PANCANCER: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.15 (cga svn revision 34144).

Summary

There were 4422 tumor samples used in this analysis: 30 significant arm-level results, 49 significant focal amplifications, and 62 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 - 49 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
--- | --- | --- | --- | ---
7p11.2 | 0 | 0 | chr7:55044034-55061448 | 1
11q13.2 | 4.7373e-198 | 8.4697e-173 | chr11:69157757-69213110 | 2
17q12 | 5.6722e-183 | 2.1898e-153 | chr17:35058337-35130413 | 5
8q24.21 | 5.0455e-153 | 5.0455e-153 | chr8:128787708-128803425 | 0 [MYC]
19q12 | 4.5299e-110 | 1.053e-90 | chr19:34950535-35013029 | 1
8p12 | 9.883e-118 | 3.2898e-88 | chr8:38326281-38349015 | 1
12q15 | 3.2776e-101 | 2.9045e-77 | chr12:67501958-67547022 | 2
4q12 | 2.7455e-49 | 4.4366e-47 | chr4:54727006-54861623 | 1
3q26.2 | 5.7133e-80 | 3.1122e-46 | chr3:170889724-170984669 | 3
12q14.1 | 1.2183e-76 | 5.8059e-41 | chr12:56450638-56502103 | 5
1q21.2 | 1.9559e-45 | 1.0393e-36 | chr1:148763481-148945656 | 5
20q13.2 | 5.915e-38 | 2.0916e-36 | chr20:51589756-51792983 | 1
1q32.1 | 4.0062e-44 | 1.6199e-34 | chr1:202660206-202806407 | 2
11q14.1 | 2.7475e-75 | 1.7656e-24 | chr11:77278969-77613835 | 8
12p12.1 | 1.666e-30 | 3.819e-23 | chr12:25221719-25405863 | 3
8p11.21 | 2.976e-52 | 1.2887e-22 | chr8:41964992-42017016 | 1
15q26.3 | 2.0446e-21 | 2.0446e-21 | chr15:96894457-97423501 | 2
1p34.2 | 6.687e-20 | 6.687e-20 | chr1:39807770-40319211 | 12
17q23.1 | 5.3061e-40 | 7.2878e-19 | chr17:55274499-55313396 | 1
3q26.33 | 3.6463e-72 | 1.7994e-18 | chr3:182584087-183291746 | 2
19p13.12 | 1.3945e-16 | 1.3945e-16 | chr19:15163321-15283141 | 3
12p13.32 | 4.3981e-18 | 4.4472e-14 | chr12:3839133-4307093 | 3
6q21 | 2.1105e-12 | 1.1703e-11 | chr6:107303733-107666415 | 5
5p15.33 | 8.9805e-11 | 8.9805e-11 | chr5:1276063-1341614 | 3
20q11.21 | 4.2182e-14 | 2.3948e-10 | chr20:29648473-29790040 | 3
19q13.2 | 2.6064e-32 | 1.988e-09 | chr19:44055704-45818266 | 57
2q21.2 | 2.7545e-09 | 1.6993e-08 | chr2:131967437-132833729 | 6
6p21.1 | 2.5734e-09 | 1.9675e-08 | chr6:43622700-44104333 | 9
7q21.2 | 5.6942e-09 | 4.22e-08 | chr7:91993046-92368284 | 5
18q11.2 | 4.7248e-08 | 4.7248e-08 | chr18:22107731-22424402 | 2
10q22.3 | 2.6106e-07 | 4.129e-06 | chr10:79208741-81674323 | 14
6p22.3 | 6.6236e-05 | 0.0003581 | chr6:18347516-22153022 | 10
4q13.3 | 7.5265e-07 | 0.00051409 | chr4:74125200-74480238 | 2
14q13.2 | 5.7228e-07 | 0.00052659 | chr14:34805650-35199811 | 5
1q44 | 6.4061e-11 | 0.00081181 | chr1:241055781-242811190 | 8
13q34 | 0.00014378 | 0.00094796 | chr13:108563148-110078078 | 6
14q11.2 | 4.5677e-06 | 0.001973 | chr14:20410492-20676586 | 12
11p13 | 0.0045761 | 0.0045761 | chr11:34333459-35362598 | 8
22q11.21 | 0.0082159 | 0.0082159 | chr22:18478545-20258915 | 36
13q12.2 | 0.0022099 | 0.010419 | chr13:27090985-27484219 | 8
2q31.2 | 0.0042046 | 0.01074 | chr2:176958202-178867670 | 10
4p16.3 | 0.015145 | 0.015145 | chr4:1401560-1962244 | 11
10q26.13 | 0.00015323 | 0.019797 | chr10:123230278-123357148 | 1
5q35.3 | 0.021375 | 0.021375 | chr5:176266376-176799881 | 13
9p13.3 | 0.022835 | 0.022835 | chr9:35231249-36050450 | 28
7q34 | 0.0063402 | 0.034983 | chr7:141944541-142213402 | 3
21q21.1 | 0.045803 | 0.045803 | chr21:15144633-17005225 | 7
2p15 | 0.10448 | 0.10448 | chr2:59969321-62989730 | 17
6q12 | 0.011181 | 0.12229 | chr6:64263615-64390811 | 1

