Breast Invasive Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16 (cga svn revision 38839).

Summary

There were 824 tumor samples used in this analysis: 29 significant arm-level results, 33 significant focal amplifications, and 53 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 33 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
11q13.3 | 7.946e-144 | 4.3342e-129 | chr11:69434304-69476265 | 1
17q12 | 4.5918e-153 | 4.0896e-110 | chr17:37837542-37876817 | 2
8p11.23 | 5.9105e-90 | 1.2463e-59 | chr8:37551407-37610505 | 3
20q13.2 | 1.0937e-38 | 1.0937e-38 | chr20:52156848-52380471 | 1
8q24.21 | 1.0562e-38 | 8.4038e-34 | chr8:128657453-128800300 | 1
17q23.1 | 5.1071e-50 | 1.8102e-29 | chr17:57919717-57958614 | 1
6q21 | 5.7491e-16 | 5.7491e-16 | chr6:107206856-107339613 | 2
12q15 | 2.3592e-15 | 2.3592e-15 | chr12:69265279-69866440 | 7
15q26.3 | 3.9555e-15 | 3.9555e-15 | chr15:98907098-99572419 | 4
1q21.3 | 2.7095e-16 | 6.706e-14 | chr1:150345471-150706805 | 11
11q14.1 | 1.4559e-60 | 1.5845e-09 | chr11:76857263-78109982 | 16
1p22.3 | 4.1166e-08 | 4.1166e-08 | chr1:85974031-86006207 | 1
8p11.23 | 8.9042e-82 | 3.4582e-07 | chr8:38134156-38274385 | 3
3q26.32 | 2.101e-06 | 2.101e-06 | chr3:176494796-179650920 | 13
19q12 | 1.2374e-06 | 6.351e-06 | chr19:30307099-30316875 | 1
8p11.21 | 2.6443e-27 | 1.1296e-05 | chr8:42155813-42256603 | 4
10q22.3 | 1.9286e-06 | 1.3547e-05 | chr10:80687652-82012440 | 17
11p13 | 0.00023303 | 0.00023303 | chr11:32772542-33741747 | 12
8q21.13 | 1.2394e-11 | 0.00024605 | chr8:80502788-81897445 | 7
12p13.33 | 0.00057546 | 0.00057546 | chr12:1-1143312 | 13
19q13.42 | 0.00011995 | 0.00059595 | chr19:55807632-56309664 | 30
17p11.2 | 0.0015525 | 0.0017453 | chr17:20898015-20924697 | 1
4q13.3 | 0.0024502 | 0.0024502 | chr4:73892436-74269687 | 2
7p11.2 | 0.0040176 | 0.0040176 | chr7:55063359-55715052 | 3
3p25.1 | 0.0059905 | 0.0059905 | chr3:14685335-15111124 | 6
14q21.1 | 0.010566 | 0.010566 | chr14:30366422-39403728 | 48
6p23 | 0.033697 | 0.033697 | chr6:13195098-13619628 | 6
1q32.1 | 0.00011134 | 0.040534 | chr1:202532314-206539650 | 71
16q12.1 | 0.046501 | 0.046501 | chr16:47645686-48057182 | 1
13q12.3 | 0.02914 | 0.063729 | chr13:30303094-31392653 | 7
13q34 | 0.017157 | 0.087476 | chr13:94510995-115169878 | 108
10p15.1 | 0.10157 | 0.10157 | chr10:5637943-5769826 | 2
10q26.13 | 0.0002416 | 0.17229 | chr10:123205358-123476012 | 1

Genes in Wide Peak

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

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

Genes
CCND1

Genes in Wide Peak

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

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

Genes
ERBB2
PGAP3

Genes in Wide Peak

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

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

Genes
ERLIN2
ZNF703
LOC728024

Genes in Wide Peak

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

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

Genes
ZNF217

Genes in Wide Peak

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

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

Genes
MYC

Genes in Wide Peak

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

Table S6. 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 6q21.

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

Genes
hsa-mir-587
LOC100422737

Genes in Wide Peak

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

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

Genes
hsa-mir-1279
CPM
LYZ
YEATS4
FRS2
CPSF6
MIR1279

Genes in Wide Peak

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

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

Genes
IGF1R
PGPEP1L
FAM169B
MIR4714

Genes in Wide Peak

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

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

Genes
hsa-mir-4257
CTSS
ECM1
ENSA
MCL1
RPRD2
ADAMTSL4
GOLPH3L
TARS2
HORMAD1
MIR4257

Genes in Wide Peak

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

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

Genes
CLNS1A
MYO7A
NDUFC2
PAK1
THRSP
GAB2
C11orf67
RSF1
USP35
KCTD14
ALG8
INTS4
GDPD4
AQP11
KCTD21
NDUFC2-KCTD14

Genes in Wide Peak

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

Table S12. 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 8p11.23.

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

Genes
FGFR1
WHSC1L1
LETM2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

Table S15. 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 8p11.21.

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

Genes
IKBKB
POLB
VDAC3
DKK4

Genes in Wide Peak

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

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

Genes
ANXA11
SFTPD
MBL1P
PPIF
ZMIZ1
FAM213A
EIF5AL1
LOC219347
PLAC9
ZCCHC24
LOC283050
LOC439990
LOC642361
LOC650623
SFTPA1
SFTPA2
LOC100288974

Genes in Wide Peak

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

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

Genes
CD59
CSTF3
HIPK3
C11orf41
TCP11L1
PRRG4
QSER1
DEPDC7
LINC00294
LOC338739
CCDC73
C11orf91

Genes in Wide Peak

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

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

Genes
TPD52
STMN2
HEY1
MRPS28
PAG1
ZBTB10
ZNF704

Genes in Wide Peak

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

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

Genes
KDM5A
NINJ2
RAD52
SLC6A12
SLC6A13
ERC1
WNK1
CCDC77
B4GALNT3
IQSEC3
LOC574538
FAM138D
LOC100288778

Genes in Wide Peak

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

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

Genes
IL11
RPL28
U2AF2
UBE2S
CCDC106
EPN1
ZNF580
ZNF581
NAT14
ISOC2
BRSK1
SUV420H2
FIZ1
ZNF628
COX6B2
TMEM190
ZNF524
ZNF784
ZNF579
NLRP11
SSC5D
TMEM150B
FAM71E2
NLRP9
RFPL4A
TMEM238
SBK2
SHISA7
SGK110
ZNF865

Genes in Wide Peak

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

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

Genes
USP22

Genes in Wide Peak

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

Table S23. 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 7p11.2.

