SNP6 Copy number analysis (GISTIC2)
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1T152H9
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 2.0.21 (Firehose task version: 127).

Summary

There were 522 tumor samples used in this analysis: 25 significant arm-level results, 29 significant focal amplifications, and 48 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 - 29 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 2.3839e-248 2.6066e-248 chr11:70075367-70220793 2
3q26.33 6.0162e-58 6.0162e-58 chr3:180888831-182802873 7
7p11.2 4.3243e-52 5.6035e-52 chr7:55022239-55373435 1
8q24.21 4.8156e-22 2.4104e-20 chr8:128198180-128493073 3
8p11.23 1.1503e-18 1.5883e-18 chr8:38159555-38270604 3
9p13.3 1.2396e-13 1.6494e-11 chr9:35438295-35855885 23
12q15 5.8118e-11 5.8118e-11 chr12:69215691-70383849 12
7q21.3 2.5921e-10 3.1556e-10 chr7:92068616-93777248 18
13q22.1 1.3369e-11 3.7361e-10 chr13:73859972-74031430 1
2q31.2 3.4147e-08 2.3838e-07 chr2:178072322-178219955 4
18p11.31 6.4312e-06 6.4312e-06 chr18:2941451-3654358 10
18q11.2 6.8933e-06 6.8933e-06 chr18:20237158-20990466 6
20q11.22 9.3622e-06 9.3622e-06 chr20:32089242-32916296 13
8q11.21 9.672e-09 3.9444e-05 chr8:49265786-49937472 2
5p15.33 7.4376e-05 7.4376e-05 chr5:1-1415403 25
17q12 0.00011601 0.00011601 chr17:37848534-37877201 2
6p12.1 0.00023649 0.00036964 chr6:53892031-54341223 2
2q11.2 5.0848e-05 0.00079694 chr2:97503963-97610929 4
9p24.1 1.4719e-10 0.00079694 chr9:4722319-6000194 15
11p13 0.00057236 0.0010909 chr11:34243783-36497593 17
12p13.33 0.0014887 0.0014887 chr12:1-1064437 11
Xq28 0.0087469 0.0087469 chrX:151490900-155270560 109
9p23 2.3785e-08 0.01278 chr9:13397807-14543657 2
6q12 0.03699 0.053741 chr6:64257063-64567239 3
13q34 0.002985 0.079616 chr13:109294458-115169878 52
15q26.3 0.12657 0.12657 chr15:95914475-102531392 46
19p13.2 0.12657 0.12657 chr19:7296453-7398264 0 [INSR]
20p12.2 0.17855 0.17855 chr20:10061633-11277459 6
9q34.3 0.1949 0.1949 chr9:107506123-141213431 452
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: Cancer Gene Census[7].

Genes
MIR548K
PPFIA1
Genes in Wide Peak

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

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

Genes
SOX2
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
ATP11B
MCCC1
Genes in Wide Peak

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

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

Genes
EGFR
Genes in Wide Peak

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

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

Genes
POU5F1B
CASC8
CCAT1
Genes in Wide Peak

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

Table S5.  Genes in bold are cancer genes as defined by The Sanger Institute: 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 9p13.3.

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

Genes
RGP1
RN7SL22P
RMRP
MIR4667
CA9
CD72
NPR2
TESK1
TLN1
TPM2
RUSC2
CREB3
SPAG8
SIT1
TMEM8B
GBA2
HINT2
ARHGEF39
ATP8B5P
CCDC107
FAM221B
MSMP
FAM166B
Genes in Wide Peak

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

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

Genes
MDM2
MYRFL
RN7SL804P
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
RAB3IP
BEST3
LRRC10
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.3.

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

Genes
CDK6
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
CALCR
GNGT1
PEX1
TFPI2
BET1
SAMD9
CCDC132
RBM48
SAMD9L
HEPACAM2
FAM133B
MIR4652
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q22.1.

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

Genes
LINC00393
Genes in Wide Peak

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

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

Genes
NFE2L2
snoU13|ENSG00000238295.1
MIR3128
HNRNPA3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.31.

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

Genes
snoU13|ENSG00000238445.1
RN7SL39P
snoU13|ENSG00000238863.1
SNORA70|ENSG00000252258.1
TGIF1
MYOM1
DLGAP1
LPIN2
MYL12A
MYL12B
Genes in Wide Peak

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

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

Genes
RN7SL745P
snoU13|ENSG00000238537.1
RBBP8
TMEM241
CABLES1
MIR4741
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.22.

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

Genes
AHCY
ASIP
E2F1
EIF2S2
CBFA2T2
PXMP4
RALY
NECAB3
ZNF341
C20orf144
CHMP4B
ACTL10
MIR4755
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.21.

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

Genes
SNAI2
EFCAB1
Genes in Wide Peak

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

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

Genes
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
SLC6A19
SLC6A18
MIR4457
MIR4456
Genes in Wide Peak

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

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

Genes
ERBB2
PGAP3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p12.1.