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

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

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

Genes
CCND1
ORAOV1

Genes in Wide Peak

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

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

Genes
ERBB2
PNMT
TCAP
STARD3
PGAP3

Genes in Wide Peak

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

Table S4. 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 8p12.

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

Genes
WHSC1L1

Genes in Wide Peak

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

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

Genes
MDM2
CPM

Genes in Wide Peak

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

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

Genes
PDGFRA

Genes in Wide Peak

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

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

Genes
TERC
MYNN
ARPM1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
METTL1
TSFM
CTDSP2
AVIL
FAM119B

Genes in Wide Peak

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

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

Genes
ENSA
MCL1
ADAMTSL4
GOLPH3L
HORMAD1

Genes in Wide Peak

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

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

Genes
ZNF217

Genes in Wide Peak

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

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

Genes
MDM4
PIK3C2B

Genes in Wide Peak

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

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

Genes
NDUFC2
THRSP
GAB2
USP35
KCTD14
ALG8
INTS4
KCTD21

Genes in Wide Peak

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

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

Genes
KRAS
CASC1
LYRM5

Genes in Wide Peak

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

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

Genes
MYST3

Genes in Wide Peak

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

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

Genes
IGF1R
LOC145814

Genes in Wide Peak

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

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

Genes
MYCL1
BMP8B
PPT1
PABPC4
PPIE
CAP1
HEYL
HPCAL4
TRIT1
OXCT2
NT5C1A
MFSD2A

Genes in Wide Peak

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

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

Genes
TUBD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
SOX2
SOX2OT

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
BRD4
NOTCH3
EPHX3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
CCND2
PARP11
C12orf5

Genes in Wide Peak

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

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

Genes
hsa-mir-587
C6orf203
PDSS2
BEND3
LOC553137

Genes in Wide Peak

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

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

Genes
TERT
SLC6A19
SLC6A18

Genes in Wide Peak

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

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

Genes
BCL2L1
ID1
COX4I2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
AKT2
hsa-mir-641
BLVRB
CLC
FBL
MAP3K10
NFKBIB
PSMC4
MRPS12
RPS16
SUPT5H
ZFP36
LTBP4
FCGBP
DYRK1B
GMFG
PAK4
DLL3
SIRT2
PLD3
LGALS13
SERTAD3
SERTAD1
PAF1
SARS2
SAMD4B
MED29
LGALS14
LRFN1
PRX
SPTBN4
PLEKHG2
CNTD2
TIMM50
SHKBP1
FBXO17
EID2B
RINL
FBXO27
C19orf47
HIPK4
TTC9B
EID2
ZNF780B
IL28A
IL28B
IL29
ZNF780A
ZNF546
NCCRP1
SYCN
LEUTX
SELV
PAPL
LOC400696
MIR641
LOC100129935

Genes in Wide Peak

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

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

Genes
hsa-mir-663b
C2orf27A
CCDC74A
LOC150776
C2orf27B
NCRNA00164

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
POLH
VEGFA
MAD2L1BP
GTPBP2
MRPS18A
XPO5
C6orf223
RSPH9
LOC100132354

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
PEX1
C7orf64
MGC16142
FAM133B

Genes in Wide Peak

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

Table S29. 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 10q22.3.

