SNP6 Copy number analysis (GISTIC2)
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1PC31D0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1PC31D0
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 2.0.22 (Firehose task version: 140).

Summary

There were 48 tumor samples used in this analysis: 12 significant arm-level results, 14 significant focal amplifications, and 27 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 - 14 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
--- | --- | --- | --- | ---
2p16.1 | 8.6529e-15 | 8.6529e-15 | chr2:61104986-61147244 | 1
1q24.2 | 0.00010764 | 0.00010764 | chr1:168767360-169269008 | 4
3q29 | 0.0045341 | 0.013525 | chr3:195032857-196137763 | 21
19q13.43 | 0.016376 | 0.016376 | chr19:55709593-57052302 | 53
8q24.23 | 0.017571 | 0.017571 | chr8:113190838-146364022 | 233
Xq27.3 | 0.022692 | 0.022692 | chrX:144689696-144696094 | 0 [SLITRK2]
3q27.3 | 0.0045371 | 0.034376 | chr3:187616647-187814476 | 0 [LPP]
12q21.1 | 0.082459 | 0.082459 | chr12:51032700-78338797 | 331
5p13.1 | 0.10188 | 0.10188 | chr5:38366134-39217225 | 6
18q21.2 | 0.12623 | 0.12623 | chr18:48582939-78077248 | 118
14q32.31 | 0.16195 | 0.16195 | chr14:100781012-101872298 | 72
7q21.3 | 0.20555 | 0.20555 | chr7:68184133-126346892 | 427
7p22.3 | 0.21389 | 0.21389 | chr7:1-4925011 | 46
16p12.2 | 0.23142 | 0.23142 | chr16:23898225-23998888 | 1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p16.1.

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

Genes
REL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q24.2.

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

Genes
RNA5SP66
LINC00970
ATP1B1
NME7

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q29.

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

Genes
TFRC
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
APOD
MUC4
PCYT1A
PPP1R2
TNK2
ACAP2
TM4SF19
ZDHHC19
SLC51A
MUC20
TCTEX1D2
LINC00885
MIR570

Genes in Wide Peak

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

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

Genes
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
IL11
PTPRH
RPL28
U2AF2
PPP6R1
HSPBP1
UBE2S
EPN1
ZNF580
ZNF581
ZNF444
NAT14
ZNF471
ZNF667
ZSCAN5A
ISOC2
BRSK1
SUV420H2
FIZ1
GALP
ZNF628
COX6B2
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
TMEM190
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
ZNF579
NLRP11
TMEM86B
SSC5D
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
SBK2
SHISA7
SGK110
ZNF865

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.23.

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

Genes
EXT1
MYC
RECQL4
ZNF252P
RN7SL395P
C8orf82
MIR1234
MIR939
TMEM249
DGAT1
SCXA
SCXB
MIR661
EPPK1
MIR937
CCDC166
7SK|ENSG00000254144.2
ZNF696
ZFP41
LY6K
JRK
ARC
LINC00051
SNORD5|ENSG00000238854.1
PTP4A3
RNA5SP278
MIR151A
CASC7
C8orf17
SNORA25|ENSG00000251744.1
SNORA40|ENSG00000212273.1
WISP1
HPYR1
OC90
SNORA72|ENSG00000252158.1
SNORA12|ENSG00000212342.1
SNORA25|ENSG00000200075.1
CCDC26
RN7SKP206
LINC00977
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
LINC00861
RN7SL590P
RN7SL329P
LINC00964
RNF139
TMEM65
RN7SKP155
snoU13|ENSG00000238422.1
U3|ENSG00000221461.1
RNY4P5
snoU13|ENSG00000238901.1
HAS2
RNA5SP277
RN7SL396P
RN7SKP153
SNORA32|ENSG00000206776.1
COLEC10
SNORA31|ENSG00000252852.1
RN7SL826P
RN7SL228P
AARD
EIF3H
RNA5SP276
LINC00536
snoU13|ENSG00000238656.1
ADCY8
ANXA13
BAI1
CYC1
CYP11B1
CYP11B2
EEF1D
GLI4
GML
GPR20
GPT
GRINA
HSF1
KCNQ3
LY6E
LY6H
NDUFB9
TONSL
NOV
TNFRSF11B
ENPP2
PLEC
PTK2
RAD21
RPL8
ST3GAL1
SLA
SNTB1
SQLE
TAF2
TG
TRPS1
TSTA3
COL14A1
ZNF7
ZNF16
PSCA
LY6D
GPAA1
FOXH1
LRRC14
MTSS1
ZNF623
KIAA0196
HHLA1
TRIB1
NDRG1
KHDRBS3
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
BOP1
SCRIB
LRRC6
FBXL6
OPLAH
MTBP
AGO2
COMMD5
MRPL13
ATAD2
CPSF1
CYHR1
ASAP1
FAM135B
PHF20L1
VPS28
FAM203A
KCNK9
THEM6
FAM49B
CHRAC1
EXOSC4
TRMT12
WDYHV1
SLC39A4
GSDMC
SLURP1
SLC45A4
ZFAT
ZNF250
DEPTOR
PYCRL
C8orf33
LYNX1
DSCC1
DERL1
SLC52A2
GSDMD
ARHGAP39
ZNF34
SHARPIN
SCRT1
TRAPPC9
TATDN1
MAF1
UTP23
PARP10
C8orf76
TIGD5
FAM83A
PPP1R16A
MED30
ZNF251
KIFC2
NAPRT1
TBC1D31
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
TOP1MT
ZNF572
LYPD2
TMEM71
FAM84B
FAM91A1
SLC30A8
COL22A1
ADCK5
TSNARE1
MAPK15
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
SPATC1
MROH5
MAFA
SAMD12
MIR30B
MIR30D
LRRC24
MROH6
FER1L6
MROH1
FAM203B
OC90
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3610
MIR4662B
MIR4663
MIR4664
MIR5194

