 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 6p24.2.

Table S7. 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 1q21.3.

Table S8. 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 3p25.1.

Table S9. 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 1q22.

Table S10. 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
SEMA4A
MEX3A
RXFP4
SCARNA4
SNORA42

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 3q26.2.

Table S12. 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 12q13.2.

Table S13. 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 17q25.1.

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

Genes
GALK1
H3F3B
ITGB4
LLGL2
RECQL5
SAP30BP
MYO15B
C17orf109
C17orf110

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
CORO1B
CARNS1
POLD4
TBC1D10C
LOC100130987

Genes in Wide Peak

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

Table S16. 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 20q11.21.

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

Genes
hsa-mir-1825
PLAGL2
KIF3B
TM9SF4
POFUT1
TSPY26P

Genes in Wide Peak

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

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

Genes
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4457
MIR4456
MIR4635

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 1q42.3.

Table S20. 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
ACTN2
ADSS
CHML
LYST
CHRM3
GNG4
HNRNPU
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
ZNF124
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZNF238
SDCCAG8
RBM34
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
PPPDE1
SCCPDH
ARID4B
KIF26B
HEATR1
ZNF692
ERO1LB
FMN2
ZNF695
ZP4
TFB2M
GREM2
SMYD3
ZNF669
ZNF672
SH3BP5L
OR2G3
OR2G2
OR2C3
EFCAB2
ZNF496
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
EDARADD
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR2W5
OR13G1
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LGALS8-AS1
MIR1537
LINC00184
MIR3123
MIR3124
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4677
MIR4671

Genes in Wide Peak

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

Table S21. 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 19p13.11.

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

Genes
JAK3
TPM4
BRD4
hsa-mir-1470
BST2
NR2F6
INSL3
KCNN1
CYP4F3
RAB8A
MYO9B
NOTCH3
RPL18A
SLC5A5
CYP4F2
AP1M1
F2RL3
MED26
AKAP8
B3GNT3
KLF2
CHERP
CYP4F8
UNC13A
FCHO1
SIN3B
PGLS
FAM32A
OR10H3
OR10H2
OR10H1
SNORA68
AKAP8L
ARRDC2
CPAMD8
BABAM1
MAP1S
USE1
ANO8
CYP4F11
EPS15L1
WIZ
RASAL3
MRPL34
CYP4F12
DDA1
TMEM38A
C19orf42
ABHD8
OCEL1
GLT25D1
EPHX3
SLC35E1
PLVAP
USHBP1
C19orf44
GTPBP3
HSH2D
HAUS8
FAM125A
PGLYRP2
CCDC124
NXNL1
CIB3
CALR3
CYP4F22
LOC126536
OR10H4
ANKLE1
FLJ25328
FAM129C
OR10H5
NWD1
SLC27A1
CYP4F24P
UCA1
TMEM221
MIR1470

Genes in Wide Peak

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

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

Genes
GLIS3

Genes in Wide Peak

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

Table S24. 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 20q13.12.

Table S25. 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 Xp11.23.

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

Genes
CDK16
RP2
UBA1
ZNF41
ZNF157
USP11
RBM10
INE1
RGN
PHF16
NDUFB11
SLC9A7
CXorf31
SNORA11C

Genes in Wide Peak

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

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

Genes
ESR1

Genes in Wide Peak

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

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

Genes
hsa-mir-718
ARHGAP4
AVPR2
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
PLXNB3
RENBP
SSR4
NAA10
TMEM187
SRPK3
PDZD4
MIR718
MIR3202-2
MIR3202-1

Genes in Wide Peak

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

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

Genes
CTPS
SCMH1
CITED4
SLFNL1
LOC100507178

Genes in Wide Peak

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

Table S30. 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 17q11.2.