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

Genes
EGFR
LANCL2
VOPP1

Genes in Wide Peak

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

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

Genes
NR2C2
C3orf19
MRPS25
C3orf20
FGD5
FGD5-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.1.

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

Genes
NKX2-1
hsa-mir-3172
hsa-mir-624
ARHGAP5
CFL2
COCH
GPR33
FOXA1
NFKBIA
PAX9
PRKD1
PSMA6
SRP54
SSTR1
AKAP6
KIAA0391
AP4S1
BAZ1A
SCFD1
HECTD1
HEATR5A
NKX2-8
STRN3
MBIP
PPP2R3C
G2E3
EAPP
SNX6
NPAS3
NUBPL
BRMS1L
INSM2
ARHGAP5-AS1
SLC25A21
EGLN3
C14orf126
MIPOL1
CLEC14A
SPTSSA
RALGAPA1
SFTA3
IGBP1P1
LOC283547
FAM177A1
MIR624
LOC100129794
LOC100506071
MIR4503

Genes in Wide Peak

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

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

Genes
SIRT5
TBC1D7
NOL7
GFOD1
PHACTR1
LOC100130357

Genes in Wide Peak

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

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

Genes
ELK4
MDM4
SLC45A3
hsa-mir-135b
ADORA1
ATP2B4
AVPR1B
CHI3L1
CHIT1
CTSE
FMOD
KISS1
MYBPH
MYOG
PPP1R12B
CDK18
PIK3C2B
PRELP
RABIF
RBBP5
REN
SNRPE
CNTN2
BTG2
PPFIA4
RAB7L1
SOX13
ZC3H11A
TMCC2
LRRN2
KDM5B
PLEKHA6
NFASC
SRGAP2
DSTYK
OPTC
ADIPOR1
CYB5R1
LAX1
KLHDC8A
ETNK2
KLHL12
NUCKS1
NUAK2
LINC00260
PPP1R15B
TMEM183A
LEMD1
SLC26A9
SYT2
LOC127841
GOLT1A
LOC148709
MFSD4
PM20D1
SLC41A1
LINC00303
LOC284576
LOC284578
LOC284581
TMEM81
LOC401980
C1orf186
MIR135B
LOC641515
TMEM183B
SNORA77
FAM72A
LOC730227
ZBED6
KDM5B-AS1

Genes in Wide Peak

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

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

Genes
PHKB

Genes in Wide Peak

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

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

Genes
ALOX5AP
HMGB1
UBL3
USPL1
KATNAL1
LOC440131
LINC00426

Genes in Wide Peak

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

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
FGF14
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
RAP2A
GRK1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
OXGR1
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
TEX29
METTL21CP1
SPACA7
RNF113B
GPR180
CLYBL
METTL21C
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
UBAC2
FAM70B
C13orf35
FLJ44054
CCDC168
FLJ41484
MIR623
LINC00460
FAM155A
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR4306
MIR3170
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4705

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.1.

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

Genes
FAM208B
ASB13

Genes in Wide Peak

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

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

Genes
FGFR2

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 - 53 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
--- | --- | --- | --- | ---
8p23.2 | 1.2009e-30 | 3.8114e-30 | chr8:2079140-6262191 | 1
1p36.13 | 1.2501e-28 | 6.1089e-28 | chr1:8876393-23038731 | 205
9p21.3 | 4.2273e-29 | 1.3958e-26 | chr9:21865498-22448737 | 4
19p13.3 | 3.1826e-25 | 3.1826e-25 | chr19:1103802-1943798 | 35
13q14.2 | 4.9562e-26 | 5.3122e-23 | chr13:48833767-49064807 | 2
10q23.31 | 1.5997e-23 | 1.3014e-21 | chr10:89617158-90034038 | 2
17p12 | 4.6317e-15 | 8.5649e-14 | chr17:11896630-12456081 | 3
4q35.2 | 1.3547e-13 | 1.3547e-13 | chr4:186877632-191154276 | 25
6q27 | 6.3323e-16 | 1.4491e-11 | chr6:167548608-169617013 | 13
21q11.2 | 1.4154e-09 | 1.4154e-09 | chr21:1-15594370 | 17
7q36.1 | 1.6274e-09 | 1.7008e-09 | chr7:151817415-152136074 | 1
11p15.5 | 1.0771e-08 | 1.752e-08 | chr11:1-3382850 | 109
15q11.2 | 1.2265e-13 | 8.9924e-08 | chr15:1-25200357 | 41
5q11.2 | 7.1029e-08 | 3.6492e-07 | chr5:55001196-57749995 | 9
14q24.3 | 7.5817e-07 | 7.2294e-07 | chr14:65287395-90424308 | 163
17q21.31 | 3.0567e-10 | 2.5342e-06 | chr17:39885492-44842087 | 138
3p21.31 | 2.3911e-12 | 3.1472e-06 | chr3:47552760-53529383 | 167
11q23.3 | 5.6212e-12 | 5.9336e-06 | chr11:104032904-128329282 | 253
3p13 | 4.3683e-10 | 5.6469e-05 | chr3:55108056-84688247 | 94
1p21.2 | 5.1627e-07 | 6.9746e-05 | chr1:85664883-115830107 | 238
7p22.3 | 8.0188e-05 | 8.0188e-05 | chr7:1-3344016 | 42
6q21 | 2.6929e-09 | 0.00020853 | chr6:107981998-109763713 | 14
15q21.1 | 1.0439e-08 | 0.00029751 | chr15:35261271-49623237 | 162
10q26.3 | 6.2365e-07 | 0.00036736 | chr10:129248643-135534747 | 57
12p13.1 | 0.00038244 | 0.00036736 | chr12:12418624-13714562 | 23
18q23 | 0.0003875 | 0.00039312 | chr18:72073957-78077248 | 27
2q37.3 | 4.5606e-13 | 0.00046032 | chr2:232785356-243199373 | 123
6p25.3 | 0.00069964 | 0.00072761 | chr6:1-7728427 | 49
11q25 | 2.0781e-13 | 0.00082032 | chr11:132204656-135006516 | 15
9p13.1 | 5.8236e-05 | 0.00089919 | chr9:38619152-71152237 | 50
12q24.32 | 3.2144e-05 | 0.00094934 | chr12:118536856-133851895 | 156
20p13 | 0.0015232 | 0.0015232 | chr20:1-815752 | 18
2q36.3 | 1.7488e-09 | 0.0036556 | chr2:220439344-243199373 | 196
5q21.3 | 0.00083731 | 0.0036556 | chr5:104425581-107194910 | 2
9p24.1 | 1.5892e-06 | 0.0039336 | chr9:7799607-12693402 | 1
13q12.11 | 3.8262e-07 | 0.0055377 | chr13:1-24737091 | 37
16p11.2 | 0.0013647 | 0.0059068 | chr16:31772318-47119148 | 23
16q23.1 | 0.00010683 | 0.0115 | chr16:78016120-79627770 | 2
2q22.3 | 0.0073609 | 0.015378 | chr2:122525427-154336496 | 116
17q12 | 3.9793e-09 | 0.025753 | chr17:29326736-35977637 | 97
8p11.21 | 0.0082091 | 0.038181 | chr8:42883855-47753079 | 4
12q23.1 | 0.0017085 | 0.047386 | chr12:99124001-100431272 | 2
6q14.3 | 2.1751e-07 | 0.061767 | chr6:64293011-105177050 | 133
8p12 | 0.0016328 | 0.062372 | chr8:22106166-37561346 | 100
16q24.3 | 6.8e-05 | 0.083074 | chr16:86613840-90354753 | 60
17p13.3 | 0.0073675 | 0.083074 | chr17:1-1826620 | 37
19q13.32 | 0.083074 | 0.083074 | chr19:45804626-49590763 | 164
22q13.31 | 0.069625 | 0.08453 | chr22:43737603-51304566 | 98
22q11.1 | 0.09055 | 0.1078 | chr22:1-18068784 | 16
4p16.3 | 0.16054 | 0.16003 | chr4:1-1215099 | 26
17p11.2 | 0.043641 | 0.16489 | chr17:21191360-25270799 | 6
11q13.1 | 0.0017354 | 0.16734 | chr11:62303823-65684611 | 152
2p25.1 | 0.21051 | 0.21158 | chr2:1-27995104 | 179