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

Genes
RPS24
MBL1P1
DLG5
PPIF
POLR3A
ZMIZ1
EIF5AL1
ZCCHC24
LOC283050
LOC642361
LOC650623
SFTPA1
SFTPA2
LOC100128292

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

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

Genes
DEK
hsa-mir-548a-1
E2F3
ID4
SOX4
CDKAL1
MBOAT1
RNF144B
FLJ22536
MIR548A1

Genes in Wide Peak

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

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

Genes
ANKRD17
COX18

Genes in Wide Peak

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

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

Genes
NFKBIA
PSMA6
KIAA0391
INSM2
RALGAPA1

Genes in Wide Peak

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

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

Genes
ADSS
CEP170
AKT3
ZNF238
SDCCAG8
C1orf100
C1orf101
LOC731275

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
COL4A1
COL4A2
IRS2
MYO16
RAB20
CARKD

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q11.2.

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

Genes
RNASE2
RNASE3
SLC39A2
ZNF219
FLJ10357
NDRG2
METT11D1
RNASE7
TPPP2
RNASE8
RNASE13
C14orf176

Genes in Wide Peak

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

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

Genes
CAT
CD44
ELF5
SLC1A2
PDHX
ABTB2
EHF
APIP

Genes in Wide Peak

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

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

Genes
hsa-mir-649
hsa-mir-1286
CRKL
SERPIND1
PI4KA
RANBP1
SLC7A4
UBE2L3
ZNF74
LZTR1
P2RX6
SNAP29
HIC2
TRMT2A
POM121L8P
ZDHHC8
MED15
DGCR8
RTN4R
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
MGC16703
LOC150197
AIFM3
RIMBP3C
POM121L4P
PI4KAP2
LOC400891
FLJ39582
P2RX6P
RIMBP3B
PI4KAP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.2.

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

Genes
CDX2
FLT3
PDX1
POLR1D
GSX1
LNX2
ATP5EP2
PRHOXNB

Genes in Wide Peak

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

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

Genes
NFE2L2
hsa-mir-1246
AGPS
PDE11A
TTC30A
OSBPL6
RBM45
TTC30B
HNRNPA3
LOC100130691

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
hsa-mir-943
LETM1
WHSC2
SLBP
TACC3
TMEM129
FAM53A
SCARNA22
MIR943

Genes in Wide Peak

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

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

Genes
FGFR2

Genes in Wide Peak

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

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

Genes
NSD1
F12
FGFR4
GRK6
SLC34A1
RGS14
LMAN2
ZNF346
PRELID1
UIMC1
RAB24
MXD3
PFN3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
CA9
CD72
NPR2
RMRP
TESK1
TLN1
TPM2
RECK
RGP1
RUSC2
CREB3
UNC13B
SPAG8
SIT1
TMEM8B
OR2S2
GBA2
HINT2
C9orf100
LOC92973
LOC158376
LOC158381
CCDC107
C9orf128
OR13J1
HRCT1
MSMP
FAM166B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q34.

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

Genes
PRSS1
PRSS2
TRY6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q21.1.

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

Genes
hsa-mir-125b-2
NRIP1
USP25
C21orf34
MIRLET7C
MIR125B2
MIR99A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p15.