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

Genes
TINAG
MLIP
Genes in Wide Peak

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

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

Genes
ANKRD39
FAM178B
SEMA4C
ANKRD23
Genes in Wide Peak

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

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

Genes
JAK2
CD274
MLANA
snoU13|ENSG00000238654.1
INSL4
AK3
RLN1
RLN2
RCL1
INSL6
PLGRKT
KIAA1432
ERMP1
PDCD1LG2
KIAA2026
Genes in Wide Peak

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

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

Genes
COMMD9
MIR3973
TRIM44
MIR1343
EHF
CAT
CD44
ELF5
SLC1A2
PDHX
FJX1
ABTB2
PAMR1
APIP
PRR5L
LDLRAD3
LINC00610
Genes in Wide Peak

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

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

Genes
KDM5A
RNU4ATAC16P
FAM138D
NINJ2
RAD52
SLC6A12
SLC6A13
WNK1
CCDC77
B4GALNT3
IQSEC3
Genes in Wide Peak

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

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

Genes
MTCP1
WASH6P|ENSG00000182484.10
WASIR1|ENSG00000185203.7
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36|ENSG00000251846.1
RN7SL687P
RN7SL667P
snoU13|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
GABRA3
GDI1
HCFC1
IDH3G
IL9R|ENSG00000124334.12
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7|ENSG00000124333.10
TAZ
VBP1
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SPRY3|ENSG00000168939.6
ZNF275
TREX2
SRPK3
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
PDZD4
FAM3A
BRCC3
H2AFB3
FAM58A
PNMA5
RAB39B
GAB3
PNCK
ZFP92
CSAG1
CTAG1A
H2AFB2
H2AFB1
OPN1MW2
MIR767
SMIM9
CMC4
PNMA6C
MIR718
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p23.

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

Genes
NFIB
LINC00583
Genes in Wide Peak

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

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

Genes
PTP4A1
PHF3
EYS
Genes in Wide Peak

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

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

Genes
MIR548AR
LINC00565
LINC00452
LINC00453
LINC00454
GRK1
DCUN1D2
LINC00403
LINC00404
SNORD44
LINC00354
LINC00346
LINC00567
snoU13|ENSG00000238629.1
RN7SL783P
RN7SKP10
LINC00676
ATP4B
COL4A1
COL4A2
F7
F10
GAS6
ING1
LAMP1
SOX1
TFDP1
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
TUBGCP3
RASA3
MYO16
ATP11A
MCF2L
TMCO3
ANKRD10
RAB20
CARKD
PCID2
UPF3A
CARS2
GRTP1
ADPRHL1
TEX29
SPACA7
CHAMP1
TMEM255B
C13orf35
MIR4502
Genes in Wide Peak

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

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

Genes
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
NR2F2
CHSY1
SYNM
OR4F4
VIMP
TTC23
LRRK1
TM2D3
ARRDC4
LINC00923
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
SPATA8
ADAMTS17
DNM1P46
CERS3
FAM169B
SPATA41
OR4F6
OR4F15
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p12.2.

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

Genes
C20orf187
JAG1
JAG1
SNAP25
MKKS
SLX4IP
Genes in Wide Peak

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

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

Genes
ABL1
NOTCH1
RALGDS
SET
TAL2
TSC1
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13|ENSG00000238530.1
MIR455
COL27A1
FKBP15
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
ABCA1
ABCA2
AK1
ALAD
AMBP
ASS1
C5
C8G
CACNA1B
CCBL1
ENTPD2
CDK9
CEL
COL5A1
SLC31A1
SLC31A2
CRAT
DBC1
DBH
SARDH
DNM1
TOR1A
LPAR1
MEGF9
ENDOG
ENG
STOM
FKTN
FCN1
FCN2
FPGS
NR5A1
FUT7
NR6A1
GLE1
GNG10
GOLGA1
GOLGA2
RAPGEF1
GRIN1
GSN
HSPA5
TNC
LCN1
LCN2
LMX1B
MUSK
NDUFA8
ODF2
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP6C
PSMB7
PSMD5
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TLR4
TRAF1
TRAF2
TTF1
TXN
VAV2
ZFP37
ZNF79
LHX3
GFI1B
IKBKAP
SSNA1
EDF1
CTNNAL1
DPM2
FUBP3
PRPF4
KLF4
GTF3C5
LHX2
MED27
PTGES
RALGPS1
ADAMTSL2
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7A
SLC27A4
CNTRL
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
PTGR1
TRIM32
SETX
ZBTB43
PMPCA
ASTN2
KIAA0368
EXOSC2
NCS1
SLC44A1
ANGPTL2
NUP188
RABGAP1
TMEM245
CIZ1
DFNB31
NELFB
NIPSNAP3A
NSMF
GPSM1
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
TRUB2
ST6GALNAC4
NDOR1
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
RAB14
C9orf78
POLE3
FBXW5
RC3H2
EPB41L4B
TBC1D13
BSPRY
TOR4A
EXD3
FAM206A
TMEM38B
NIPSNAP3B
STRBP
RABL6
CDK5RAP2
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
SLC46A2
ZNF462
PRDM12
SUSD1
DDX31
FAM129B
C9orf16
MAPKAP1
EHMT1
SVEP1
PTGES2
AKNA
ARPC5L
HDHD3
AIF1L
UCK1
FSD1L
GARNL3
HSDL2
NTNG2
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
TMEM141
C9orf37
MVB12B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
MRRF
ARRDC1
DPH7
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
RNF183
NACC2
C9orf116
LCN8
PTRH1
PIP5KL1
OR1L8
OR1N2
OR1N1
SLC34A3
DAB2IP
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
ZNF483
C9orf84
KIAA1958
C9orf96
OLFML2A
QSOX2
C9orf91
NAIF1
CDC26
PHYHD1
MORN5
OR1L4
TXNDC8
C9orf43
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
FAM78A
GPR144
QRFP
OR1J1
OR1B1
GLT6D1
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR147A
MIR181A2
MIR181B2
MIR199B
C9orf173
NRARP
DNAJC25
MIR600HG
MIR602
RNF208
CARD9
MIR3154
MIR3689A
MIR3911
MIR3927
MIR3689B
MIR3689D1
MIR3689F
MIR3960
MIR4674
MIR4478
MIR3689C
MIR3689D2
MIR3689E
MIR548AW