Genes in Wide Peak

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

Table S34. 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 1p36.13.

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

Genes
PAX7
SDHB
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
ALPL
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
TNFRSF8
CDA
CDC42
CLCN6
CLCNKA
CLCNKB
CORT
DDOST
DFFA
ECE1
EPHA2
ENO1
EPHA8
MTOR
HSPG2
HTR6
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
RAP1GAP
RSC1A1
SLC2A5
SRM
TNFRSF1B
ZBTB17
PRDM2
AKR7A2
ALDH4A1
EIF4G3
DHRS3
H6PD
CROCC
ZBTB40
MFN2
CELA3A
ANGPTL7
UBE4B
MAD2L2
PDPN
MASP2
MST1P2
MST1P9
PADI2
CTRC
CLSTN1
AKR7A3
SPEN
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
PADI4
C1orf144
FBXO2
FBXO6
PLA2G2D
HSPB7
LINC00339
UBIAD1
PADI1
PLA2G2E
HP1BP3
CELA2B
MRTO4
PADI3
WNT4
FBXO42
RNF186
FBLIM1
PQLC2
CASZ1
TMEM51
ARHGEF10L
VPS13D
CAMK2N1
NBPF1
NECAP2
RCC2
CTNNBIP1
AGTRAP
PTCHD2
KIF17
MIIP
CELA2A
PLA2G2F
NMNAT1
PINK1
PRAMEF1
PRAMEF2
EFHD2
RSG1
MUL1
AGMAT
GPR157
SPSB1
TAS1R2
ACTL8
USP48
NBPF3
SLC25A33
DDI2
LZIC
CROCCP2
IGSF21
KIAA2013
C1orf158
FBXO44
CROCCP3
FHAD1
RBP7
LRRC38
AADACL3
IFFO2
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf127
C1orf64
SLC2A7
FAM43B
TMEM201
C1orf126
AKR7L
TMCO4
SLC25A34
ESPNP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
APITD1
TMEM82
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
PRAMEF3
LDLRAD2
MIR34A
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
PRAMEF7
C1orf200
PRAMEF19
PRAMEF20
LOC649330
PRAMEF22
PRAMEF15
PRAMEF16
SNORA59B
SNORA59A
PRAMEF14
FLJ37453
NPPA-AS1
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4632

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
STK11
TCF3
hsa-mir-1909
ATP5D
CIRBP
EFNA2
GAMT
GPX4
RPS15
APC2
UQCR11
SBNO2
DAZAP1
MBD3
PCSK4
C19orf24
REXO1
FAM108A1
KLF16
MUM1
MIDN
REEP6
SCAMP4
ADAT3
PLK5
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
ADAMTSL5
NDUFS7
ONECUT3
MEX3D
LOC100288123
MIR1909

Genes in Wide Peak

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

Table S38. 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 10q23.31.

Table S39. 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 17p12.

Table S40. 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 4q35.2.

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

Genes
DUX4
F11
FAT1
FRG1
HSP90AA4P
KLKB1
MTNR1A
TLR3
FAM149A
DUX2
ZFP42
TRIML2
CYP4V2
LOC285441
LOC339975
TRIML1
LOC401164
DUX4L4
FRG2
FLJ38576
DUX4L6
DUX4L5
DUX4L3
DUX4L2
LOC100288255

Genes in Wide Peak

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

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

Genes
MLLT4
GPR31
KIF25
TCP10
C6orf123
UNC93A
SMOC2
FRMD1
TTLL2
DACT2
TCP10L2
MLLT4-AS1
HGC6.3

Genes in Wide Peak

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

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

Genes
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
TPTE
C21orf15
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
LIPI
POTED
ANKRD20A11P
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

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

Table S44. 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 11p15.5.

Table S45. 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
PHLDA2
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
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
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
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 15q11.2.