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

Genes
REL
BCL11A
PEX13
XPO1
USP34
CCT4
B3GNT2
EHBP1
PAPOLG
FAM161A
KIAA1841
AHSA2
COMMD1
PUS10
TMEM17
C2orf74
SNORA70B

Genes in Wide Peak

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

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

Genes
PTP4A1

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 0 | 0 | chr9:21545227-23680570 | 6
3p14.2 | 1.4675e-201 | 1.3875e-191 | chr3:59009803-61522370 | 1
19p13.3 | 1.9874e-148 | 1.9874e-148 | chr19:1-3178101 | 114
6q26 | 4.4845e-143 | 5.8389e-137 | chr6:161613089-163073197 | 1
10q23.31 | 3.6819e-138 | 9.4819e-129 | chr10:89607138-90024018 | 2
5q11.2 | 1.6352e-113 | 7.9375e-106 | chr5:58296055-59823742 | 3
20p12.1 | 1.9199e-83 | 1.9199e-83 | chr20:14250876-15984135 | 2
13q14.2 | 1.5871e-93 | 5.6441e-81 | chr13:47731768-47962808 | 2
8p23.2 | 1.9982e-82 | 1.4377e-74 | chr8:2080589-6255647 | 1
16p13.3 | 2.6065e-66 | 2.6065e-66 | chr16:5085718-7704198 | 1
22q13.31 | 2.0373e-64 | 1.9557e-64 | chr22:44619793-49691432 | 62
16q23.1 | 4.7488e-71 | 2.1117e-60 | chr16:76686559-78185271 | 1
1p36.31 | 2.2114e-132 | 8.5771e-60 | chr1:4741841-6621560 | 19
4q35.2 | 8.4559e-72 | 2.5868e-58 | chr4:187416481-191273063 | 15
4q22.1 | 6.7696e-61 | 1.0799e-51 | chr4:91092757-93459528 | 2
2q37.3 | 3.6677e-69 | 1.2447e-51 | chr2:240612612-242951149 | 39
2q22.1 | 1.3128e-56 | 5.1535e-47 | chr2:139248662-143354308 | 1
1p36.11 | 5.6009e-112 | 4.19e-46 | chr1:26773226-27028008 | 2
11p15.5 | 5.8208e-46 | 5.8208e-46 | chr11:303924-699860 | 22
15q15.1 | 1.3483e-46 | 1.5268e-29 | chr15:39620202-40067954 | 10
17q11.2 | 4.5763e-25 | 6.4875e-25 | chr17:26350862-26746744 | 4
18q23 | 6.3111e-22 | 6.3892e-22 | chr18:75847612-76117153 | 4
6p25.3 | 1.3158e-17 | 1.276e-17 | chr6:1553836-2569051 | 2
7p22.3 | 3.0596e-16 | 3.0031e-16 | chr7:1-2370980 | 28
11q25 | 7.688e-25 | 1.5244e-13 | chr11:133637835-134452384 | 3
14q23.3 | 9.4327e-15 | 1.6066e-10 | chr14:66032906-66727865 | 1
7q31.1 | 5.6741e-12 | 4.0103e-10 | chr7:109386704-111163100 | 2
17p12 | 1.1122e-14 | 8.1069e-09 | chr17:15405082-15555845 | 2
8p21.2 | 2.0267e-19 | 1.5292e-08 | chr8:25952364-26418943 | 2
9q34.3 | 4.4863e-08 | 1.6459e-07 | chr9:135882980-137515965 | 8
9p24.1 | 7.6044e-29 | 8.6713e-07 | chr9:7786330-12683402 | 2
16q24.3 | 7.9361e-25 | 9.1416e-07 | chr16:87821235-88104546 | 1
5q21.3 | 2.9594e-17 | 2.5119e-06 | chr5:96541228-110437864 | 23
3p21.31 | 7.22e-28 | 2.7496e-06 | chr3:46424169-46515615 | 1
17p12 | 5.1458e-11 | 7.0842e-06 | chr17:11837355-12512565 | 3
13q12.11 | 2.4089e-18 | 8.5284e-06 | chr13:18336832-18646348 | 2
10q26.3 | 2.8588e-12 | 9.3401e-06 | chr10:133644852-135374737 | 35
12q23.1 | 2.8468e-09 | 1.1521e-05 | chr12:97648132-98955403 | 2
12q24.33 | 6.75e-10 | 7.6795e-05 | chr12:128949565-132349534 | 33
11q22.3 | 3.9924e-11 | 0.0003181 | chr11:103538114-116807149 | 94
14q13.1 | 2.3406e-05 | 0.00042106 | chr14:32371600-33463751 | 1
15q11.2 | 1.2942e-25 | 0.00059554 | chr15:1-25674918 | 121
2p25.3 | 0.00076929 | 0.00076498 | chr2:1-1775996 | 9
19q13.43 | 1.6214e-08 | 0.00076498 | chr19:63068201-63811651 | 32
9p13.1 | 1.1044e-10 | 0.00083688 | chr9:38609152-70342057 | 46
10q11.23 | 1.3664e-06 | 0.0019073 | chr10:52314091-53747935 | 5
1q44 | 0.0028076 | 0.0027941 | chr1:243931413-244771113 | 1
10p15.3 | 0.0031534 | 0.0031284 | chr10:1766485-3169967 | 1
6q21 | 7.4211e-09 | 0.0037227 | chr6:83826859-116893709 | 137
7q36.1 | 0.00024405 | 0.012476 | chr7:151448348-151767007 | 1
12p13.1 | 0.013703 | 0.013724 | chr12:12378793-13605829 | 21
21q11.2 | 1.4756e-12 | 0.013724 | chr21:1-16028074 | 16
21q22.3 | 0.00018777 | 0.013933 | chr21:41749349-41973771 | 1
1p13.2 | 1.5959e-05 | 0.015736 | chr1:79233223-119715206 | 256
3q26.31 | 0.0084121 | 0.015933 | chr3:175482500-178221491 | 1
19q13.32 | 1.8049e-06 | 0.020781 | chr19:51538519-52909734 | 31
3q13.31 | 0.028027 | 0.055721 | chr3:117644353-120103518 | 1
3p26.3 | 1.3185e-06 | 0.11101 | chr3:1-4999770 | 11
21q21.1 | 3.9176e-06 | 0.13657 | chr21:16901626-25682320 | 8
17p13.3 | 0.00068927 | 0.16415 | chr17:1-261062 | 1
14q32.32 | 8.1189e-06 | 0.16507 | chr14:90951922-106368585 | 243
1p33 | 2.5344e-06 | 0.24756 | chr1:48707867-50287554 | 2