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 - 48 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 6.6634e-264 6.4674e-241 chr9:21931610-22003135 2
8p23.2 2.2608e-98 2.2608e-98 chr8:3548028-4251283 2
4q35.2 5.4589e-35 1.7797e-32 chr4:187475875-191154276 16
2q22.1 9.2957e-42 2.047e-28 chr2:140708948-143637838 2
18q23 8.5261e-28 2.2321e-23 chr18:74301825-78077248 18
11q23.1 1.5927e-21 1.5793e-21 chr11:109298128-112835143 39
19p13.3 1.7709e-19 1.6836e-19 chr19:1060134-1272039 8
7q36.1 3.2498e-22 5.8875e-19 chr7:148117946-153767963 78
1p13.2 4.7599e-19 1.2507e-17 chr1:112530734-149881397 152
13q12.11 3.1303e-23 2.3106e-15 chr13:1-23727991 46
5q12.1 6.5965e-18 7.1304e-15 chr5:58151172-59818245 3
9p23 1.416e-39 1.3799e-14 chr9:8885227-12687261 2
10p11.21 1.7994e-14 9.3008e-14 chr10:34059131-35328087 1
2q36.2 4.6565e-25 9.5632e-14 chr2:215261791-243199373 281
2q21.2 9.9549e-30 3.0622e-12 chr2:133423352-134161285 1
Xq21.33 2.251e-11 2.262e-11 chrX:96134519-96599519 2
10q23.31 7.2816e-11 7.0036e-11 chr10:89617158-90034038 3
Xp21.3 1.1594e-10 3.7515e-10 chrX:28999803-29639108 2
13q14.2 4.1405e-17 1.9052e-09 chr13:48666829-49563699 7
3p12.1 1.011e-10 6.3345e-08 chr3:78209676-85012839 6
17q25.3 2.6665e-06 2.9732e-06 chr17:80698053-80902410 2
16q23.3 4.7996e-09 7.625e-06 chr16:82485689-83542835 3
4q22.1 1.3377e-08 1.1391e-05 chr4:91271445-93240505 1
4p15.2 1.5047e-05 1.5047e-05 chr4:20726855-22351071 1
1p36.21 1.6161e-06 3.7188e-05 chr1:1-27864255 459
21q22.3 0.00032453 0.00031208 chr21:41298805-43485528 20
11p15.5 0.00044692 0.0004485 chr11:1-6518784 190
7q31.1 2.1321e-09 0.00061067 chr7:108535383-111366370 4
5q35.3 0.00010942 0.0009079 chr5:176521457-176731866 2
6p25.3 0.0012217 0.0012446 chr6:1-12718155 86
9q34.3 0.0012426 0.0012446 chr9:139376600-139456211 4
14q11.2 0.0073065 0.01372 chr14:1-28735041 268
16q23.1 1.6098e-05 0.013993 chr16:78098006-79299841 3
14q32.32 0.0049674 0.014853 chr14:81998189-107349540 282
Xp22.2 0.010192 0.029605 chrX:9751329-10420184 3
3p14.2 1.2944e-06 0.035583 chr3:59705136-62306281 4
1q44 0.043479 0.042921 chr1:245290228-247047608 7
4q21.3 1.7216e-05 0.046702 chr4:86921750-87746054 4
9q21.11 2.7424e-07 0.059687 chr9:38619152-71152237 57
10p15.3 0.029605 0.08634 chr10:1-5197880 32
15q15.1 0.10249 0.10509 chr15:1-57887323 361
19q13.43 0.11016 0.11102 chr19:57100222-59128983 76
17p11.2 0.13976 0.15897 chr17:20330075-25626166 18
3p26.2 0.023934 0.17511 chr3:3220635-4535479 3
5q15 1.2501e-09 0.18126 chr5:92929447-93956985 4
18q21.2 1.9168e-11 0.19906 chr18:48255169-67073349 77
12q24.33 0.22797 0.22514 chr12:71029284-133851895 489
3p24.1 0.00093669 0.31298 chr3:28799677-30767809 3
Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53
Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251
Genes in Wide Peak

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

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
FAT1
FRG1
ZFP42
TRIML2
TRIML1
DUX4L4
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B
Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
MBP
NFATC1
ZNF236
CTDP1
TXNL4A
ADNP2
KCNG2
PQLC1
PARD6G
ATP9B
HSBP1L1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.1.