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

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
NBEAP1
NDN
MKRN3
CYFIP1
C15orf2
MAGEL2
NIPA2
TUBGCP5
NIPA1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8IP
WHAMMP3
POTEB
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
CHEK2P2
LOC646214
CXADRP2
REREP3
LOC653061
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
HERC2P7
GOLGA8DP
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3

Genes in Wide Peak

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

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

Genes
IL6ST
MAP3K1
DDX4
GPBP1
ANKRD55
C5orf35
IL31RA
MIER3
ACTBL2

Genes in Wide Peak

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

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

Genes
TSHR
GPHN
hsa-mir-1260
hsa-mir-625
ACTN1
ACYP1
ARG2
ZFP36L1
ENTPD5
FOXN3
DIO2
DLST
EIF2S1
ERH
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
LTBP2
MAX
MAP3K9
ALDH6A1
PGF
PIGH
PSEN1
ABCD4
RAD51B
SEL1L
SRSF5
SLC8A3
SLC10A1
TGFB3
DPF3
GPR65
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
NRXN3
SPTLC2
RGS6
KIAA0247
KIAA0317
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
PTPN21
C14orf1
VASH1
SNW1
PCNX
TTLL5
ANGEL1
ZFYVE26
TTC9
FLRT2
SIPA1L1
DCAF4
PLEK2
MLH3
PRO1768
POMT2
COQ6
FCF1
RDH11
COX16
ATP6V1D
ZFYVE1
KCNK10
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
SPATA7
YLPM1
C14orf162
ADCK1
TMEM63C
GALNTL1
PLEKHH1
ZNF410
NGB
RBM25
C14orf133
SMOC1
IRF2BPL
MPP5
ZC2HC1C
C14orf169
ZC3H14
C14orf45
SLIRP
DNAL1
RPS6KL1
STON2
KIAA1737
PAPLN
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
IFT43
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
RDH12
ADAM21P1
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
FAM71D
TMEM229B
SAMD15
EML5
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
C14orf55
SNORD56B
VSX2
RAB15
HEATR4
PLEKHD1
LOC400236
LINC00238
ACOT1
ACOT6
LOC645431
SYNDIG1L
SNORA79
LOC731223
LOC100289511
MIR1260A
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
LOC100628307

Genes in Wide Peak

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

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

Genes
BRCA1
ETV4
hsa-mir-4315-1
hsa-mir-2117
ACLY
AOC2
ARL4D
ATP6V0A1
FMNL1
CNP
CRHR1
DHX8
DUSP3
EZH1
FZD2
G6PC
KAT2A
GFAP
CCR10
GRN
HCRT
HSD17B1
IFI35
ITGA2B
JUP
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
NAGLU
NMT1
NSF
PPY
PYY
RAB5C
RPL27
SLC4A1
STAT3
STAT5A
STAT5B
MLX
DNAJC7
TUBG1
UBTF
RND2
CNTNAP1
AOC3
BECN1
MAP3K14
EFTUD2
PLEKHM1
LRRC37A
HDAC5
GJC1
PSME3
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
C1QL1
RUNDC3A
GPATCH8
KCNH4
FAM215A
TUBG2
NKIRAS2
CCDC56
PSMC3IP
SOST
ARL17A
SLC25A39
HIGD1B
LRRC37A4
KLHL11
ATXN7L3
FKBP10
WNK4
C17orf53
TMUB2
DHX58
ACBD4
DCAKD
PLEKHH3
DBF4B
COASY
AARSD1
TTC25
VPS25
TMEM101
GHDC
AOC4
G6PC3
ASB16
HSPB9
PLCD3
TMEM106A
NT5C3L
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
CD300LG
KIF18B
RUNDC1
C17orf69
NAGS
FAM134C
IMP5
ARHGAP27
ZNF385C
STH
KIAA1267
C17orf105
FAM171A2
C17orf104
PTRF
KLHL10
C17orf65
LOC388387
CCDC103
MGC57346
LRRC37A2
LOC644172
LOC644246
NSFP1
LOC100128977
LOC100130148
LOC100130581
LOC100133991
LOC100190938
MIR2117
MIR4315-2
MIR4315-1
ARL17B

Genes in Wide Peak

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

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

Genes
BAP1
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
ACY1
ALAS1
AMT
APEH
RHOA
SLC25A20
CAMP
CDC25A
CISH
COL7A1
DAG1
DOCK3
DUSP7
CELSR3
GNAI2
GNAT1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
MAP4
MST1
MST1R
PFKFB4
PLXNB1
PRKAR2A
PRKCD
QARS
RPL29
SEMA3F
SMARCC1
NEK4
TCTA
TKT
TNNC1
UBA7
USP4
UQCRC1
IFRD2
MAPKAPK3
SEMA3B
MANF
HYAL3
HYAL2
BSN
RRP9
CACNA2D2
VPRBP
IP6K1
PARP3
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CSPG5
USP19
SLC38A3
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
LAMB2P1
RAD54L2
STAB1
NAT6
ABHD14A
POC1A
NDUFAF3
DNAH1
GNL3
SPCS1
RBM15B
GMPPB
C3orf18
SHISA5
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
P4HTM
QRICH1
DALRD3
DCP1A
GLT8D1
SEMA3G
PCBP4
RNF123
CCDC71
NT5DC2
SLC26A6
CAMKV
CCDC51
WDR82
ATRIP
NICN1
MON1A
ABHD14B
UCN2
RFT1
GPR62
IQCF1
GLYCTK
PPM1M
C3orf45
KLHDC8B
FBXW12
CCDC36
C3orf62
TMEM110
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR191
TMEM89
IQCF6
C3orf78
MIR425
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
SNORD19B
C3orf74
BSN-AS2
MIR1226
MIR711
MIR4271
IQCF4
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4443
LUST

Genes in Wide Peak

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

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

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
VWA5A
MCAM
NCAM1
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
DCPS
DDX25
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
MPZL3
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
CARD17
HEPN1
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
CASP12
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4493
MIR4491
MIR4492
LOC100652768

Genes in Wide Peak

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

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

Genes
FHIT
MITF
FOXP1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
ARF4
C3orf51
DNASE1L3
FLNB
GBE1
GPR27
CNTN3
PDHB
PTPRG
ROBO1
ROBO2
ATXN7
TMF1
WNT5A
SLMAP
ACOX2
CADPS
SUCLG2
HESX1
UBA3
MAGI1
PSMD6
ARL6IP5
RPP14
FAM107A
PDZRN3
FRMD4B
FAM208A
RYBP
LRIG1
ERC2
APPL1
ARHGEF3
IL17RD
PXK
FEZF2
EBLN2
SHQ1
LMOD3
ADAMTS9
ABHD6
C3orf14
PROK2
THOC7
ID2B
KBTBD8
SLC25A26
FAM3D
C3orf49
SNTN
SYNPR
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
LOC201617
DNAH12
PDE12
FAM116A
C3orf64
CCDC66
LOC285401
EIF4E3
SPATA12
LOC401074
FAM19A1
FLJ20518
FAM86DP
MIR548A2
GXYLT2
ZNF717
LOC100287879
FRG2C
MIR1284
MIR1324
MIR3136
MIR4272
MIR4273
MIR3938
LOC100506994
LOC100507062
ADAMTS9-AS2
MIR4444-1
LOC100652759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p21.2.