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
MTAP
C9orf53
DMRTA1
CDKN2BAS

Genes in Wide Peak

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

Table S50. 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 19p13.3.

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

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

Genes in Wide Peak

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

Table S52. 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 10q23.31.

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

Genes
PTEN
KILLIN

Genes in Wide Peak

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

Table S54. 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 20p12.1.

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

Genes
FLRT3
MACROD2

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
A2BP1

Genes in Wide Peak

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

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

Genes
hsa-let-7b
ACR
ARSA
CHKB
CPT1B
TYMP
PPARA
MAPK11
MAPK12
SBF1
WNT7B
CELSR1
SAPS2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
FAM19A5
NCAPH2
GTSE1
MOV10L1
TTC38
C22orf26
MIOX
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC150381
C22orf40
CN5H6.4
TTLL8
RPL23AP82
C22orf34
CHKB-CPT1B
LOC400931
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
C22orf41
LOC730668
LOC100144603
LOC100271722

Genes in Wide Peak

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

Table S60. 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 1p36.31.

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

Genes
RPL22
ZBTB48
KCNAB2
TNFRSF25
KLHL21
ACOT7
ICMT
CHD5
HES2
PLEKHG5
NOL9
TAS1R1
ESPN
THAP3
PHF13
NPHP4
GPR153
RNF207
HES3

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
TMSL3
FAM190A

Genes in Wide Peak

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

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

Genes
hsa-mir-149
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
SEPT2
PDCD1
PPP1R7
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
RNPEPL1
GAL3ST2
C2orf54
ING5
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
C2orf85
DUSP28
AQP12A
OR6B2
MIR149
PRR21
AQP12B
D2HGDH
LOC728323
PP14571

Genes in Wide Peak

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

Table S65. 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 S66. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ARID1A
PIGV

Genes in Wide Peak

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

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

Genes
HRAS
hsa-mir-210
DRD4
IRF7
RNH1
SCT
RASSF7
IFITM1
IFITM3
DEAF1
PKP3
MUPCDH
PHRF1
SIGIRR
PTDSS2
LRRC56
LOC143666
C11orf35
TMEM80
ANO9
B4GALNT4
MIR210

Genes in Wide Peak

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

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

Genes
hsa-mir-626
TYRO3
JMJD7-PLA2G4B
MAPKBP1
MGA
EHD4
SPTBN5
MIR626
JMJD7
PLA2G4B

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG

Genes in Wide Peak

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

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

Genes
ADNP2
C18orf22
PARD6G
LOC100130522

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
B3GAT1
GLB1L2
GLB1L3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
GPHN

Genes in Wide Peak

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

Table S75. 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 17p12.