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

Genes
ALDOC
RPL23A
SDF2
SUPT6H
FOXN1
SLC13A2
UNC119
TRAF4
KIAA0100
SPAG5
SARM1
SNORD4B
SNORD4A
SNORD42B
SNORD42A
C17orf63
RAB34
PIGS
SLC46A1
TLCD1
SGK494
PROCA1
NEK8
SPAG5-AS1
RAB34

Genes in Wide Peak

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

Table S32. 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 S33. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CREB3L1
hsa-mir-3160-2
ARHGAP1
CHRM4
MDK
DGKZ
ATG13
AMBRA1
HARBI1
MIR3160-2
MIR3160-1
MIR4688

Genes in Wide Peak

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

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

Genes
IRF2BPL
C14orf166B

Genes in Wide Peak

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

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

Genes
hsa-mir-3200
LIF
LIMK2
OSM
SMTN
TCN2
MTMR3
GAL3ST1
SF3A1
MORC2
PES1
SEC14L2
OSBP2
INPP5J
PLA2G3
MTFP1
TUG1
TBC1D10A
KIAA1656
RNF185
SELM
HORMAD2
DUSP18
MORC2-AS1
RNF215
SEC14L3
SEC14L4
SLC35E4
SDC4P
CCDC157
GATSL3
SEC14L6
MIR3200
MIR3928

Genes in Wide Peak

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

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

Genes
hsa-mir-647
NPBWR2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
PCMTD2
SLC2A4RG
ZNF512B
C20orf195
PPDPF
DNAJC5
ZGPAT
PRIC285
ZBTB46
SAMD10
ABHD16B
LINC00266-1
C20orf201
LINC00176
MIR647
UCKL1-AS1
MIR941-1
MIR941-4
MIR941-2
MIR941-3
MIR1914
LOC100505815
RTEL1-TNFRSF6B

Genes in Wide Peak

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

Table S37. 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 18p11.31.

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

Genes
TGIF1
MYOM1
DLGAP1
MYL12A
MYL12B
FLJ35776

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
VDR
RAPGEF3
HDAC7
SLC48A1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

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

Genes
DBN1
F12
GRK6
SLC34A1
PDLIM7
RGS14
LMAN2
DDX41
FAM193B
DOK3
PRR7
LOC340037
PFN3

Genes in Wide Peak

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

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

Genes
hsa-mir-106b
AZGP1
MCM7
TAF6
ZNF3
ZKSCAN1
ZSCAN21
AP4M1
STAG3
COPS6
C7orf43
PVRIG
GAL3ST4
GPC2
CNPY4
MBLAC1
GJC3
GATS
C7orf59
MIR106B
MIR25
MIR93
AZGP1P1
MIR4658

Genes in Wide Peak

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

Table S43. 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 14q32.33.