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

Genes
SDHD
POU2AF1
SDHD
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
CRYAB
DLAT
FDX1
IL18
PPP2R1B
PTS
RDX
TIMM8B
BTG4
C11orf57
TEX12
ARHGAP20
C11orf1
BCO2
DIXDC1
ZC3H12C
FDXACB1
C11orf52
C11orf93
PIH1D2
LAYN
C11orf53
C11orf92
C11orf88
MIR34B
MIR34C
MIR4491
Genes in Wide Peak

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

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

Genes
STK11
POLR2E
ATP5D
GPX4
SBNO2
HMHA1
MIDN
C19orf26
Genes in Wide Peak

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

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

Genes
EZH2
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
AOC1
GBX1
KCNH2
NOS3
RARRES2
RHEB
SLC4A2
SMARCD3
XRCC2
ZNF212
ZNF282
CUL1
ASIC3
PDIA4
ABCF2
FASTK
ABCB8
GIMAP2
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ZNF398
KMT2C
GALNT11
LRRC61
ZNF767
TMUB1
KRBA1
ZBED6CL
AGAP3
ZNF786
ASB10
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
GALNTL5
GIMAP7
ZNF467
GIMAP1
C7orf33
ZNF775
ATG9B
WDR86
GIMAP6
ZNF862
ACTR3C
ZNF783
Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
LINC00622
snoU13|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
AMPD1
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD58
FCGR1A
FMO5
GJA5
GJA8
HMGCS2
HSD3B1
HSD3B2
IGSF3
MOV10
NGF
NHLH2
PDZK1
PRKAB2
PTGFRN
SLC16A1
SYCP1
TBX15
TSHB
CSDE1
HIST2H2AC
HIST2H2BE
HIST2H4A
ITGA10
PEX11B
CD101
CHD1L
RBM8A
TSPAN2
BCAS2
WARS2
PIAS3
POLR3C
TXNIP
AP4B1
PHTF1
ADAM30
CD160
NBPF14
PTPN22
PHGDH
BOLA1
HAO2
GPR89B
RSBN1
GDAP2
FAM46C
ST7L
SLC22A15
CTTNBP2NL
OLFML3
DCLRE1B
VTCN1
SIKE1
TRIM45
VANGL1
REG4
POLR3GL
ZNF697
MAB21L3
LIX1L
SYT6
HFE2
ANKRD35
NBPF12
PPIAL4A
NBPF11
SPAG17
HIPK1
MAGI3
FAM19A3
NBPF16
ANKRD34A
HIST2H2AB
PPM1J
C1orf137
NOTCH2NL
NBPF9
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
NBPF20
MIR320B1
Genes in Wide Peak

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

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

Genes
RNY3P4
LINC00621
SNORD36|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27|ENSG00000252128.1
snoU13|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
FGF9
GJA3
GJB2
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
LATS2
CRYL1
IL17D
MPHOSPH8
XPO4
MRP63
TPTE2
N6AMT2
SKA3
MICU2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

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

Genes
FKSG52
MIR582
PDE4D
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
RN7SL5P
SNORD27|ENSG00000251699.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

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

Genes
PARD3
Genes in Wide Peak

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

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

Genes
ACSL3
ATIC
PAX3
FEV
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
snoU13|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
SNORD82
SNORD20
SNORA75|ENSG00000206885.1
NCL
MIR4777
RN7SL834P
RNY4P19
RN7SKP283
SNORD112|ENSG00000251801.1
SNORA25|ENSG00000272237.1
RNA5SP121
SNORA48|ENSG00000212391.1
MIR4439
RN7SL807P
snoU13|ENSG00000238852.1
SGPP2
RN7SKP213
RN7SL764P
MIR3131
LINC00608
U3|ENSG00000252805.1
RN7SKP38
VIL1
MIR26B
snoU13|ENSG00000238736.1
snoU13|ENSG00000238428.1
CXCR2P1
DIRC3
RN7SKP43
RNA5SP120
RPL37A
MREG
LINC00607
snoU13|ENSG00000238663.1
SNORA70|ENSG00000207274.1
VWC2L
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
INHA
INPP5D
IRS1
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
NMUR1
STK25
CAPN10
SP140
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ASIC4
DOCK10
PECR
C2orf83
MFF
ACKR3
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
CCDC140
SLC23A3
GPBAR1
SLC16A14
LINC00471
DAW1
C2orf57
TIGD1
CCDC108
C2orf72
RUFY4
DUSP28
MROH2A
ESPNL
C2orf62
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
MIR375
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4268
MIR3132
MIR4269
MIR4786
MIR5001
MIR5702
MIR5703
Genes in Wide Peak

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

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

Genes
RN7SKP154
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
RN7SL74P
RPA4
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.3.