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q21.1.

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

Genes
ATF1
CDK4
DDIT3
HOXC11
HOXC13
MDM2
NACA
HMGA2
WIF1
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
U8|ENSG00000201809.1
RAB21
SNORA17|ENSG00000212461.1
MYRFL
RN7SL804P
SLC35E3
SNORA70G
DYRK2
CAND1
snoU13|ENSG00000238528.1
RN7SKP166
TMBIM4
RNA5SP362
RPSAP52
RNU6ATAC42P
snoU13|ENSG00000238592.1
MIR548C
SNORD83
XPOT
snoU13|ENSG00000238440.1
RPS11P6
AVPR1A
LDHAL6CP
snoU13|ENSG00000238475.1
SNORD112|ENSG00000252883.1
SNORA19|ENSG00000251822.1
RN7SKP65
MIR26A2
snoU13|ENSG00000238436.1
RN7SL312P
MIR1228
HBCBP
RDH16
SNORA48|ENSG00000212383.1
RN7SL809P
SNORD59A
RBMS2
RNF41
RN7SL770P
MMP19
TMEM198B
ORMDL2
GLYCAM1
RN7SL744P
MIR148B
RN7SL390P
MIR615
HOXC8
HOTAIR
HOXC12
RN7SKP289
SNORD81|ENSG00000223213.1
KRT121P
LINC00592
C12orf80
OR7E47P
POU6F1
U6|ENSG00000272028.1
HIGD1C
RN7SL519P
ACVR1B
ACVRL1
AMHR2
APOF
ATP5B
ATP5G2
CD63
CDK2
CPM
CS
CSRP2
CYP27B1
DGKA
EIF4B
CELA1
ERBB3
B4GALNT1
BLOC1S1
GLI1
GNS
NCKAP1L
NR4A1
HNRNPA1
HOXC4
HOXC5
HOXC6
HOXC9
HOXC10
IFNG
IGFBP6
INHBC
ITGA5
ITGA7
ITGB7
KCNC2
KIF5A
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LRP1
LYZ
MARS
METTL1
MIP
MYL6
MYO1A
NAB2
NAP1L1
NFE2
CNOT2
SLC11A2
PA2G4
PCBP2
PDE1B
PFDN5
PPP1R1A
PRIM1
PTPRB
PTPRR
RAB5B
RAP1B
RARG
RDH5
RPL41
RPS26
TSPAN31
SCN8A
SHMT2
PMEL
SMARCC2
SP1
STAT2
STAT6
SUOX
TAC3
TARBP2
TFCP2
TSPAN8
MAP3K12
AAAS
YEATS4
SOAT2
LGR5
NPFF
HSD17B6
TIMELESS
KRT75
SLC16A7
SLC4A8
ESPL1
DAZAP2
TESPA1
ZBTB39
PAN2
USP15
TSFM
CTDSP2
GDF11
TMEM5
CNPY2
DCTN2
CCT2
AVIL
PTGES3
FRS2
OS9
ATF7
CPSF6
KRR1
BAZ2A
IRAK3
GALNT6
NXPH4
GPR182
COPZ1
R3HDM2
MON2
TMEM194A
TBC1D30
ESYT1
TENC1
ZDHHC17
GRIP1
CBX5
SMUG1
LEMD3
METTL7A
LETMD1
METTL21B
ZNF385A
GLS2
KCNMB4
TBK1
TRHDE
IL22
KRT76
CSAD
BIN2
IL23A
TMBIM4
GPR84
PRR13
TMEM19
IL26
MDM1
NDUFA4L2
NUP107
SMAGP
PPM1H
SRGAP1
DIP2B
CALCOCO1
NEUROD4
C12orf10
C12orf44
ARHGAP9
IKZF4
TBC1D15
SLC26A10
NABP2
BBS10
PIP4K2C
CSRNP2
THAP2
INHBE
LLPH
WIBG
SARNP
CAPS2
ZC3H10
SPRYD3
MFSD5
DNAJC14
NAV3
LACRT
XRCC6BP1
HELB
MARCH9
COQ10A
KRT71
MBD6
OSBPL8
ARHGEF25
C12orf56
AGAP2
DCD
RAB3IP
MUCL1
OR2AP1
OR10P1
SDR9C7
LRIG3
TPH2
SP7
GTSF1
OR10A7
KRT74
MYL6B
KRT72
GLIPR1L2
BEST3
E2F7
KRT80
C12orf66
GRASP
KRT78
DTX3
METTL7B
ZFC3H1
STAC3
MSRB3
OR6C74
OR6C3
GLIPR1L1
ZNF740
RASSF3
OR6C6
ANKRD52
SLC39A5
SPRYD4
C12orf61
DPY19L2
TMPRSS12
KRT6C
KRT73
KRT79
FAM19A2
ANKRD33
OR6C2
OR6C4
KRT77
LRRC10
OR6C1
OR6C75
OR6C76
OR6C70
OR6C65
OR6C68
MIRLET7I
MIR196A2
OR9K2
ATXN7L3B
MIR616