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

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP5F1
BRDT
CAPZA1
CD53
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
OVGP1
PKN2
PSMA5
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
LMO4
CDC14A
RTCD1
SLC16A4
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
TSPAN2
BCAS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
KIAA1107
SLC35A3
LRRC8B
DDAH1
RWDD3
PTPN22
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
RPAP2
DENND2D
SIKE1
GPR61
ZNF644
LRRC8C
PROK1
PSRC1
FAM40A
DNAJA1P5
HENMT1
GBP4
GBP5
OLFM3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
C1orf52
TMEM56
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
HIPK1
AKR7A2P1
EPHX4
AKNAD1
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
GBP7
C1orf146
FAM69A
SLC6A17
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682

Genes in Wide Peak

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

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

Genes
CARD11
hsa-mir-339
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
EIF3B
ADAP1
IQCE
SUN1
INTS1
SNX8
FTSJ2
GET4
CYP2W1
HEATR2
CHST12
FAM20C
MICALL2
TTYH3
PSMG3
C7orf50
ZFAND2A
COX19
KIAA1908
GPR146
AMZ1
TMEM184A
BRAT1
TFAMP1
UNCX
ELFN1
FLJ44511
LOC442497
MIR339
LOC100288524
MIR4648
MIR4655

Genes in Wide Peak

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

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

Genes
FOXO3
NR2E1
SNX3
CD164
SEC63
SESN1
OSTM1
ARMC2
CCDC162P
LACE1
SCML4
CEP57L1
PPIL6
LINC00222

Genes in Wide Peak

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

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

Genes
BUB1B
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
B2M
CAPN3
CKMT1B
DUT
EPB42
FBN1
GALK2
GANC
GATM
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
SLC12A1
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
SLC28A2
COPS2
TGM5
PPIP5K1
SECISBP2L
LCMT2
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
CEP152
MAPKBP1
RTF1
MGA
VPS39
CCNDBP1
EID1
C15orf63
TMEM87A
RPAP1
PLDN
RPUSD2
TUBGCP4
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
PPP1R14D
ZNF770
HAUS2
FAM82A2
DNAJC17
PAK6
CASC5
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
SPRED1
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
PLA2G4F
LRRC57
HMGN2P46
SLC24A5
FAM98B
PLA2G4D
MRPL42P5
C15orf52
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
MIR626
MIR627
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100131089
ANKRD63
JMJD7
PLA2G4B
MIR1282
LOC100306975
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4510
MIR4716

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
ADAM8
BNIP3
CYP2E1
ECHS1
INPP5A
MGMT
MKI67
PTPRE
UTF1
GLRX3
DPYSL4
TUBGCP2
DUX2
VENTX
CALY
TTC40
PPP2R2D
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
CTAGE7P
CLRN3
C10orf91
PWWP2B
PAOX
EBF3
TCERG1L
C10orf125
JAKMIP3
STK32C
LOC387723
FOXI2
FLJ46300
LOC399829
SPRNP1
FRG2B
SPRN
MIR202
NPS
LOC619207
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
MIR378C
MIR4297
MIR3944

Genes in Wide Peak

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

Table S58. 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
MANSC1
GPRC5D
KIAA1467
DUSP16
APOLD1
GSG1
HTR7P1
LOH12CR1
C12orf36
RPL13AP20
LOH12CR2
MIR613
MIR614
LOC100506314

Genes in Wide Peak

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

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

Genes
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TSHZ1
TXNL4A
ADNP2
KCNG2
SALL3
ZNF407
CNDP2
RBFA
PQLC1
PARD6G
CNDP1
FAM69C
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400657
HSBP1L1
LOC100130522
LOC100131655

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
KCNJ13
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PPP1R7
SAG
SPP2
DGKD
PER2
LRRFIP1
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
NGEF
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
EFHD1
ILKAP
ING5
MGC16025
AGAP1
TWIST2
DIS3L2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
MSL3P1
TIGD1
LOC200772
CXXC11
DUSP28
ESPNL
ECEL1P2
RBM44
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
PRSS56
AQP12B
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

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

Genes
IRF4
BPHL
DSP
SERPINB1
F13A1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TUBB2A
RIPK1
PRPF4B
CDYL
LY86
ECI2
FARS2
RPP40
FAM50B
NRN1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
RIOK1
FOXQ1
HUS1B
SNRNP48
C6orf195
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
PSMG4
DKFZP686I15217
C6orf201
PPP1R3G
MIR3691
LOC100507194
LOC100508120
MIR4645

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

Table S63. 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
FAM201A
CBWD5
LOC286297
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
FAM74A1
FAM74A4
ZNF658B
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.32.

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

Genes
BCL7A
hsa-mir-4304
hsa-mir-1178
ACADS
SCARB1
COX6A1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
P2RX4
P2RX7
PEBP1
PLA2G1B
POLE
PRKAB1
PSMD9
PXMP2
PXN
RAN
RPLP0
CLIP1
SFSWAP
HNF1A
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
ULK1
DENR
OASL
DYNLL1
SRSF9
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RNF10
MPHOSPH9
CAMKK2
ZNF268
TMED2
GCN1L1
RAB35
SNRNP35
CIT
FZD10
MLXIP
P2RX2
SETD1B
ANKLE2
SIRT4
ABCB9
RIMBP2
ATP6V0A2
HSPB8
HCAR1
GALNT9
ARL6IP4
TAOK3
POP5
ANAPC5
TRIAP1
RHOF
SBNO1
ZCCHC8
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
SUDS3
C12orf43
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
RNF34
CCDC92
PUS1
COQ5
SRRM4
CCDC62
KDM2B
UNC119B
ORAI1
C12orf65
TMEM132C
CCDC64
TMEM132B
LOC116437
TMEM132D
SLC15A4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
LOC144742
CCDC60
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
MORN3
GATC
HNF1A-AS1
DDX51
HCAR2
LOC338799
EP400NL
RILPL1
IL31
TMEM233
SETD8
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
LOC647589
SNORA49
LOC100128554
LOC100130238
LOC100190940
ZNF605
MIR1178
MIR4304
MIR3612
MIR3908
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4498
MIR4700

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q36.3.