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

Genes
MIR4666B
RNA5SP500
Genes in Wide Peak

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

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

Genes
RB1
LINC00462
LINC00441
RCBTB2
ITM2B
LPAR6
CYSLTR2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.1.

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

Genes
LINC00971
RN7SL751P
RN7SKP61
GBE1
ROBO1
MIR3923
Genes in Wide Peak

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

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

Genes
TBCD
ZNF750
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
MIR3182
RN7SL134P
snoU13|ENSG00000238321.1
Genes in Wide Peak

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

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

Genes
RN7SKP248
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.2.

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

Genes
KCNIP4
Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18|ENSG00000252691.1
SCARNA17|ENSG00000252190.1
MAN1C1
snoU13|ENSG00000238889.1
SYF2
snoU13|ENSG00000238986.1
RN7SL857P
snoU13|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16|ENSG00000252404.1
RN7SL451P
SNORA77|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
MTOR
FUCA1
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RHCE
RHD
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
NR0B2
MMP23B
KCNAB2
FCN3
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
AUNIP
EFHD2
MMEL1
RSG1
MUL1
NOL9
LIN28A
LINC00115
MORN1
FAM110D
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
C1orf170
SYTL1
IGSF21
KIAA2013
THAP3
STPG1
UBXN11
FBXO44
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
C1orf234
OR4F29
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697
Genes in Wide Peak

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

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

Genes
TMPRSS2
SNORA3|ENSG00000251778.1
LINC00112
LINC00111
snoU13|ENSG00000252771.1
SNORA32|ENSG00000207503.1
FAM3B
LINC00323
SNORA51|ENSG00000207147.1
MIR4760
DSCAM
MX1
MX2
BACE2
C2CD2
ZBTB21
RIPK4
PRDM15
LINC00479
MIR3197
Genes in Wide Peak

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

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

Genes
CARS
HRAS
NUP98
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62|ENSG00000201980.1
OR51C1P
SNORA7|ENSG00000206976.1
snoU13|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
CNGA4
CTSD
DRD4
DUSP8
HBB
HBD
HBE1
HBG2
HPX
IGF2
INS
IRF7
KCNQ1
LSP1|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
RNH1
MRPL23
RRM1
SMPD1
TRIM21
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IFITM2
TRIM3
PKP3
SIRT3
OR52A1
ARFIP2
TIMM10B
PGAP2
TRPM5
UBQLN3
BET1L
CEND1
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
FAM160A2
TRIM5
SYT8
PRKCDBP
OSBPL5
LRRC56
MRGPRE
ART5
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR52W1
OR56A4
OR56A1
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
SCGB1C1
C11orf42
NLRP6
OR56B4
OR52B2
C11orf35
OR51F1
OR51V1
EFCAB4A
ANO9
B4GALNT4
OR52L1
OR52B6
PDDC1
MRGPRG
IFITM5
FAM99A
OR56B1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
MUC5B
MIR4298
MIR4686
MIR4687
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238922.1
FLJ00325
LRRN3
IMMP2L
Genes in Wide Peak

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

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

Genes
NSD1
RAB24
Genes in Wide Peak

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

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

Genes
IRF4
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CDYL
EEF1E1
ECI2
FARS2
RPP40
FAM50B
SLC35B3
NRN1
TMEM14C
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
SMIM13
SYCP2L
PXDC1
FAM217A
CAGE1
MYLK4
TUBB2B
PSMG4
C6orf201
PPP1R3G
TMEM170B
MIR4645
MIR5689
MIR5683
Genes in Wide Peak

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

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

Genes
NOTCH1
MIR4673
C9orf163
MIR4674
Genes in Wide Peak

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

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

Genes
CCNB1IP1
LINC00645
SNORD37|ENSG00000212270.1
TM9SF1
RNA5SP383
DHRS4L1
LINC00596
RN7SKP205
MIR208B
MIR208A
PABPN1
C14orf164
SNORA73|ENSG00000252114.1
SNORD41|ENSG00000212302.1
OR6J1
TRAC
TRAJ1
TRAJ2
TRAJ3
TRAJ4
TRAJ5
TRAJ6
TRAJ7
TRAJ8
TRAJ9
TRAJ10
TRAJ11
TRAJ12
TRAJ13
TRAJ14
TRAJ16
TRAJ17
TRAJ18
TRAJ19
TRAJ20
TRAJ21
TRAJ22
TRAJ23
TRAJ24
TRAJ25
TRAJ26
TRAJ27
TRAJ28
TRAJ29
TRAJ30
TRAJ31
TRAJ32
TRAJ33
TRAJ34
TRAJ35
TRAJ36
TRAJ37
TRAJ38
TRAJ39
TRAJ40
TRAJ41
TRAJ42
TRAJ43
TRAJ44
TRAJ45
TRAJ46
TRAJ47
TRAJ48
TRAJ49
TRAJ50
TRAJ52
TRAJ53
TRAJ54
TRAJ56
TRAJ57
TRAJ58
TRAJ59
TRAJ61
TRDV3
TRDC
TRDJ3
TRDJ2
TRDJ4
TRDJ1
TRDD3
TRDD2
TRDD1
TRDV2
TRAV41
TRAV40
TRAV39
TRAV36DV7
TRAV35
TRAV34
TRAV30
TRAV29DV5
TRAV27
TRAV25
TRAV24
TRDV1
TRAV23DV6
TRAV22
TRAV21
TRAV20
TRAV19
TRAV18
TRAV17
TRAV16
TRAV14DV4
TRAV10
TRAV7
TRAV6
TRAV5
TRAV4
TRAV3
TRAV2
RN7SL650P
SNORD8
SNORD9
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
OR4Q2
snoU13|ENSG00000238492.1
MED15P6
LINC00516
MED15P1
ANG
APEX1
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
NRL
OXA1L
PCK2
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TGM1
AP1G2
SLC7A7
CPNE6
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
SUPT16H
ACIN1
KHNYN
SLC7A8
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
SLC39A2
EMC9
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR4K1
IPO4
DCAF11
OR4K15
JPH4
RNASE7
RAB2B
AJUBA
ZFHX2
LRRC16B
PPP1R3E
TMEM55B
DHRS1
CMTM5
RNASE11
TPPP2
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
NOP9
ADCY4
TSSK4
DHRS4L2
RNASE10
OR6S1
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
TMEM253
CBLN3
MIR4307
MIR4707
Genes in Wide Peak