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

Genes
CKB
KLC1
MARK3
BAG5
APOPT1
TRMT61A

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 - 49 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 | 2.7415e-43 | 6.3694e-43 | chr19:3560635-4230222 | 25
5q11.2 | 1.1414e-27 | 1.1225e-27 | chr5:58260298-59787985 | 3
4q34.3 | 1.6769e-30 | 1.5543e-23 | chr4:178911874-183060693 | 1
10q23.31 | 3.1429e-20 | 3.1429e-20 | chr10:89617158-90034038 | 2
Xp21.2 | 2.9903e-17 | 2.9903e-17 | chrX:30870233-34644819 | 4
16q23.1 | 4.0545e-16 | 2.7212e-14 | chr16:78129058-79627770 | 1
2q22.1 | 3.2759e-15 | 9.1633e-14 | chr2:139655617-143637838 | 1
1p36.11 | 4.4631e-18 | 3.6156e-11 | chr1:26900639-27433459 | 11
8p23.2 | 1.0988e-09 | 1.0988e-09 | chr8:1-6262191 | 15
6q26 | 2.8062e-08 | 2.8265e-08 | chr6:161693099-163153207 | 1
3p14.2 | 4.5929e-08 | 4.5257e-08 | chr3:59034763-61547330 | 1
22q13.32 | 3.0197e-16 | 5.7532e-08 | chr22:48026910-51304566 | 46
17q11.2 | 2.4953e-09 | 1.9588e-06 | chr17:29326736-29722618 | 5
18q23 | 3.3698e-06 | 3.5563e-06 | chr18:62012003-78077248 | 46
12q23.1 | 3.8284e-07 | 1.3071e-05 | chr12:99124001-100107912 | 2
11p15.5 | 2.8167e-05 | 2.8285e-05 | chr11:1-3679657 | 114
7p22.3 | 6.1336e-05 | 6.1336e-05 | chr7:1-2556638 | 34
13q14.2 | 3.2561e-06 | 6.4121e-05 | chr13:48833767-49281290 | 3
15q15.1 | 7.3842e-07 | 0.0001029 | chr15:26093402-51004695 | 239
16p13.3 | 0.00050639 | 0.00051475 | chr16:3764793-4013466 | 1
19q13.43 | 0.00085572 | 0.00083518 | chr19:57359801-59128983 | 71
11q25 | 2.1459e-05 | 0.00088336 | chr11:119368304-135006516 | 128
20p12.1 | 0.0016328 | 0.0015912 | chr20:14302876-16252980 | 3
11q14.1 | 0.00076547 | 0.0023582 | chr11:82995735-85348794 | 2
1p36.21 | 6.5524e-11 | 0.0028398 | chr1:1-23637694 | 361
22q13.31 | 2.4745e-19 | 0.0030013 | chr22:47571204-48018269 | 1
17q21.2 | 5.3971e-06 | 0.0054414 | chr17:38323662-43511537 | 190
4p16.3 | 0.00016477 | 0.0070083 | chr4:1-1511830 | 31
4q22.1 | 6.4121e-05 | 0.0082882 | chr4:90844993-94753878 | 3
4p15.31 | 0.00058909 | 0.010503 | chr4:18017993-21845560 | 6
9p24.1 | 0.01923 | 0.01884 | chr9:7799607-12693402 | 1
12q24.33 | 0.00035945 | 0.0213 | chr12:121015462-133851895 | 126
7q31.1 | 0.00021349 | 0.021975 | chr7:109599468-111366370 | 2
2q37.3 | 0.00030004 | 0.031537 | chr2:223149669-243199373 | 191
16q21 | 0.00020537 | 0.043211 | chr16:31772318-69350160 | 224
17p12 | 0.00020497 | 0.053647 | chr17:9147260-18289032 | 97
9q34.11 | 0.061593 | 0.062353 | chr9:91929461-141213431 | 593
3q13.31 | 0.06594 | 0.066325 | chr3:116161663-118620828 | 1
14q13.1 | 0.065402 | 0.066325 | chr14:33301849-34394000 | 1
19p12 | 0.00089539 | 0.1107 | chr19:23939307-28240493 | 4
17p13.3 | 0.0012664 | 0.13673 | chr17:1-1201203 | 17
7q36.3 | 0.0013459 | 0.15268 | chr7:117882615-159138663 | 336
17p11.2 | 0.0011746 | 0.15676 | chr17:19651612-25270516 | 19
13q11 | 0.003515 | 0.17357 | chr13:1-24043829 | 30
2p25.3 | 0.20885 | 0.20885 | chr2:1-27588658 | 163
22q11.1 | 0.0018485 | 0.20885 | chr22:1-18249022 | 21
15q23 | 0.001195 | 0.23476 | chr15:26376327-92398023 | 660
1q43 | 0.25102 | 0.25282 | chr1:186954518-249250621 | 489
7q11.22 | 0.0066745 | 0.25282 | chr7:66780207-70601215 | 1
22q12.1 | 0.041014 | 0.29126 | chr22:29192671-29455701 | 1

Genes in Wide Peak

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

Table S45. 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
HMG20B
ZFR2
PIP5K1C
SNORD37
TJP3
ITGB1BP3
ZBTB7A
SIRT6
PIAS4
C19orf29
CREB3L3
RAX2
ATCAY
MRPL54
GIPC3
ANKRD24
C19orf29-AS1
MIR637

Genes in Wide Peak

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

Table S46. 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 S47. 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 S48. 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 Xp21.2.

Table S49. 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 S50. 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 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 1p36.11.

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

Genes
ARID1A
SFN
NR0B2
NUDC
GPN2
PIGV
GPATCH3
ZDHHC18
FAM46B
C1orf172
TRNP1

Genes in Wide Peak

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

Table S53. 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 6q26.

Table S54. 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 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 22q13.32.

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

Genes
hsa-mir-3201
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC284933
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR3201
MIR4535

Genes in Wide Peak

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

Table S57. 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 18q23.

Table S58. 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 12q23.1.

Table S59. 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 11p15.5.

Table S60. 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 7p22.3.