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.1.

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

Genes
LIFR
FYB
OSMR
EGFLAM
RICTOR
MIR3650

Genes in Wide Peak

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

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

Genes
BCL2
MALT1
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
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
CDH7
CYB5A
KDSR
GRP
LMAN1
SMAD4
MBP
MC4R
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
ONECUT2
VPS4B
TSHZ1
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
CDH20
CDH19
TIMM21
RAX
ST8SIA3
MEX3C
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
PQLC1
CCDC68
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
GTSCR1
DOK6
LINC00305
DYNAP
BOD1L2
LINC00908
HMSD
CPLX4
ATP9B
LINC00909
MIR122
HSBP1L1
C18orf63
MIR4529
MIR5011

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.31.

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

Genes
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
WARS
DLK1
BEGAIN
WDR25
SLC25A47
LINC00523
RTL1
MIR127
MIR136
MIR154
MIR323A
MIR337
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
MIR1197
MIR1193
MIR2392

Genes in Wide Peak

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

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

Genes
CDK6
ELN
HIP1
MET
AKAP9
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1|ENSG00000271739.1
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13|ENSG00000238922.1
FLJ00325
U3|ENSG00000238297.1
snoU109|ENSG00000238832.1
RNA5SP236
SNORD112|ENSG00000251911.1
RN7SL8P
LHFPL3
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
MIR4658
MIR106B
MIR93
MIR25
AZGP1P1
SNORA40|ENSG00000222966.1
CYP3A4
snoU13|ENSG00000239133.1
MYH16
snoU13|ENSG00000238459.1
MIR3609
RN7SL13P
RN7SL478P
RN7SKP104
RN7SL252P
SHFM1
MIR591
PON1
snoU13|ENSG00000238384.1
RN7SKP129
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
snoU13|ENSG00000238739.1
DPY19L2P4
SNORA67|ENSG00000207094.1
snoU13|ENSG00000238587.1
LINC00972
SEMA3A
RNA5SP235
MIR1255B1
RN7SL35P
RN7SL869P
RNA5SP234
RSBN1L
snoU13|ENSG00000238453.1
RN7SL212P
snoU13|ENSG00000238935.1
TMEM120A
SNORA14A
CCL24
RN7SL642P
NSUN5P1
STAG3L1
GATSL2
GATSL1
STAG3L2
RNA5SP233
MIR590
LINC00035
RN7SL265P
GTF2IRD2P1
NCF1B
RN7SL625P
RN7SL377P
RNA5SP232
RN7SKP75
RN7SL371P
RNA5SP231
ACHE
ASNS
AZGP1
CACNA2D1
CALCR
CAV1
CAV2
KRIT1
CD36
CFTR
AP1S1
COL1A2
CLDN4
CLDN3
CUX1
CYP3A7
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
SLC26A3
EPHB4
EPO
GNAI1
GNB2
GNGT1
GPR22
GRM3
GRM8
GTF2I
HGF
AGFG2
HSPB1
KCND2
LAMB1
LIMK1
LRCH4
MCM7
DNAJB9
MDH2
NDUFA5
NPTX2
NRCAM
OCM2
ORC5
SERPINE1
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PMS2P3
POLR2J
PON2
PON3
POR
PPP1R3A
PRKAR2B
RELN
PSMC2
PTPN12
PTPRZ1
RFC2
SLC13A1
SPAM1
SRI
SRPK2
STX1A
SYPL1
TAC1
TAF6
TFR2
TRIP6
VGF
ZAN
EIF4H
CLIP2
LAT2
WNT2
YWHAG
ZNF3
ZKSCAN1
ZSCAN21
ZP3
MTERF
TFPI2
ST7
TRRAP
FZD1
FZD9
FKBP6
BUD31
SGCE
WASL
PLOD3
BAZ1B
CLDN12
AP4M1
BCL7B
PMPCB
ATP5J2
GTF2IRD1
SEMA3E
DOCK4
MAGI2
POM121
DMTF1
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
BET1
CCL26
FAM3C
COG5
ZNHIT1
SEMA3C
ARPC1A
STAG3
FGL2
CPSF4
DBF4
COPS6
DUS4L
ZNF277
TP53TG1
PDAP1
TFEC
LAMB4
LMTK2
POMZP3
PEG10
HYAL4
TSPAN12
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
AUTS2
TES
FBXO24
TBL2
STEAP1
HBP1
DNAJC2
PCLO
MDFIC
PILRA
PNPLA8
TAS2R16
FIS1
MLXIPL
WNT16
ACTL6B
SRRT
STYXL1
ASB4
ADAM22
GSAP
GPR85
ANKIB1
PUS7
ING3
LRRN3
CROT
ALKBH4
SAMD9
ZCWPW1
C7orf43
PPP1R9A
CCDC132
NSUN5
KMT2E
BAIAP2L1
SLC25A40
BCAP29
MEPCE
ANKRD7
SLC12A9
ACN9
SMURF1
PHTF2
RHBDD2
CCDC146
RINT1
WBSCR17
MOSPD3
GIGYF1
CYP3A43
CASD1
ZNF655
PVRIG
TMEM243
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
CPED1
ORAI2
UPK3B
OR2AE1
WBSCR16
TSC22D4
TRIM56
ABHD11
CALN1
ARMC10
IMMP2L
CTTNBP2
RBM48
ZNF394
GTF2IRD2
DNAJC30
TMEM60
GTPBP10
TRIM4
MYL10
CADPS2
FOXP2
DTX2
WBSCR22
WBSCR28
TRIM50
COL26A1
SRCRB4D
ASZ1
MUC17
ASB15
RUNDC3B
C7orf60
IQUB
C7orf66
WBSCR27
VPS37D
RNF133
THAP5
CCDC71L
BHLHA15
SAMD9L
C7orf62
ZNF804B
ZSCAN25
FAM200A
PPP1R35
GPC2
SRRM3
KIAA1324L
LRWD1
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
MBLAC1
FAM133B
NSUN5P2
STEAP2
ZNF789
LSMEM1
GNAT3
MOGAT3
GJC3
DPY19L2P2
GATS
TRIM73
NAT16
SLC26A5
TRIM74
RNF148
GTF2IRD2B
LAMTOR4
FEZF1
RPL13AP17
LRRD1
C7orf76
KPNA7
C7orf61
UFSP1
TYW1B
SPDYE3
SPDYE2
STAG3L3
LMOD2
POLR2J3
NCF1
TMEM229A
POM121C
EFCAB10
UPK3BL
RASA4B
SPDYE2B
MIR548O
MIR4284
MIR4652
MIR4651
MIR5692C2
MIR5692A1

Genes in Wide Peak

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

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

Genes
CARD11
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
EIF3B
ADAP1
IQCE
SUN1
INTS1
SNX8
FTSJ2
GET4
CYP2W1
HEATR2
CHST12
RADIL
PAPOLB
MICALL2
TTYH3
PSMG3
C7orf50
ZFAND2A
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MIR4656

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p12.2.