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

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

Genes
RNA5SP431
PIH1
WWOX
Genes in Wide Peak

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

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

Genes
AKT1
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
GALC
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
GPR68
DLK1
MTA1
RPS6KA5
BAG5
C14orf2
CDC42BPB
TCL1B
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
PTPN21
RCOR1
PACS2
PPP1R13B
FLRT2
KIF26A
TMEM251
GPR132
SERPINA10
EVL
GSKIP
CINP
ASB2
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
DDX24
UNC79
BEGAIN
PPP4R4
MOAP1
INF2
OTUB2
ZFYVE21
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
HHIPL1
C14orf142
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
TTC8
TC2N
SLC25A29
GSC
SERPINA12
PRIMA1
TTC7B
SYNE3
EML5
NUDT14
LINC00521
SERPINA11
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
SERPINA9
COX8C
ASPG
SERPINA13P
C14orf64
RTL1
TMEM179
C14orf180
MIR127
MIR136
MIR154
MIR203
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1197
MIR1193
MIR4309
MIR3173
MIR151B
MIR4710
MIR2392
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.2.

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

Genes
SHROOM2
CLCN4
WWC3
Genes in Wide Peak

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

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

Genes
FHIT
PTPRG
U3|ENSG00000212211.1
NPCDR1
Genes in Wide Peak

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

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

Genes
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
SCCPDH
KIF26B
TFB2M
SMYD3
CNST
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.3.

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

Genes
RN7SKP96
MAPK10
PTPN13
MIR4452
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.11.

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

Genes
CBWD3
PGM5P2
RNA5SP284
SNORA70|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
PGM5
ZNF658
SPATA31A7
CNTNAP3
ANKRD20A1
CBWD5
FOXD4L3
FOXD4L4
SPATA31A6
FAM74A4
ANKRD20A3
ANKRD20A2
FAM27A
SPATA31A2
SPATA31A4
CBWD6
SPATA31A1
FOXD4L6
FOXD4L5
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR4477A
Genes in Wide Peak

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

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

Genes
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
KLF6
AKR1C2
IDI1
PFKP
AKR1C3
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
AKR1E2
IDI2
LINC00200
PRR26
Genes in Wide Peak

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

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

Genes
BUB1B
TCF12
LINC00926
snoU13|ENSG00000239035.1
RN7SL568P
snoU13|ENSG00000238513.1
PYGO1
MIR628
RSL24D1
ONECUT1
MIR1266
U6|ENSG00000272337.1
RN7SL354P
RNA5SP395
U6|ENSG00000271819.1
RN7SL494P
RNA5SP394
FGF7
RN7SL307P
RN7SL577P
RN7SKP139
FKSG62
RN7SKP101
SNORD11|ENSG00000238819.1
SNORA41|ENSG00000207516.1
HMGN2P46
snoU13|ENSG00000238583.1
SLC30A4
SNORA11|ENSG00000261709.2
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13|ENSG00000238494.1
snoU13|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13|ENSG00000238564.1
THBS1
FAM98B
U3|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77|ENSG00000212415.1
snoU13|ENSG00000238342.1
RN7SL286P
RN7SL539P
GOLGA8O
U8|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18|ENSG00000206849.1
MIR211
RN7SL82P
U8|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
RNA5SP391
LINC00929
SNORA48|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64|ENSG00000270704.2
SNHG14
SNURF
snoU13|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13|ENSG00000239083.1
CHEK2P2
RN7SL584P
ACTC1
APBA2
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO5A
NDN
NEDD4
OCA2
PLCB2
MAPK6
RAB27A
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SPINT1
SRP14
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
EIF3J
SNAP23
HERC2
USP8
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
BCL2L10
RASGRP1
GNB5
ARPP19
SLC27A2
GPR176
CHP1
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
EID1
NPAP1
SERF2
TMEM87A
RPAP1
BLOC1S6
GREM1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
ZNF280D
TRPM7
PPP1R14D
MTMR10
ZNF770
HAUS2
RMDN3
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
EMC7
PAK6
DTWD1
CASC5
AVEN
STARD9
VPS18
SQRDL
ZNF106
RFX7
SPATA5L1
CHAC1
KATNBL1
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
C15orf43
C15orf65
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
FAM227B
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
SLC24A5
PRTG
GOLGA6L2
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
GLDN
FMN1
USP50
TEX9
C15orf52
TNFAIP8L3
GOLGA8EP
OR4M2
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
HERC2P9
GOLGA8B
EIF2AK4
UNC13C
CKMT1A
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
POTEB2
MIR1282
MIR4508
MIR4510
MIR4716
MIR4713
MIR4712
POTEB
Genes in Wide Peak