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

Genes
hsa-mir-339
GPER
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
EIF3B
ADAP1
SUN1
INTS1
SNX8
FTSJ2
GET4
CYP2W1
HEATR2
CHST12
FAM20C
MICALL2
PSMG3
C7orf50
ZFAND2A
COX19
KIAA1908
GPR146
TMEM184A
TFAMP1
UNCX
ELFN1
FLJ44511
LOC442497
MIR339
LOC100288524
MIR4655

Genes in Wide Peak

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

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

Genes
RB1
RCBTB2
LPAR6

Genes in Wide Peak

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

Table S63. 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
ACTC1
APBA2
B2M
CAPN3
CHRM5
CHRNA7
CKMT1B
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
OCA2
PLCB2
RAD51
RYR3
SCG5
SLC12A1
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
USP8
SLC28A2
COPS2
TGM5
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
FAM189A1
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
TRPM7
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
DTWD1
CASC5
AVEN
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
HMGN2P46
SLC24A5
LOC283710
FAM98B
PLA2G4D
GOLGA8G
FMN1
MRPL42P5
USP50
C15orf52
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
MIR211
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC646278
LOC653075
MIR626
MIR627
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100128714
LOC100129387
LOC100131089
ANKRD63
GOLGA8F
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4510
MIR4716
MIR4509-3
MIR4712
MIR4715
TMCO5B

Genes in Wide Peak

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

Table S64. 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 19q13.43.

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

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

Genes in Wide Peak

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

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

Genes
FLI1
ARHGEF12
hsa-mir-3167
hsa-mir-100
ACRV1
APLP2
CHEK1
ETS1
GRIK4
HSPA8
STT3A
KCNJ1
KCNJ5
VWA5A
NFRKB
NRGN
OPCML
PVRL1
SC5DL
ST3GAL4
SORL1
SRPR
ST14
TECTA
ZNF202
BARX2
EI24
FEZ1
ARHGAP32
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
FAM118B
C11orf61
CLMP
C11orf63
CCDC15
PUS3
JAM3
KIRREL3
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
PANX3
TMEM45B
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
LINC00167
HEPN1
LOC649133
LOC100128239
PATE3
MIR3167
LOC100507392
MIR4697
MIR4493

Genes in Wide Peak

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

Table S67. 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 11q14.1.

Table S68. 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 1p36.21.

Table S69. 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-3115
hsa-mir-4253
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
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
TNFRSF8
CDA
CDK11B
CDC42
CLCN6
CLCNKA
CLCNKB
CORT
DDOST
DFFA
DFFB
DVL1
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
MTOR
GABRD
GNB1
ZBTB48
HSPG2
HTR1D
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
LUZP1
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
KDM1A
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
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417

Genes in Wide Peak

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

Table S70. 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 17q21.2.

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

Genes
BRCA1
ETV4
RARA
hsa-mir-2117
ACLY
AOC2
ARL4D
ATP6V0A1
FMNL1
CDC6
CCR7
CNP
DHX8
DUSP3
EZH1
GAST
FZD2
G6PC
KAT2A
GFAP
CCR10
GRN
HCRT
HSD17B1
IFI35
IGFBP4
ITGA2B
JUP
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
NBR1
ADAM11
MEOX1
MPP2
MPP3
NAGLU
NMT1
PPY
PYY
RAB5C
RPL27
SLC4A1
SMARCE1
STAT3
STAT5A
STAT5B
MLX
TOP2A
DNAJC7
TUBG1
UBTF
RND2
CNTNAP1
AOC3
BECN1
KRT38
KRT37
KRT36
HAP1
MAP3K14
EFTUD2
HDAC5
GJC1
PSME3
EIF1
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
C1QL1
RUNDC3A
GPATCH8
KCNH4
FAM215A
KRT23
TUBG2
NKIRAS2
CCDC56
PSMC3IP
SOST
RAPGEFL1
SLC25A39
HIGD1B
KRT20
KLHL11
ATXN7L3
FKBP10
WNK4
C17orf53
TMUB2
DHX58
ACBD4
DCAKD
PLEKHH3
DBF4B
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
AOC4
G6PC3
ASB16
HSPB9
PLCD3
TMEM106A
NT5C3L
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
GJD3
KRT222
KRT40
CD300LG
KIF18B
RUNDC1
LOC147093
WIPF2
KRT25
TMEM99
NAGS
FAM134C
KRT28
KRT24
ARHGAP27
ZNF385C
C17orf105
FAM171A2
C17orf104
KRT42P
PTRF
KLHL10
C17orf65
KRT27
KRT26
LOC388387
CCDC103
KRT39
KRTAP4-11
KRTAP4-8
KRTAP2-2
KRTAP9-1
LOC730755
LOC100130581
KRTAP4-9
KRTAP4-7
LOC100133991
LOC100190938
MIR2117
KRTAP16-1
LOC100505782

Genes in Wide Peak

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

Table S72. 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 4q22.1.