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

Genes
PRKCB

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 - 27 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 | 4.6366e-22 | 4.6366e-22 | chr9:21931610-22448737 | 3
15q21.1 | 7.2452e-05 | 7.2452e-05 | chr15:44953604-45026122 | 2
6q23.3 | 3.8116e-07 | 0.00044539 | chr6:137860913-138410514 | 2
10q23.31 | 0.00049123 | 0.00049123 | chr10:90534760-91090085 | 8
1p13.1 | 0.00025934 | 0.00052806 | chr1:116959687-117120066 | 2
1q43 | 0.001789 | 0.001789 | chr1:93485263-249250621 | 1417
6q14.1 | 0.00025712 | 0.001789 | chr6:76307902-111139036 | 163
2q23.1 | 0.011502 | 0.011502 | chr2:122489933-168731067 | 187
6p21.32 | 0.011937 | 0.011937 | chr6:31167499-33114170 | 85
17q24.1 | 0.013269 | 0.013752 | chr17:62970616-63525081 | 2
5q33.3 | 0.017027 | 0.017027 | chr5:157281809-158744166 | 4
13q14.2 | 0.017027 | 0.017027 | chr13:48875329-49064807 | 2
3p21.31 | 0.017027 | 0.017213 | chr3:42578769-50196417 | 163
8q12.1 | 0.023211 | 0.021103 | chr8:54752291-66514953 | 55
16p13.13 | 0.026332 | 0.02379 | chr16:10910547-11030197 | 1
19p13.2 | 0.032454 | 0.032335 | chr19:8000602-8118949 | 1
7q33 | 0.035109 | 0.034296 | chr7:117853365-159138663 | 348
4q35.1 | 0.037489 | 0.040791 | chr4:167652787-191154276 | 112
1p36.32 | 0.011937 | 0.057531 | chr1:1-48649489 | 789
6q22.32 | 0.00052806 | 0.066847 | chr6:96022438-139502638 | 252
19q13.2 | 0.069584 | 0.072612 | chr19:42567946-42801342 | 9
12p13.2 | 0.12173 | 0.12704 | chr12:1-22595769 | 273
16q23.1 | 0.15034 | 0.15181 | chr16:78098006-79299841 | 3
8p23.2 | 0.17714 | 0.1656 | chr8:1-33334473 | 257
17p13.1 | 0.18242 | 0.1944 | chr17:1-62229443 | 1096
22q13.31 | 0.2126 | 0.21964 | chr22:41635693-51304566 | 138
Xq28 | 0.21501 | 0.21964 | chrX:57927912-155270560 | 669

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53

Genes in Wide Peak

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

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

Genes
B2M
PATL2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q23.3.

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

Genes
TNFAIP3
SNORD112|ENSG00000252476.1

Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238991.1
ANKRD22
ACTA2
FAS
IFIT2
CH25H
STAMBPL1
LIPM