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

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

Genes
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
A1BG
PEG3
RPS5
AURKC
ZNF8
ZNF17
MZF1
ZNF132
ZNF135
ZNF154
UBE2M
TRIM28
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
SLC27A5
ZIM2
ZNF324
CHMP2A
ZNF544
ZNF586
ZNF416
ZNF446
VN1R1
ZNF304
USP29
ZSCAN18
RPL23AP79
ZNF329
ZNF419
ZNF552
ZNF671
ZNF606
ZBTB45
ZNF587
ZNF551
ZNF835
ZIM3
ZNF837
ZNF543
C19orf18
ZNF418
ZNF497
ZNF550
ZNF584
ZSCAN4
ZNF549
ZNF547
ZIK1
ZNF776
ZSCAN1
ZSCAN22
ZNF530
ZNF773
ZNF749
ZNF324B
ZNF772
ZNF587B
MIR4754
Genes in Wide Peak

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

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

Genes
MTND1P15
UBBP4
RN7SL426P
TMEM11
KRT16P3
NOS2P3
KCNJ12
MAP2K3
USP22
DHRS7B
CDRT15L2
C17orf103
FAM27L
LGALS9B
CCDC144NL
C17orf51
MTRNR2L1
MIR4522
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.2.

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

Genes
SETMAR
LRRN1
SUMF1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
FAM172A
POU5F2
KIAA0825
MIR2277
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
BCL2
MALT1
snoU13|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8|ENSG00000199713.1
RN7SL112P
SNORD28|ENSG00000252284.1
FECH
U3|ENSG00000212539.1
TXNL1
SNORA73|ENSG00000201816.1
RNA5SP459
SNORA37
DCC
snoU13|ENSG00000238885.1
RN7SL695P
ME2
CDH7
KDSR
GRP
LMAN1
SMAD4
MC4R
NARS
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
RAB27B
SERPINB3
SERPINB4
TCF4
SERPINB7
TNFRSF11A
MBD2
ONECUT2
VPS4B
POLI
PHLPP1
NEDD4L
WDR7
PIGN
CDH20
CDH19
RAX
ST8SIA3
MEX3C
TMX3
ZCCHC2
ZNF532
ELAC1
KIAA1468
CCDC102B
CCDC68
MRO
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
STARD6
CCBE1
C18orf54
LINC00305
DYNAP
BOD1L2
HMSD
CPLX4
MIR122
MIR4529
MIR5011
Genes in Wide Peak

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

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

Genes
BCL7A
BTG1
ALDH2
PTPN11
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13|ENSG00000238822.1
RN7SL534P
snoU13|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38|ENSG00000201042.1
RNA5SP374
HRK
MAP1LC3B2
LINC00173
MIR620
SNORD56|ENSG00000200112.1
RN7SL865P
SNORA27|ENSG00000252459.1
RN7SKP216
LHX5
RN7SKP71
MIR3657
ADAM1A
U7|ENSG00000272215.1
RNA5SP373
RN7SL387P
PPTC7
SNORD50|ENSG00000202335.1
RN7SL769P
RN7SL441P
RN7SKP250
RNA5SP372
MIR619
SNORA40|ENSG00000264043.2
FICD
RNA5SP371
SNORD74|ENSG00000200897.1
C12orf45
MIR3922
RNA5SP370
HCFC2
MIR3652
snoU13|ENSG00000238914.1
U8|ENSG00000212594.1
LINC00485
RN7SL793P
RNA5SP369
snoU13|ENSG00000238940.1
RNA5SP368
RNA5SP367
snoU13|ENSG00000238800.1
SLC5A8
snoU13|ENSG00000238748.1
RN7SL176P
RNA5SP366
SNORA53
RN7SL179P
SLC9A7P1
RMST
C12orf63
C12orf55
RN7SKP11
ELK3
RN7SL88P
SNRPF
PGAM1P5
KRT19P2
RN7SL483P
RN7SL330P
RN7SKP263
RN7SL630P
RN7SL737P
UBE2N
snoU13|ENSG00000239073.1
SNORD74|ENSG00000201502.1
snoU13|ENSG00000238361.1
snoU13|ENSG00000238865.1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
U8|ENSG00000201809.1
RAB21
SNORA17|ENSG00000212461.1
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PTPRR
PXMP2
PXN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
RAB35
KERA
KRR1
PRDM4
CIT
PWP1
NUDT4
FZD10
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
UTP20
MRPL42
IFT81
CCDC59
FAM216A
TRHDE
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SVOP
STAB2
VEZT
GOLGA2B
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
METTL25
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
RNFT2
FAM222A
C12orf52
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
CCDC64
SDSL
OSBPL8
IQCD
DEPDC4
CCDC38
TMEM132D
SLC15A4
TPH2
NEDD1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
RAD9B
FAM109A
TMTC2
TMTC3
C12orf50
ALDH1L2
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
CCER1
SLC17A8
LRRC43
TCP11L2
C12orf79
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
GAS2L3
MYO1H
HECTD4
KSR2
DDX51
MMAB
HCAR2
TMEM119
C12orf74
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
C12orf76
MIR135A2
PLEKHG7
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
C12orf73
ZNF605
MIR1251
MIR4303
MIR3685
MIR3908
MIR4495
MIR4419B
MIR4700
MIR4497
MIR5188
MIR5700
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p24.1.