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

Genes
ATOH1
GRID2
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

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

Genes
hsa-mir-218-1
SLIT2
KCNIP4
PACRGL
MIR218-1
SLIT2-IT1

Genes in Wide Peak

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

Table S75. 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 12q24.33.

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

Genes
BCL7A
hsa-mir-4304
ACADS
SCARB1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
P2RX4
P2RX7
POLE
PSMD9
PXMP2
RAN
CLIP1
SFSWAP
HNF1A
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
ULK1
DENR
OASL
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
MPHOSPH9
CAMKK2
ZNF268
TMED2
SNRNP35
FZD10
MLXIP
P2RX2
SETD1B
ANKLE2
ABCB9
RIMBP2
ATP6V0A2
HCAR1
GALNT9
ARL6IP4
POP5
ANAPC5
RHOF
SBNO1
ZCCHC8
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
C12orf43
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
RNF34
CCDC92
PUS1
CCDC62
KDM2B
UNC119B
ORAI1
C12orf65
TMEM132C
TMEM132B
LOC116437
TMEM132D
SLC15A4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
MORN3
HNF1A-AS1
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
MIR4700

Genes in Wide Peak

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

Table S77. 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 2q37.3.

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

Genes
ACSL3
PAX3
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
SNORD20
SAG
CCL20
SP100
SPP2
SCG2
CUL3
DGKD
PER2
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
HDAC4
FARP2
FARSB
ARL4C
RAMP1
NMUR1
STK25
COPS8
CAPN10
SP140
PASK
ATG4B
SH3BP4
KCNE4
NGEF
SNORD82
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
USP40
HJURP
HES6
DOCK10
C2orf83
MFF
CXCR7
RNPEPL1
WDFY1
NYAP2
GAL3ST2
RAB17
COPS7B
MRPL44
TRPM8
MLPH
IQCA1
FAM124B
TM4SF20
C2orf54
ARMC9
EFHD1
SPHKAP
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
MGC16025
DNER
B3GNT7
SP140L
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
CCDC140
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
C2orf72
CXXC11
DUSP28
ESPNL
ECEL1P2
LOC348761
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
MIR1471
MIR1244-1
BOK-AS1
MIR1244-3
MIR1244-2
MIR4269
UBE2F-SCLY
MIR4439
MIR4777
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

Table S79. 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 17p12.

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

Genes
MAP2K4
GAS7
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
COX10
DNAH9
DRG2
FLII
LLGL1
MEIS3P1
MYH1
MYH2
MYH3
MYH4
MYH8
PMP22
RCVRN
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
COPS3
MYH13
GLP2R
STX8
PIGL
NCOR1
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
TRIM16
RAI1
MPRIP
TNFRSF13B
SNORD49A
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
NT5M
C17orf48
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
LRRC48
MGC12916
ATPAF2
MYOCD
CDRT7
CDRT15P1
USP43
C17orf76-AS1
ZSWIM7
SMCR7
SMCR5
SMCR8
SMCR9
TOM1L2
CDRT15
WDR16
USP32P1
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
FLJ34690
CDRT4
TBC1D26
CDRT1
TMEM220
SHISA6
FAM211A
KRT16P2
PIRT
CDRT15P2
SNORD49B
SNORD65
MIR33B
MIR744
FAM106CP
LOC100289255
MIR1288
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