Table S66. 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
hsa-mir-4268
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
DTYMK
EPHA4
GBX2
GPC1
GPR35
HDLBP
AGFG1
HTR2B
SP110
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
SNORD20
SAG
CCL20
SLC4A3
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
STK11IP
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
MIR4268
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 5q21.3.

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

Genes
EFNA5
RAB9BP1

Genes in Wide Peak

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

Table S68. 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 13q12.11.

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

Genes
hsa-mir-2276
FGF9
GJA3
GJB2
MIPEP
SGCG
TUBA3C
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
PSPC1
TNFRSF19
XPO4
MRP63
TPTE2
N6AMT2
SKA3
EFHA1
ZDHHC20
PHF2P1
ANKRD20A9P
LINC00442
C1QTNF9B
C1QTNF9B-AS1
BASP1P1
ANKRD26P3
LINC00421
MIR2276
LINC00327
MIR4499

Genes in Wide Peak

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

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

Genes
hsa-mir-1826
DNAJA2
ZNF267
ORC6
TP53TG3
VPS35
SHCBP1
GPT2
MYLK3
ANKRD26P1
LOC146481
LOC283914
SLC6A10P
C16orf87
LOC390705
FLJ26245
HERC2P4
UBE2MP1
LINC00273
TP53TG3C
LOC729264
TP53TG3B
LOC100130700

Genes in Wide Peak

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

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

Genes
CLEC3A
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.3.

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

Genes
ERCC3
hsa-mir-128-1
hsa-mir-663b
ACVR2A
BIN1
RND3
CACNB4
CCNT2
DARS
GPR17
GPR39
GYPC
HNMT
KIF5C
LCT
MCM6
MGAT5
MYO7B
NEB
ORC4
POLR2D
PROC
TNFAIP6
CXCR4
KYNU
NMI
HS6ST1
ZEB2
STAM2
MAP3K2
NXPH2
RAB3GAP1
UBXN4
R3HDM1
EPC2
ARL5A
PTPN18
MMADHC
C2orf27A
ARHGEF4
LRP1B
PLEKHB2
RIF1
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
CFC1
RPRM
UGGT1
SAP130
GTDC1
MZT2B
YSK4
THSD7B
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
SFT2D3
CCDC74A
CCDC74B
IMP4
TUBA3E
TUBA3D
FMNL2
LYPD1
CNTNAP5
ACMSD
FAM168B
LYPD6
LYPD6B
LOC150527
LOC150776
WTH3DI
ARL6IP6
FAM123C
LOC285103
SPOPL
CYP27C1
NCKAP5
GPR148
RBM43
LOC389033
LOC389043
LOC401010
DKFZp686O1327
MIR128-1
C2orf27B
LOC440905
LOC440910
POTEKP
POTEE
ANKRD30BL
LOC646743
LOC647012
CFC1B
MZT2A
POTEF
PABPC1P2
LOC100129961
LOC100131320
CYP4F30P
LOC100216479
ZEB2-AS1
MIR663B
MIR3679
LOC100507600
MIR4783
MIR4784
MIR4773-1
MIR4773-2

Genes in Wide Peak

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

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

Genes
NF1
TAF15
SUZ12
hsa-mir-2909
hsa-mir-632
hsa-mir-365-2
ACACA
ACCN1
AP2B1
EVI2A
EVI2B
LHX1
LIG3
MYO1D
OMG
PEX12
PSMD11
RAD51D
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SH3GL1P1
TADA2A
ZNF207
CDK5R1
ZNHIT3
CCL4L1
CCT6B
DUSP14
SYNRG
TMEM98
AATF
NLE1
FNDC8
SLFN12
RHOT1
C17orf79
UTP6
LYZL6
C17orf75
MMP28
DHRS11
GGNBP2
MRM1
MYO19
RAB11FIP4
ZNF830
SLFN11
RASL10B
LRRC37B
RFFL
TMEM132E
SPACA3
C17orf50
SLFN13
SLC35G3
UNC45B
SLFN5
RHBDL3
RDM1
GAS2L2
C17orf66
PIGW
C17orf78
SLFN14
CCL14-CCL15
CCL4L2
C17orf102
MIR193A
TBC1D3B
TBC1D3C
CCL3L3
ARGFXP2
TBC1D3G
SNORD7
MIR632
TBC1D3H
MIR365B
MIR2909
AA06
SLFN12L
RAD51L3-RFFL
MIR4724
MIR4733
MIR4725

Genes in Wide Peak

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

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

Genes
FNTA
SGK196
HGSNAT
POTEA

Genes in Wide Peak

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

Table S75. 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 6q14.3.

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

Genes
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
GABRR1
GABRR2
GRIK2
HTR1B
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
POU3F2
RNY4
SIM1
ELOVL4
MAP3K7
TPBG
TTK
RNGTT
TBX18
HMGN3
FHL5
SNAP91
CASP8AP2
SYNCRIP
SLC35A1
FUT9
PNRC1
ASCC3
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
MDN1
UFL1
PHF3
ORC3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
NDUFAF4
CYB5R4
UBE2J1
COQ3
PHIP
AKIRIN2
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
C6orf162
LYRM2
SNX14
FAM135A
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
MCHR2
FAXC
GJA10
USP45
C6orf7
UBE2CBP
MRAP2
RWDD2A
KLHL32
MB21D1
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
PRSS35
LCA5
C6orf163
MMS22L
DPPA5
EYS
GJB7
SNHG5
C6orf147
MIR30A
MIR30C2
OOEP
MCART3P
TSG1
SNORD50B
LOC728012
KHDC1L
LOC100130890
LOC100288198
MIR2113
MIR548H3
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
WRN
hsa-mir-3148
hsa-mir-4288
hsa-mir-4287
hsa-mir-548h-4
ADRA1A
BNIP3L
CHRNA2
CLU
DPYSL2
DUSP4
EGR3
EPHX2
EXTL3
PTK2B
GNRH1
GSR
GTF2E2
NRG1
LOXL2
NEFM
NEFL
NKX3-1
PNOC
PPP2CB
PPP2R2A
PPP3CC
STC1
FZD3
UBXN8
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
ENTPD4
SORBS3
DCTN6
PNMA2
ADAM28
RBPMS
TRIM35
RHOBTB2
KIF13B
LEPROTL1
SLC39A14
ADAMDEC1
PURG
SLC25A37
SCARA3
TMEM66
KCTD9
PIWIL2
ELP3
CCDC25
INTS9
PBK
ZNF395
BIN3
TEX15
KIAA1967
PDLIM2
EBF2
DUSP26
HMBOX1
RNF122
DOCK5
FLJ14107
ZNF703
TTI2
STMN4
MAK16
FUT10
CHMP7
NKX2-6
UNC5D
PEBP4
CDCA2
ESCO2
FBXO16
KCNU1
R3HCC1
LOC254896
LOC286059
SCARA5
LOC286135
LOC389641
C8orf80
C8orf58
C8orf75
MBOAT4
LOC100128750
MIR4287
MIR3148
MIR4288
MIR3622A
MIR3622B
LOC100507156
LOC100507341
MIR548O2