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

Genes
U3|ENSG00000199927.1
TGFBR2
RBMS3
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 25 significant results found. The significance cutoff is at Q value=0.25.

Arm # Genes Amp Frequency Amp Z score Amp Q value Del Frequency Del Z score Del Q value
1p 1300 0.14 -0.383 1 0.14 0.0763 0.853
1q 1195 0.24 5.26 4.22e-07 0.11 -2.44 1
2p 624 0.19 -1.55 1 0.09 -6.56 1
2q 967 0.15 -1.6 1 0.11 -4.06 1
3p 644 0.17 -1.42 1 0.71 26.4 0
3q 733 0.50 14.6 0 0.35 6.16 1.58e-09
4p 289 0.11 -6.21 1 0.41 7.81 1.65e-14
4q 670 0.09 -5.69 1 0.32 5.47 8.02e-08
5p 183 0.38 5.02 1.29e-06 0.25 -0.918 1
5q 905 0.14 -2.13 1 0.39 11.2 0
6p 710 0.17 -1.95 1 0.17 -2.24 1
6q 556 0.13 -4.76 1 0.15 -3.76 1
7p 389 0.36 5.87 1.41e-08 0.11 -6.03 1
7q 783 0.25 2.85 0.00784 0.12 -3.96 1
8p 338 0.36 4.1 8.09e-05 0.58 15.3 0
8q 551 0.61 19.6 0 0.24 0.405 0.685
9p 301 0.28 1.18 0.341 0.45 9.42 0
9q 700 0.30 4.35 3.07e-05 0.25 2.14 0.0458
10p 253 0.10 -7.09 1 0.33 3.58 0.000536
10q 738 0.08 -6.26 1 0.23 1.47 0.177
11p 509 0.16 -3.12 1 0.32 4.21 4.22e-05
11q 975 0.19 0.699 0.646 0.39 11.5 0
12p 339 0.29 2.18 0.0484 0.12 -6.12 1
12q 904 0.18 -0.681 1 0.08 -5.5 1
13q 560 0.16 -3.17 1 0.36 6.99 6.83e-12
14q 938 0.32 7.81 2.78e-14 0.16 -1.24 1
15q 810 0.17 -1.44 1 0.23 1.74 0.11
16p 559 0.23 -0.0114 1 0.16 -3.26 1
16q 455 0.24 0.0365 1 0.20 -1.89 1
17p 415 0.15 -4.33 1 0.24 0.0243 0.853
17q 972 0.17 -0.561 1 0.09 -4.97 1
18p 104 0.26 -0.709 1 0.29 0.645 0.573
18q 275 0.12 -5.32 1 0.47 10.7 0
19p 681 0.12 -4.43 1 0.22 0.341 0.698
19q 935 0.17 -0.875 1 0.20 1.13 0.303
20p 234 0.39 6.33 9.97e-10 0.16 -4.46 1
20q 448 0.39 7.94 1.33e-14 0.12 -5.2 1
21q 258 0.10 -6.59 1 0.38 5.88 8.31e-09
22q 564 0.25 1.24 0.331 0.18 -2.09 1
Xq 668 0.18 -1.8 1 0.23 0.606 0.573
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

  • Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

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/HNSC-TP/11447292/GDAC_MergeDataFiles_11449966/HNSC-TP.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_GENCODE_v18_20140127.mat

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

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 522 Input Tumor Samples.

Tumor Sample Names
TCGA-4P-AA8J-01A-11D-A390-01
TCGA-BA-4074-01A-01D-1432-01
TCGA-BA-4075-01A-01D-1432-01
TCGA-BA-4076-01A-01D-1432-01
TCGA-BA-4077-01B-01D-1432-01
TCGA-BA-4078-01A-01D-1432-01
TCGA-BA-5149-01A-01D-1510-01
TCGA-BA-5151-01A-01D-1432-01
TCGA-BA-5152-01A-02D-1869-01
TCGA-BA-5153-01A-01D-1432-01

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)
[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)
[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)