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

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

Genes
ABL1
FANCC
NOTCH1
OMD
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
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
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
ABCA1
ABCA2
ABO
AK1
ALAD
ALDOB
AMBP
ASS1
AUH
BAAT
C5
C8G
CACNA1B
CCBL1
TNFSF8
ENTPD2
CDK9
CEL
CELP
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL2
CYLC2
DBC1
DBH
SARDH
DNM1
ECM2
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSD17B3
HSPA5
TNC
IARS
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PHF2
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
UGCG
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
LHX2
MED27
PTGES
ATP6V1G1
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7B
ACTL7A
GADD45G
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
FAM120A
PMPCA
ASTN2
BICD2
FKBP15
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
RABGAP1
C9orf5
C9orf4
CIZ1
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
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
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
FAM22F
DIRAS2
ASPN
BSPRY
C9orf167
TEX10
LPPR1
EXD3
FAM206A
STX17
NOL8
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
C9orf86
CDK5RAP2
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
BDAG1
ZBTB26
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
PRDM12
CARD9
SUSD1
IPPK
DDX31
FAM129B
MRPL41
WNK2
SECISBP2
C9orf16
MAPKAP1
GALNT12
EHMT1
SVEP1
PTGES2
AKNA
MIR600HG
URM1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
GARNL3
HSDL2
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
C9orf30
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
LOC158257
FAM120AOS
LINC00475
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
C9orf96
OLFML2A
QSOX2
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CDC26
LOC253039
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
LINC00256A
FAM78A
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
LOC340508
LOC340515
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR32
C9orf106
LCN10
LOC441454
LOC441455
FAM22G
LOC441461
C9orf173
NRARP
C9orf129
PALM2-AKAP2
DNAJC25
DNAJC25-GNG10
MIR455
NRON
FAM163B
FLJ40292
TUBBP5
RNF224
C9orf29
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA84
SNORA70C
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
UNQ6494
LOC100129316
LOC100129722
LOC100130954
LOC100131193
LOC100132077
FAM157B
LOC100132781
RNU6ATAC
LINC00092
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3154
MIR2861
MIR4291
MIR4290
MIR3134
C9orf174
LOC100499484
MIR3621
MIR3910-1
MIR3689A
MIR3911
MIR3910-2
MIR3689B
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506599
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4670
MIR4672
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
LSAMP-AS3

Genes in Wide Peak

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

Table S83. 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 19p12.

Table S84. 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 17p13.3.

Table S85. 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 S86. 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 17p11.2.

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

Genes
KCNJ12
MAP2K3
TMEM11
ULK2
AKAP10
USP22
DHRS7B
SPECC1
CDRT15L2
C17orf103
FAM27L
FLJ36000
LGALS9B
CCDC144NL
C17orf51
CCDC144C
KRT16P3
KCNJ18
MTRNR2L1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q11.

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

Genes
FGF9
GJA3
GJB2
SGCG
TUBA3C
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
PSPC1
XPO4
MRP63
TPTE2
N6AMT2
SKA3
EFHA1
ZDHHC20
PHF2P1
ANKRD20A9P
LINC00442
BASP1P1
ANKRD26P3
LINC00421
MIR4499

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 22q11.1.

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

Genes
hsa-mir-3198
ATP6V1E1
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
HSFY1P1
CECR6
CECR5
CECR3
CECR2
CECR1
OR11H1
SLC25A18
GAB4
CCT8L2
XKR3
TPTEP1
CECR7
CECR5-AS1
MIR3198-1