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

Genes
TRIM16
CDRT1

Genes in Wide Peak

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

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

Genes
BNIP3L
PPP2R2A

Genes in Wide Peak

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

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

Genes
BRD3
COL5A1
FCN1
FCN2
RXRA
OLFM1
WDR5
RNU6ATAC

Genes in Wide Peak

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

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

Genes
PTPRD
C9orf123

Genes in Wide Peak

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

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

Genes
ANKRD11

Genes in Wide Peak

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

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

Genes
hsa-mir-548f-3
hsa-mir-548p
CHD1
EFNA5
FER
MAN2A1
PAM
ST8SIA4
RAB9P1
PJA2
HISPPD1
GIN1
FBXL17
NUDT12
C5orf30
SLC25A46
SLCO6A1
RGMB
FAM174A
SLCO4C1
TMEM232
MIR548C
LOC100133050

Genes in Wide Peak

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

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

Genes
LTF

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
MIR744

Genes in Wide Peak

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

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

Genes
DKFZp686A1627
LOC348021

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-202
ADAM8
CYP2E1
ECHS1
INPP5A
UTF1
DPYSL4
TUBGCP2
VENTX
CALY
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
C10orf91
PWWP2B
PAOX
C10orf93
C10orf125
JAKMIP3
STK32C
FRG2B
SPRN
MIR202
LOC619207
LOC653543
LOC653544
LOC653545
LOC653548
LOC728410

Genes in Wide Peak

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

Table S86. 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 12q24.33.

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

Genes
STX2
GOLGA3
MMP17
POLE
PXMP2
RAN
SFRS8
ZNF10
ZNF26
ZNF84
ZNF140
ULK1
PIWIL1
ZNF268
FZD10
P2RX2
ANKLE2
RIMBP2
GALNT9
CHFR
EP400
FBRSL1
NOC4L
PUS1
LOC116437
PGAM5
GPR133
DDX51
EP400NL
SNORA49
LOC100130238
LOC100190940
ZNF605

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

Genes
ATM
DDX10
PAFAH1B2
POU2AF1
SDHD
PCSK7
hsa-mir-34c
ACAT1
APOA1
APOA4
APOC3
CASP1
CASP4
CASP5
CRYAB
DLAT
DRD2
FDX1
GRIA4
GUCY1A2
HSPB2
HTR3A
IL18
NCAM1
NNMT
NPAT
PPP2R1B
PTS
RDX
SLN
TAGLN
ZBTB16
CUL5
ZNF259
HTR3B
ZW10
RBM7
CEP164
EXPH5
SIK2
SIK3
BACE1
CADM1
REXO2
TIMM8B
SIDT2
C11orf71
SLC35F2
RAB39
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
TEX12
ARHGAP20
USP28
CARD18
AASDHPPT
C11orf1
ALG9
TMPRSS5
BCO2
KIAA1826
BUD13
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
APOA5
CASP12
C11orf93
PIH1D2
FAM55A
FAM55B
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
ANKK1
RNF214
C11orf53
C11orf34
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CARD17
LOC643923
CLDN25

Genes in Wide Peak

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

Table S89. 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 15q11.2.

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

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

Genes in Wide Peak

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

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

Genes
ACP1
TPO
PXDN
SH3YL1
SNTG2
TMEM18
FAM150B
C2orf90
FAM110C

Genes in Wide Peak

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

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

Genes
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF256
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
ZSCAN18
MGC2752
ZNF329
ZNF606
ZBTB45
ZNF837
C19orf18
ZNF418
ZNF417
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
NCRNA00181
ZNF814
LOC100131691

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p13.1.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.23.

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

Genes
hsa-mir-605
PRKG1
DKK1
CSTF2T
MIR605

Genes in Wide Peak

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

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

Genes
SMYD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

Table S96. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PFKP

Genes in Wide Peak

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

Table S97. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
CCNC
CGA
CNR1
COL10A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1E
LAMA4
MARCKS
ME1
NT5E
PGM3
POU3F2
PREP
REV3L
SIM1
SMPD2
MAP3K7
NR2E1
TSPYL1
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDC2L6
MDN1
TSPYL4
KIAA0776
ORC3L
SFRS18
FBXL4
SNORD50A
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
UBE2J1
COQ3
SOBP
AKIRIN2
QRSL1
NCRNA00120
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
BEND3
RRAGD
PRDM13
BACH2
C6orf164
POPDC3
MICAL1
MANEA
GPR63
SPACA1
ARMC2
RPF2
MCHR2
C6orf168
GJA10
RTN4IP1
USP45
SLC22A16
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
SLC16A10
RIPPLY2
PM20D2
SFRS13B
C6orf165
PRSS35
C6orf163
C6orf185
AKD1
NT5DC1
HS3ST5
LACE1
C6orf167
SCML4
C6orf182
PPIL6
FLJ34503
GJB7
SNHG5
LIN28B
FAM26F
LOC442245
RFPL4B
LOC553137
C6orf225
TSG1
SNORD50B
LOC728402
C6orf186