Genes in Wide Peak

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

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

Genes
MIR548AC
CD58

Genes in Wide Peak

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

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

Genes
SDHC
ABL2
ARNT
BCL9
ELK4
FCGR2B
FH
MDM4
MUC1
NOTCH2
NRAS
NTRK1
PBX1
PRCC
TPM3
TPR
PDE4DIP
TRIM33
RBM15
SLC45A3
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13|ENSG00000239094.1
snoU13|ENSG00000238545.1
MIR4742
snoU13|ENSG00000238856.1
MIR320B2
SNORA72|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13|ENSG00000238576.1
snoU13|ENSG00000238798.1
U3|ENSG00000221673.1
RNA5SP76
SLC30A10
U3|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
SERTAD4
MIR4260
MIR205HG
MIR29B2
MIR29C
snoU13|ENSG00000238401.1
FAIM3
IL20
SNORD112|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72|ENSG00000201944.1
SNORD112|ENSG00000252946.1
SCARNA20|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77|ENSG00000221643.1
RABIF
PCAT6
SNORA70|ENSG00000253042.1
U6|ENSG00000272262.1
snoU13|ENSG00000239046.1
snoU13|ENSG00000238571.1
PTPRVP
GPR37L1
SNORA70|ENSG00000206637.1
MIR1231
MIR5191
RPS10P7
ASCL5
LINC00862
MIR181A1HG
MIR4735
U3|ENSG00000252241.1
MIR1278
snoU109|ENSG00000238754.1
RN7SKP126
RNA5SP73
RN7SKP156
RNA5SP72
SNORD112|ENSG00000252790.1
RN7SL654P
RNA5SP71
RN7SKP229
RNA5SP70
KIAA1614
U6|ENSG00000272292.1
MIR3121
LHX4
RN7SL230P
IFRG15
RN7SL374P
SNORA67|ENSG00000201619.1
SNORA67|ENSG00000212338.1
TOR3A
SNORA63|ENSG00000201791.1
RNA5SP69
C1orf220
LINC00083
MIR488
SCARNA3
snoU13|ENSG00000238872.1
RNA5SP68
RNA5SP67
SNORD78|ENSG00000208317.1
GAS5
RN7SKP160
snoU13|ENSG00000238430.1
ANKRD45
snoU13|ENSG00000251817.1
TNFSF18
SNORD112|ENSG00000252354.1
DNM3OS
SCARNA20|ENSG00000253060.1
RN7SL425P
snoU13|ENSG00000238859.1
RN7SL269P
RN7SL333P
C1orf112
F5
RNA5SP66
LINC00970
LINC00626
ANKRD36BP1
SFT2D2
MIR1255B2
snoU13|ENSG00000238325.1
RNA5SP65
POGK
MIR921
RNA5SP64
UCK2
TMCO1
SNORD112|ENSG00000252359.1
U3|ENSG00000212538.1
RNA5SP63
RNA5SP62
SNORD112|ENSG00000252740.1
RN7SL861P
C1orf111
MIR556
RNA5SP61
MIR4654
RN7SL466P
RPL31P11
FCGR2C
MIR5187
ADAMTS4
ACA64|ENSG00000238934.1
F11R
DCAF8
KCNJ9
SNORD64|ENSG00000212161.1
OR10J4
RNA5SP60
RN7SL612P
MIR765
snoU13|ENSG00000238843.1
BGLAP
SNORA26|ENSG00000252236.1
SCARNA4|ENSG00000252808.1
SNORA42|ENSG00000207475.1
snoU13|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
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