Genes in Wide Peak

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

Table S91. 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
FLJ27352
C15orf55
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
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
ACTC1
ADAM10
ACAN
ANPEP
ANXA2
APBA2
AQP9
B2M
BBS4
BCL2A1
BNC1
BNIP2
CA12
CAPN3
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
IL16
IREB2
ISG20
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2A2
MAN2C1
MAP1A
MEIS2
MFAP1
MFGE8
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NEDD4
NEO1
NMB
OAZ2
OCA2
FURIN
PDE8A
PKM2
PLCB2
PLIN1
POLG
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RLBP1
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SH3GL3
SLC12A1
SNX1
SORD
SPINT1
SRP14
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
SLC30A4
AP3B2
ANP32A
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
PEX11A
IQGAP1
ALDH1A2
HERC2
HERC1
PSTPIP1
PRC1
USP8
CCNB2
SLC28A2
SLC28A1
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
HOMER2
PIGB
KIF23
IGDCC3
ZNF592
PPIP5K1
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
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
ACSBG1
KIAA1024
MGA
DMXL2
VPS39
FAM189A1
TMED3
AP4E1
SEC11A
CCNDBP1
DAPK2
EID1
GABARAPL3
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
VPS33B
GREM1
MRPL46
NPTN
FOXB1
RPUSD2
TUBGCP4
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
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
DNAJC17
FANCI
IMP3
LARP6
MNS1
DNAJA4
NOP10
GOLGA6B
MESP1
UNC45A
MYO5C
NDNL2
FAM214A
C15orf24
C15orf39
THAP10
PAK6
WDR93
PARP6
DTWD1
CASC5
AVEN
C15orf17
ADAMTSL3
KIAA1199
GJD2
STARD9
ALPK3
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
ZFP106
KLHL25
CPEB1
AEN
IQCH
ISL2
RFX7
MRPS11
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
AAGAB
LMAN1L
C15orf29
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
AGSK1
SPG11
ELL3
PLEKHO2
WDR61
CD276
STARD5
POLR2M
C15orf44
C15orf5
ADPGK
APH1B
FAM103A1
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
WDR73
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf42
C15orf57
C15orf23
BMF
SHF
DUOXA1
RCCD1
LOC91450
CALML4
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
DIS3L
TGM7
CATSPER2
LEO1
C15orf40
SENP8
MTFMT
OSTBETA
HIGD2B
C15orf27
AGBL1
AGPHD1
WHAMM
FSD2
PLA2G4E
TRIM69
C15orf43
LOC145663
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145837
LOC145845
C15orf61
HAPLN3
MESP2
TMCO5A
NRG4
LINC00052
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
RHOV
SCAMP5
C15orf33
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
SPESP1
LOC253044
LPCAT4
LOC254559
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
HMGN2P46
SLC24A5
PRTG
LOC283663
LINC00277
C15orf60
C15orf37
LOC283688
LOC283692
LOC283693
LOC283710
FAM154B
LOC283731
LOC283738
FAM98B
PLA2G4D
LOC283761
GOLGA8G
FBXL22
TMEM202
LOC338963
GLDN
GOLGA6A
TMC3
ZNF774
FMN1
RBPMS2
ANKDD1A
C15orf38
MRPL42P5
USP50
TEX9
GOLGA6L5
KIF7
ZNF710
HDDC3
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
LOC388152
UBE2Q2P1
KBTBD13
UBAP1L
SKOR1
ANKRD34C
C15orf58
LOC390660
SHC4
CTXN2
C15orf53
C15orf54
ST20
DUOXA2
MIR184
MIR190A
MIR211
MIR7-2
MIR9-3
C15orf50
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC645752
LOC646278
SH2D7
LOC646938
GOLGA6L10
LOC648809
LOC653075
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA15
SCARNA14
FBXO22-AS1
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
ANP32AP1
LOC727849
LOC727915
LOC728758
OIP5-AS1
LOC729739
LOC729911
MIR147B
DNM1P35
LOC100129387
LOC100130855
LOC100131089
ANKRD63
GOLGA8F
LOC100132724
UBE2Q2P3
UBE2Q2P2
JMJD7
PLA2G4B
LOC100287559
LOC100287616
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1276
MIR1233-1
MIR1272
MIR1266
MIR1179
MIR1282
LOC100306975
MIR548H4
MIR2116
MIR1233-2
MIR4311
MIR4312
MIR4310
MIR4313
MIR3942
RPS17L
LOC100505648
LOC100505679
LOC100506686
LOC100506874
LOC100507466
C15orf38-AP3S2
ST20-MTHFS
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4514
MIR4513
MIR4509-1
MIR4509-2
MIR3529
MIR4510
MIR4716
MIR4713
MIR4511
MIR4509-3
MIR4712
MIR4515
TMCO5B
MYZAP

Genes in Wide Peak

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

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

Genes
ELK4
FH
MDM4
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ARF1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PIK3C2B
PKP1
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS1
RGS2
RGS7
RGS13
RNPEP
RYR2
SNRPE
SRP9
TROVE2
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
B3GALT2
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GPR37L1
GGPS1
SOX13
IKBKE
TMEM63A
TOMM20
URB2
CEP170
ZC3H11A
TMCC2
LPGAT1
KIF14
AKT3
BPNT1
TIMM17A
LRRN2
ZNF238
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NFASC
FBXO28
CAMSAP2
SRGAP2
CRB1
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
GLRX2
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
UCHL5
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
LAX1
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
KLHL12
LGR6
TFB2M
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
NUAK2
DDX59
RASSF5
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
WNT3A
NAV1
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
ASPM
PGBD2
OR2L13
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
HNRNPU-AS1
LIN9
VN1R5
FAM5C
ZNF678
PRSS38
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
IRF2BP2
ZBTB41
MIA3
C1orf95
FAM89A
RPS10P7
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR181B1
MIR194-1
MIR205
MIR181A1
MIR215
MIR29B2
MIR29C
RGS21
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SNORA14B
SNORA36B
SNORA77
SNORA16B
LOC728463
FAM72A
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR1231
MIR1278
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
KDM5B-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4735
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.22.