Genes in Wide Peak

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

Table S98. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MLL3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

Table S99. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-614
hsa-mir-613
CDKN1B
CREBL2
EMP1
GPR19
GPRC5A
HEBP1
DDX47
GPRC5D
KIAA1467
DUSP16
APOLD1
GSG1
HTR7P
LOH12CR1
C12orf36
RPL13AP20
LOH12CR2
MIR613
MIR614

Genes in Wide Peak

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

Table S100. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BAGE
HSPA13
TPTE
NRIP1
RBM11
C21orf15
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
C21orf99
LIPI
ABCC13
POTED
C21orf81

Genes in Wide Peak

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

Table S101. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TMPRSS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

Table S102. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
PTPN22
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
C1orf103
CTTNBP2NL
C1orf183
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
SPATA1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
C1orf203
FAM40A
C1orf59
GBP4
GBP5
SSX2IP
OLFM3
WDR63
C1orf161
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
LOC149620
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AFARP1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
LOC400759
MIR137
MIR197
C1orf180
BCL2L15
LOC441897
LOC492303
RBMXL1
CYMP
LOC648740
NBPF6
SCARNA2
MIR553
MIR942
MIR760

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

Table S103. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NAALADL2

Genes in Wide Peak

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

Table S104. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
C5AR1
CALM3
AP2S1
GRLF1
NPAS1
PPP5C
PTGIR
SLC1A5
SLC8A2
NAPA
DHX34
SAE1
KPTN
ZC3H4
PRKD2
CCDC9
BBC3
GPR77
STRN4
GLTSCR1
TMEM160
PNMAL1
MEIS3
PNMAL2
FKRP
CCDC8
ZNF541
GNG8
DACT3
PRR24
SNAR-E

Genes in Wide Peak

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

Table S105. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LOC285194

Genes in Wide Peak

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

Table S106. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IL5RA
ITPR1
SETMAR
CHL1
CNTN6
TRNT1
CRBN
LRRN1
CNTN4
SUMF1
EGOT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

Table S107. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CXADR
NCAM2
PRSS7
BTG3
NCRNA00157
C21orf91
CHODL
C21orf131

Genes in Wide Peak

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

Table S108. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
RPH3AL

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.32.

Table S109. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
AKT1
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-770
hsa-mir-345
hsa-mir-342
SERPINA3
BDKRB1
BDKRB2
SERPINA6
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
RAGE
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ADAM6
DLK1
CCNK
MTA1
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
C14orf109
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
CDCA4
ATG2B
UBR7
MEG3
SMEK1
BTBD7
ZNF839
C14orf132
DDX24
KIAA1409
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
C14orf139
CLMN
CATSPERB
RIN3
TMEM121
AMN
IFI27L2
SETD3
C14orf153
HHIPL1
C14orf142
FAM181A
BTBD6
C14orf73
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
TC2N
SLC24A4
SLC25A29
DEGS2
C14orf72
GSC
SERPINA12
PRIMA1
C14orf49
MGC23270
NUDT14
C14orf48
SERPINA11
C14orf86
SNHG10
C14orf177
C14orf68
C14orf70
KIAA0284
C14orf80
CCDC85C
NCRNA00203
SERPINA9
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
FLJ45244
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
MIR323
MIR337
MIR342
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR453
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
C14orf184
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORD112
MIR411
MIR654
MIR655
MIR656
SNORD113-1
SNORD113-2
SNORD113-3
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-8
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100133469

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p33.