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
ABCA4
ACTA1
ACTN2
ADAR
ADORA1
ADORA3
PARP1
ADSS
AGL
AGT
ALDH9A1
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
APCS
APOA2
FASLG
ARF1
RHOC
ASTN1
SERPINC1
ATF3
ATP1A1
ATP1A2
ATP1A4
ATP1B1
ATP2B4
C4BPA
C4BPB
CACNA1E
CACNA1S
CAPN2
CAPZA1
CASQ1
CASQ2
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD247
CD5L
CD34
CD48
CD53
CD58
CENPF
CHI3L1
CHI3L2
CHIT1
CHML
LYST
CHRNB2
CKS1B|ENSG00000173207.8
CLK2
CNN3
COL11A1
COPA
CR1
CR1L
CR2
CRABP2
CRP
CSF1
CSRP1
CTSE
CTSK
CTSS
CD55
DBT
DHX9
DPT
DPYD
ECM1
S1PR1
EIF2D
EFNA1
EFNA3
EFNA4
CELSR2
ELF3
ENSA
EPHX1
EPRS
ESRRG
ETV3
EXTL2
F3
F13B
FCER1A
FCER1G
FCGR1A
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO1
FMO2
FMO3
FMO4
FMO5
FMOD
NR5A2
DARC
GALNT2
GBA
GJA5
GJA8
GLUL
GNAT2
GNG4
GPR25
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GUK1
H3F3A
HDGF
CFH
CFHR1
CFHR2
MR1
HMGCS2
HNRNPU
HSD3B1
HSD3B2
HSD11B1
HSPA6
IGSF3
IFI16
IL6R
IL10
ILF2
INSRR
IRF6
ITPKB
IVL
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
KCNJ10
KCNK1
KCNK2
KCNN3
KISS1
LAD1
LAMB3
LAMC1
LAMC2
LBR
LGALS8
LMNA
LMX1A
LOR
LY9
MARK1
MCL1
CD46
SMCP
MEF2D
MGST3
MNDA
MOV10
MPZ
MTR
MTX1
MYBPH
MYOC
MYOG
PPP1R12B
NCF2
NDUFS2
NEK2
NGF
NHLH1
NHLH2
NID1
NIT1
NPR1
DDR2
NVL
OVGP1
CDK18
PDC
PDZK1
PFDN2
PFKFB2
PIGC
PIGR
PIK3C2B
PI4KB
PKLR
PKP1
PLA2G4A
PLXNA2
PRRX1
POU2F1
PPOX
PPP2R5A
PRELP
PRKAB2
PROX1
PSEN2
PSMA5
PSMB4
PSMD4
PTGFRN
PTGS2
QSOX1
PTPN7
PTPN14
PTPRC
PEX19
ABCD3
RAB4A
RAB13
RAP1A
RBBP5
REN
RFX5
RGS1
RGS2
RGS4
RGS7
RGS13
RGS16
RIT1
RNASEL
RNF2
RNPEP
RORC
RPS27
RXRG
RYR2
S100A1
SORT1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SARS
XCL1
SELE
SELL
SELP
SHC1
SLAMF1
SLC16A1
SOAT1
UAP1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SRP9
TROVE2
SSR2
STXBP3
XCL2
SYCP1
TARBP1
CNTN2
TBCE
TBX15
VPS72
TGFB2
LEFTY2
THBS3
TCHH
TLR5
GPR137B
TNNI1
TNNT2
TNR
TP53BP2
TRAF5
CCT3
TSHB
TSNAX
TUFT1
TNFSF4
USF1
USH2A
VCAM1
ZNF124
CSDE1
DAP3
NPHS2
BTG2
HIST3H3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
BCAR3
ANXA9
GNPAT
DYRK3
CDC42BPA
RGS5
PPFIA4
ITGA10
BLZF1
CDC14A
DEGS1
KMO
RTCA
VAMP4
PEA15
B4GALT3
B3GALT2
ADAM15
PEX11B
CREG1
CD84
RAB7L1
SELENBP1
TAF1A
MPZL1
SH2D2A
ANGPTL1
TBX19
SLC16A4
PRPF3
EXO1
ARHGEF2
DEDD
XPR1
MAPKAPK2
GPR52
CD101
AIM2
GGPS1
RASAL2
CHD1L
SOX13
PRDX6
IKBKE
SLC25A44
KIAA0040
NOS1AP
TMEM63A
TOMM20
URB2
ARHGEF11
CEP350
CEP170
SETDB1
ZC3H11A
SMG7
LPPR4
UBAP2L
SV2A
DENND4B
RABGAP1L
TMCC2
FAM20B
LPGAT1
KIF14
RBM8A
NR1I3
AKT3
SCAMP3
ARPC5
TSPAN2
PRG4
GPA33