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

Genes
AUTS2

Genes in Wide Peak

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

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

Genes
ZNRF3

Arm-level results

Table 3. Get Full Table Arm-level significance table - 30 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.07 | -1.16 | 1 | 0.05 | -2.86 | 1
1q | 1955 | 0.33 | 18.2 | 0 | 0.05 | -2.28 | 1
2p | 924 | 0.17 | 4.41 | 2.55e-05 | 0.03 | -5.42 | 1
2q | 1556 | 0.14 | 3.43 | 0.00133 | 0.03 | -4.63 | 1
3p | 1062 | 0.09 | -1.42 | 1 | 0.10 | -0.465 | 1
3q | 1139 | 0.15 | 2.73 | 0.0127 | 0.08 | -1.94 | 1
4p | 489 | 0.03 | -5.83 | 1 | 0.20 | 5.41 | 1.54e-07
4q | 1049 | 0.02 | -5.83 | 1 | 0.20 | 6.18 | 2.19e-09
5p | 270 | 0.10 | -1.88 | 1 | 0.12 | -0.361 | 1
5q | 1427 | 0.04 | -4.44 | 1 | 0.14 | 3.22 | 0.00183
6p | 1173 | 0.14 | 2.19 | 0.0517 | 0.04 | -4.44 | 1
6q | 839 | 0.11 | -0.159 | 1 | 0.05 | -4.03 | 1
7p | 641 | 0.12 | 0.473 | 0.848 | 0.10 | -1.23 | 1
7q | 1277 | 0.12 | 1.41 | 0.242 | 0.09 | -0.815 | 1
8p | 580 | 0.23 | 7.19 | 2.23e-12 | 0.20 | 5.27 | 2.75e-07
8q | 859 | 0.30 | 12.6 | 0 | 0.07 | -2.83 | 1
9p | 422 | 0.03 | -5.54 | 1 | 0.21 | 5.75 | 2.53e-08
9q | 1113 | 0.01 | -5.92 | 1 | 0.23 | 8.9 | 0
10p | 409 | 0.24 | 7.42 | 4.57e-13 | 0.11 | -0.964 | 1
10q | 1268 | 0.22 | 8.13 | 2.22e-15 | 0.10 | -0.447 | 1
11p | 862 | 0.05 | -4.28 | 1 | 0.14 | 2.01 | 0.0556
11q | 1515 | 0.04 | -4.24 | 1 | 0.13 | 2.64 | 0.0111
12p | 575 | 0.13 | 0.741 | 0.655 | 0.09 | -1.86 | 1
12q | 1447 | 0.09 | -0.616 | 1 | 0.07 | -2.04 | 1
13q | 654 | 0.06 | -3.57 | 1 | 0.17 | 3.63 | 0.000434
14q | 1341 | 0.07 | -2 | 1 | 0.12 | 1.23 | 0.231
15q | 1355 | 0.02 | -5.19 | 1 | 0.20 | 7.33 | 1.11e-12
16p | 872 | 0.05 | -3.87 | 1 | 0.18 | 4.82 | 2.67e-06
16q | 702 | 0.02 | -5.48 | 1 | 0.26 | 9.78 | 0
17p | 683 | 0.03 | -5.45 | 1 | 0.24 | 8.34 | 0
17q | 1592 | 0.06 | -2.49 | 1 | 0.17 | 5.29 | 2.66e-07
18p | 143 | 0.11 | -1.18 | 1 | 0.14 | 0.688 | 0.468
18q | 446 | 0.07 | -3.21 | 1 | 0.15 | 1.67 | 0.112
19p | 995 | 0.10 | -0.778 | 1 | 0.12 | 0.71 | 0.468
19q | 1709 | 0.10 | 0.223 | 1 | 0.11 | 1.25 | 0.231
20p | 355 | 0.20 | 5.27 | 3.8e-07 | 0.05 | -4.28 | 1
20q | 753 | 0.24 | 8.38 | 0 | 0.03 | -5.24 | 1
21q | 509 | 0.07 | -2.98 | 1 | 0.10 | -1.04 | 1
22q | 921 | 0.07 | -2.5 | 1 | 0.22 | 7.27 | 1.39e-12
Xq | 1312 | 0.13 | 1.89 | 0.0969 | 0.16 | 4.26 | 3.42e-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/1971823/2.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 492 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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