Table S110. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BEND5
AGBL4

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 | 1731 | 0.11 | -0.522 | 1 | 0.11 | -0.833 | 1
1q | 1572 | 0.28 | 32.4 | 0 | 0.05 | -13.1 | 1
2p | 753 | 0.11 | -7.61 | 1 | 0.04 | -20.5 | 1
2q | 1235 | 0.09 | -7.48 | 1 | 0.04 | -17.2 | 1
3p | 853 | 0.10 | -8.75 | 1 | 0.23 | 14.4 | 0
3q | 917 | 0.20 | 9.83 | 0 | 0.09 | -9.68 | 1
4p | 366 | 0.04 | -20.6 | 1 | 0.21 | 6.59 | 5.11e-11
4q | 865 | 0.03 | -19.7 | 1 | 0.20 | 8.49 | 0
5p | 207 | 0.21 | 5.13 | 7.21e-07 | 0.12 | -8.59 | 1
5q | 1246 | 0.13 | 0.251 | 1 | 0.17 | 7.37 | 2.13e-13
6p | 937 | 0.13 | -2.92 | 1 | 0.11 | -6.2 | 1
6q | 692 | 0.08 | -12.4 | 1 | 0.19 | 5 | 5.73e-07
7p | 508 | 0.34 | 30.4 | 0 | 0.08 | -12.1 | 1
7q | 1071 | 0.32 | 33.6 | 0 | 0.06 | -12.4 | 1
8p | 495 | 0.15 | -1.5 | 1 | 0.36 | 32.8 | 0
8q | 697 | 0.32 | 29.3 | 0 | 0.14 | -2.73 | 1
9p | 343 | 0.10 | -11.1 | 1 | 0.27 | 16.5 | 0
9q | 916 | 0.08 | -11.3 | 1 | 0.22 | 12.4 | 0
10p | 312 | 0.12 | -7.88 | 1 | 0.21 | 6.54 | 6.59e-11
10q | 1050 | 0.07 | -11.7 | 1 | 0.23 | 15.8 | 0
11p | 731 | 0.06 | -16.3 | 1 | 0.14 | -2.29 | 1
11q | 1279 | 0.07 | -11.1 | 1 | 0.16 | 5.57 | 2.67e-08
12p | 484 | 0.17 | 1.29 | 0.386 | 0.09 | -12.6 | 1
12q | 1162 | 0.14 | -0.128 | 1 | 0.08 | -10.3 | 1
13q | 554 | 0.15 | -2.48 | 1 | 0.24 | 13.8 | 0
14q | 1144 | 0.06 | -12.7 | 1 | 0.21 | 13.9 | 0
15q | 1132 | 0.04 | -17.1 | 1 | 0.18 | 7.97 | 2.02e-15
16p | 719 | 0.13 | -3.93 | 1 | 0.18 | 3.71 | 0.000192
16q | 562 | 0.09 | -11.1 | 1 | 0.25 | 15.8 | 0
17p | 575 | 0.06 | -15.4 | 1 | 0.34 | 31.9 | 0
17q | 1321 | 0.12 | -1.46 | 1 | 0.17 | 8.06 | 9.28e-16
18p | 117 | 0.09 | -13.4 | 1 | 0.27 | 14.4 | 0
18q | 340 | 0.07 | -15.4 | 1 | 0.28 | 19.2 | 0
19p | 870 | 0.15 | -0.585 | 1 | 0.13 | -3.78 | 1
19q | 1452 | 0.15 | 4.16 | 6.93e-05 | 0.12 | -1.16 | 1
20p | 295 | 0.29 | 19.6 | 0 | 0.10 | -11 | 1
20q | 627 | 0.34 | 31.4 | 0 | 0.07 | -13.2 | 1
21q | 422 | 0.08 | -14.5 | 1 | 0.15 | -3.14 | 1
22q | 764 | 0.06 | -14.4 | 1 | 0.27 | 20 | 0

Methods & Data
Input

Table 4. Get Full Table First 10 out of 4422 Input Tumor Samples.

Tumor Sample Names
TCGA-02-0001-01C-01D-0182-01
TCGA-02-0003-01A-01D-0182-01
TCGA-02-0006-01B-01D-0182-01
TCGA-02-0007-01A-01D-0182-01
TCGA-02-0009-01A-01D-0182-01
TCGA-02-0010-01A-01D-0182-01
TCGA-02-0011-01B-01D-0182-01
TCGA-02-0014-01A-01D-0182-01
TCGA-02-0021-01A-01D-0182-01
TCGA-02-0024-01B-01D-0182-01

Figure 3. Segmented copy number profiles in the input data

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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

- Maintainer = Dan DiCara

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