STX6
SF3B4
BCAS2
WARS2
BPNT1
CEPT1
PIAS3
TIMM17A
LRRN2
VAV3
HAX1
ZBTB18
C1orf61
SEMA6C
LAMTOR5
SLC19A2
POLR3C
IVNS1ABP
TXNIP
LEFTY1
SPHAR
PMVK
FAM189B
AP4B1
PHTF1
CAPN9
NES
KDM5B
AHCYL1
SDCCAG8
CFHR4
CFHR3
OCLM
JTB
MTMR11
SLC27A3
IL24
TDRKH
ADAM30
CD160
DDX20
DUSP10
PMF1
DUSP12
VPS45
COG2
MTF2
NTNG1
PLEKHA6
KIAA0907
WDR47
KIFAP3
ATF6
RBM34
KIF21B
NMNAT2
NFASC
POGZ
COLGALT2
CLCC1
RGL1
SYT11
PRRC2C
FBXO28
RPRD2
CAMSAP2
SMG5
NCSTN
CRB1
GPR161
SLC35A3
ABCB10
ZNF281
SNAPIN
OPN3
PHLDA3
RUSC1
CA14
DSTYK
RAB3GAP2
CCDC19
LMOD1
NBPF14
MPC2
INTS7
OLFML2B
AHCTF1
C1orf43
NSL1
RWDD3
DNM3
TOR1AIP1
CHTOP
PTPN22
PHGDH
LCE2B
OR2M4
OR2L2
OPTC
OR10J1
OR2T1
RPS6KC1
USP21
DIEXF
TAF5L
CACYBP
CHIA
SLC39A1
DISC1
KLHL20
LAMTOR2
FLVCR1
UBE2T
CNIH4
TMOD4
GPSM2
PYCR2
NME7
NENF
IL19
CERS2
SLC25A24
CRNN
G0S2
DCAF8
F11R
TMED5
RRP15
GLRX2
BOLA1
DESI2
ZBTB7B
RRNAD1
ADIPOR1
SCCPDH
APH1A
TRIM17
KCTD3
PLEKHO1
HAO2
IER5
SNX7
UCHL5
SUCO
GPR89B
HSD17B7
UFC1
DTL
METTL13
OAZ3
CYB5R1
ARID4B
CD244
GPR88
DPM3
MRPS21
TRMT13
ADAMTSL4
CRCT1
EGLN1
MAP10
RSBN1
SWT1
GDAP2
FAM46C
GON4L
GPATCH4
PALMD
FNBP1L
ST7L
LAX1
DUSP23
C1orf27
C1orf56
MARC2
SUSD4
KIF26B
RALGPS2
GPATCH2
PRPF38B
HEATR1
MSTO1
DARS2
PRMT6
GOLPH3L
KLHDC8A
ETNK2
KIRREL
TMEM206
YY1AP1
SLC22A15
YOD1
BATF3
UBE2Q1
RNPC3
ITLN1
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
LRIF1
FAM63A
ADCY10
DCAF6
ASH1L
LENEP
CTTNBP2NL
FAM212B
SLC50A1
ERO1LB
FMN2
SLAMF8
CDC42SE1
UBQLN4
OLFML3
SMYD2
LHX9
ADCK3
RAB25
PGLYRP4
ZNF695
RHBG
SCYL3
GJC2
CAMK1G
ATP8B2
VANGL2
PBXIP1
S100A14
GATAD2B
AMIGO1
CGN
IGSF9
SIPA1L2
ZNF687
HCN3
FAM5B
CCDC181
SLAMF7
CADM3
PTBP2
RHOU
PRUNE
KLHL12
LGR6
HAPLN2
PAPPA2
BCAN
TNN
MRPS14
TFB2M
SEMA4A
RFWD2
GREM2
RGS18
HIAT1
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
DCLRE1B
MRPL9
JMJD4
INTS3
SCNM1
WDR77
C1orf116
C1orf35
FCRL2
TTC13
EPS8L3
CDC73
MRPL24
PGBD5
TNFAIP8L2
C1orf54
VTCN1
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PAQR6
PCNXL2
TRIM46
MROH9
SIKE1
TARS2
WDR26
TRIM45
EDEM3
FLAD1
TRAF3IP3
SH3BP5L
NPL
OR6N2
OR6K2
OR2L5
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
C1orf21
PVRL4
SNX27
ANP32E
SHCBP1L
TRMT1L
NUAK2
VANGL1
ISG20L2
FCRL5
FCRL4
DDX59
NUF2
RASSF5
HMCN1
GPR61
MIXL1
SPRTN
FCAMR
REG4
OBSCN
TEX35
HORMAD1
TOMM40L
POLR3GL
TMEM79
EFCAB2
ACBD6
PROK1
MLK4
ZBTB37
LCE3D
PSRC1
LINC00467
FCRLA
ZNF496
C1orf198
PPP1R15B
MAEL
DISP1
STRIP1
RGS8
WNT3A
NAV1
SEC16B
AQP10
SLAMF9
PYGO2
ANGEL2
ZNF697
IGFN1
NUP210L
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
TMEM183A
HIST3H2A
PIGM
IGSF8