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
AFG3L1P
APRT
C16orf3
CA5A
CDH15
CYBA
DPEP1
GALNS
GAS8
MC1R
MVD
CHMP1A
RPL13
SPG7
SLC7A5
CDK10
C16orf7
PIEZO1
TUBB3
PRDM7
TCF25
ZCCHC14
CPNE7
IL17C
ANKRD11
TRAPPC2L
KLHDC4
DEF8
BANP
JPH3
DBNDD1
FBXO31
CDT1
MAP1LC3B
SPIRE2
ZNF469
CENPBD1
ZNF276
RNF166
SPATA2L
C16orf55
ZC3H18
SLC22A31
ZFPM1
MGC23284
ZNF778
ACSF3
LINC00304
SNAI3
CTU2
PABPN1L
LOC400558
SNORD68
LOC100128881
LOC100130015
LOC100287036
C16orf95
MIR4722

Genes in Wide Peak

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

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

Genes
hsa-mir-22
hsa-mir-3183
ABR
CRK
MYO1C
SERPINF1
PITPNA
SERPINF2
RPA1
YWHAE
DOC2B
SCARF1
RPH3AL
PRPF8
TIMM22
GEMIN4
GLOD4
INPP5K
RNMTL1
VPS53
NXN
FAM57A
RILP
MIR22HG
SMYD4
SLC43A2
WDR81
TUSC5
FAM101B
C17orf97
MIR22
BHLHA9
TLCD2
DBIL5P
LOC100306951
MIR3183
LOC100506388

Genes in Wide Peak

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

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

Genes
ERCC2
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
BAX
BCAT2
C5AR1
CA11
CALM3
CGB
CKM
AP2S1
CRX
DBP
DMPK
DMWD
EMP3
ERCC1
FOSB
FTL
FUT1
FUT2
GIPR
GPR4
GRIN2D
ARHGAP35
GYS1
FOXA3
KCNA7
KCNJ14
LHB
LIG1
NOVA2
NPAS1
NTF4
NUCB1
PPP5C
PTGIR
RPL18
RTN2
SEPW1
SLC1A5
SLC8A2
SNRPD2
SULT2B1
SULT2A1
TULP2
VASP
SYMPK
PLA2G4C
NAPA
PGLYRP1
CYTH2
DHX34
SAE1
PPP1R13L
CD3EAP
RUVBL2
KDELR1
KPTN
CARD8
ZC3H4
FBXO46
SYNGR4
PPP1R15A
EML2
PRKD2
CCDC9
IRF2BP1
FGF21
BBC3
GPR77
DHDH
STRN4
GLTSCR2
GLTSCR1
EHD2
HSD17B14
QPCTL
FAM83E
RASIP1
TMEM160
PNMAL1
TMEM143
CABP5
SPHK2
MEIS3
PNMAL2
PLEKHA4
ELSPBP1
HIF3A
FKRP
OPA3
RSPH6A
GRWD1
CCDC8
ZNF541
CCDC114
DKFZp434J0226
CGB5
CGB7
CGB8
GNG8
CGB1
CGB2
LMTK3
NTN5
PPM1N
KLC3
DACT3
SIX5
IGFL2
ZNF114
SPACA4
PRR24
TPRX1
MAMSTR
IZUMO1
MYPOP
NANOS2
IGFL1
LOC388553
IGFL3
MIR330
IGFL4
SEC1
SNORD23
MIR642A
CCDC61
MIR769
SNAR-G1
SNAR-A1
SNAR-A2
SNAR-A12
BSPH1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-C1
SNAR-C3
SNAR-G2
SNAR-A14
LOC100287177
MIR3191
MIR3190
MIR320E
MIR642B
LOC100505681
LOC100505812
LOC100506012
LOC100506068

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
MPPED1
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
SMC1B
PARVB
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
PARVG
CERK
EFCAB6
ALG12
CRELD2
ADM2
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
PNPLA5
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
LINC00229
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

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

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

Genes
IL17RA
ANKRD62P1-PARP4P3
POTEH
HSFY1P1
CECR6
CECR5
CECR3
CECR2
CECR1
OR11H1
GAB4
CCT8L2
XKR3
TPTEP1
CECR7
CECR5-AS1

Genes in Wide Peak

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

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

Genes
hsa-mir-571
ATP5I
DGKQ
GAK
IDUA
MYL5
PDE6B
ZNF141
PCGF3
SPON2
CPLX1
SLC26A1
FGFRL1
PIGG
ABCA11P
MFSD7
TMEM175
ZNF595
ZNF721
ZNF718
RNF212
ZNF876P
ZNF732
LOC100129917
LOC100130872
TMED11P

Genes in Wide Peak

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

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

Genes
KCNJ12
FAM27L
FLJ36000
C17orf51
KCNJ18
MTRNR2L1

Genes in Wide Peak

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

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

Genes
MEN1
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
ARL2
BAD
C11orf2
MRPL49
ZNHIT2
CAPN1
CFL1
CHRM1
COX8A
CTSW
EEF1G
MARK2
ESRRA
FAU
FKBP2
GNG3
DNAJC4
LTBP3
MAP3K11
OVOL1
PLCB3
POLR2G
PPP2R5B
PYGM
MAP4K2
RARRES3
RELA
DPF2
ROM1
SIPA1
SLC3A2
STX5
TM7SF2
VEGFB
SF1
ZFPL1
FOSL1
RPS6KA4
FIBP
MTA2
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
SLC22A6
SLC22A8
NRXN2
NAALADL1
KCNK7
RASGRP2
RTN3
CDC42EP2
NXF1
KAT5
SSSCA1
TAF6L
EHD1
STIP1
CCDC85B
PLA2G16
ATG2A
GANAB
FAM89B
SNHG1
POLA2
FLRT1
PRDX5
C11orf20
ATL3
B3GAT3
PPP1R14B
BSCL2
MACROD1
SAC3D1
SNX15
EFEMP2
KCNK4
UBXN1
TRMT112
WDR74
HRASLS2
CDC42BPG
OTUB1
SLC22A11
GPR137
SCYL1
TUT1
C11orf95
TMEM223
C11orf48
NAA40
ZBTB3
MUS81
INTS5
FERMT3
TRPT1
FRMD8
RNASEH2C
NUDT22
SYVN1
LGALS12
DKFZp761E198
CDCA5
SLC22A9
BATF2
SLC22A12
HRASLS5
C11orf84
GPHA2
TIGD3
LRRN4CL
HNRNPUL2
LOC254100
EHBP1L1
SNX32
EML3
C11orf85
SLC25A45
NEAT1
CCDC88B
TTC9C
SLC22A24
RCOR2
TMEM179B
MALAT1
SLC22A25
SLC22A10
SPDYC
PCNXL3
MIR192
MIR194-2
SLC22A20
SNORA57
MIR612
METTL12
C11orf83
LOC100130348
MIR1237
MIR3654
MIR3680-1
ARL2-SNX15
HNRNPUL2-BSCL2
MIR4489
MIR4690

Genes in Wide Peak

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

Table S86. 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
FTH1P3
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
GPN1
MAPRE3
SLC4A1AP
EFR3B
MYT1L
LPIN1
PUM2
NTSR2
IFT172
SH3YL1
TRIB2
GRHL1
NRBP1
ITSN2
TRAPPC12
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
HS1BP3
FNDC4
COLEC11
CENPO
CCDC121
SMC6
NOL10
C2orf44
FAM49A
C2orf16
ZNF512
ABHD1
EPT1
RSAD2
CCDC164
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
FAM84A
GDF7
GPR113
UBXN2A
CYS1
KRTCAP3
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

Arm-level results

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

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.14 | 1.25 | 0.413 | 0.19 | 5.53 | 4.74e-08
1q | 1955 | 0.59 | 37.9 | 0 | 0.20 | 4.28 | 2.16e-05
2p | 924 | 0.07 | -6.33 | 1 | 0.09 | -5.01 | 1
2q | 1556 | 0.04 | -7.79 | 1 | 0.10 | -2.86 | 1
3p | 1062 | 0.06 | -6.61 | 1 | 0.18 | 2.42 | 0.0127
3q | 1139 | 0.14 | -1.09 | 1 | 0.08 | -5.37 | 1
4p | 489 | 0.05 | -7.87 | 1 | 0.24 | 5.02 | 7.29e-07
4q | 1049 | 0.04 | -7.95 | 1 | 0.19 | 2.76 | 0.00484
5p | 270 | 0.22 | 3.55 | 0.00094 | 0.15 | -1.37 | 1
5q | 1427 | 0.14 | -0.322 | 1 | 0.18 | 3.04 | 0.00209
6p | 1173 | 0.15 | 0.115 | 1 | 0.19 | 3.13 | 0.00163
6q | 839 | 0.10 | -4.11 | 1 | 0.25 | 6.84 | 1.54e-11
7p | 641 | 0.20 | 2.62 | 0.0191 | 0.11 | -3.92 | 1
7q | 1277 | 0.16 | 0.938 | 0.617 | 0.12 | -2.12 | 1
8p | 580 | 0.25 | 4.76 | 5.51e-06 | 0.53 | 25.9 | 0
8q | 859 | 0.50 | 25.1 | 0 | 0.21 | 3.16 | 0.00155
9p | 422 | 0.10 | -4.67 | 1 | 0.26 | 6.32 | 4.72e-10
9q | 1113 | 0.07 | -5.64 | 1 | 0.20 | 3.85 | 0.000126
10p | 409 | 0.16 | -0.705 | 1 | 0.14 | -1.87 | 1
10q | 1268 | 0.05 | -7.32 | 1 | 0.16 | 1.35 | 0.137
11p | 862 | 0.07 | -5.97 | 1 | 0.26 | 7.79 | 1.4e-14
11q | 1515 | 0.07 | -4.53 | 1 | 0.37 | 18.2 | 0
12p | 575 | 0.14 | -1.62 | 1 | 0.14 | -1.96 | 1
12q | 1447 | 0.12 | -1.98 | 1 | 0.10 | -3.27 | 1
13q | 654 | 0.08 | -5.39 | 1 | 0.34 | 12.9 | 0
14q | 1341 | 0.10 | -3.24 | 1 | 0.19 | 3.63 | 0.000296
15q | 1355 | 0.06 | -6.18 | 1 | 0.21 | 4.99 | 7.9e-07
16p | 872 | 0.32 | 11 | 0 | 0.36 | 13.7 | 0
16q | 702 | 0.11 | -2.96 | 1 | 0.54 | 28.2 | 0
17p | 683 | 0.09 | -4.07 | 1 | 0.51 | 26.4 | 0
17q | 1592 | 0.22 | 5.79 | 2.29e-08 | 0.26 | 9.52 | 0
18p | 143 | 0.11 | -4.3 | 1 | 0.25 | 4.9 | 1.15e-06
18q | 446 | 0.10 | -4.55 | 1 | 0.25 | 5.54 | 4.74e-08
19p | 995 | 0.09 | -4.76 | 1 | 0.12 | -2.73 | 1
19q | 1709 | 0.11 | -1.8 | 1 | 0.10 | -2.93 | 1
20p | 355 | 0.27 | 6.94 | 1.56e-11 | 0.11 | -4.14 | 1
20q | 753 | 0.32 | 12 | 0 | 0.06 | -6.64 | 1
21q | 509 | 0.14 | -2.15 | 1 | 0.12 | -3.5 | 1
22q | 921 | 0.06 | -6 | 1 | 0.36 | 15.7 | 0

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.

- 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/BRCA/1444330/2.GDAC_MergeDataFiles.Finished/BRCA.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 = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 824 Input Tumor Samples.

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

Figure 3. Segmented copy number profiles in the input data

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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