LEMD1
C1orf85
HENMT1
NLRP3
PGLYRP3
SLAMF6
SLC26A9
FCRL1
FCRL3
FMO9P
COX20
TSEN15
FAM129A
SNAP47
TADA1
SH2D1B
OLFM3
GABPB2
TCHHL1
RPTN
TDRD10
SHE
CCSAP
KLHDC9
AXDND1
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
OR10J5
LRRC39
DCST2
DNAH14
OR2B11
ZNF648
TEDDM1
ARL8A
SYT2
GOLT1A
UHMK1
FCRLB
WDR64
C1orf131
LIX1L
EDARADD
TSACC
IQGAP3
APOA1BP
MRPL55
HIST3H2BB
DRAM2
PIFO
C1orf162
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
TATDN3
S100A16
NEK7
ITLN2
SYT6
C1orf74
CREB3L4
BROX
C1orf51
TMEM56
NBPF4
SLC35F3
HFE2
ANKRD35
FAM163A
B3GALNT2
MFSD4
PM20D1
GCSAML
SLC30A7
NBPF12
LELP1
RC3H1
DCST1
CNIH3
METTL11B
FAM78B
SHISA4
EXOC8
BNIPL
LRRC71
CHIAP2
PYHIN1
C1orf227
FAM71A
FNDC7
DENND1B
TDRD5
TOR1AIP2
SPRR4
SASS6
SDE2
CNST
PPIAL4A
TTC24
C1orf65
UBL4B
LCE4A
NBPF11
PLD5
C1orf100
SPAG17
KRTCAP2
CRTC2
IBA57
HIPK1
TMEM9
AKNAD1
SLC41A1
OR2T6
LCE5A
SYT14
C1orf101
ARHGAP30
C1orf192
ASPM
MAGI3
TIPRL
FAM19A3
RIIAD1
THEM5
OR2L13
SLC9C2
OR14A16
NBPF16
LINC00303
FAM102B
SYPL2
CYB561D1
ANKRD34A
C1orf204
LIN9
HIST2H2AB
PPM1J
S100A7A
RXFP4
FAM5C
PRSS38
C1orf110
RD3
CCDC18
OR6F1
OR2W3
OR2T8
OR2T3
MYBPHL
OR10R2
FCRL6
KCNT2
OR2T29
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
RGSL1
IRF2BP2
ZBTB41
PEAR1
MIA3
C1orf95
FAM89A
ILDR2
SLC6A17
C1orf137
NOTCH2NL
LYSMD1
HRNR
FLG2
FMO6P
LINC00272
C1orf53
TMEM81
COA6
C1orf229
FRRS1
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf226
C1ORF220
NBPF9
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
APOBEC4
MIR181B1
MIR197
MIR199A2
MIR181A1
MIR214
MIR215
C1orf132
RGS21
HIST2H2BF
ETV3L
LRRC52
TRIM67
MAP1LC3C
OR10J3
OR13G1
MIR135B
KPRP
LCE6A
HIST2H4B
C1orf145
PRR9
C1orf148
PPIAL4G
PPIAL4D
MT1HL1
NBPF6
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
MIR557
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
MIR760
C1orf68
TSTD1
C2CD4D
NBPF20
MIR320B1
MIR1537
MIR1295A
MIR3123
MIR3124
MIR4257
MIR3916
MIR4666A
MIR378G
MIR4424
MIR137HG

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q14.1.

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

Genes
PRDM1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
snoU13|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18|ENSG00000252249.1
U3|ENSG00000221455.1
U3|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73|ENSG00000222145.1
RN7SL183P
snoU13|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70|ENSG00000206886.1
RNA5SP210
SNORD112|ENSG00000252932.1
HTR1B
U6|ENSG00000272445.1
snoU13|ENSG00000239132.1
RNA5SP209
RN7SKP163
AIM1
BCKDHB
CCNC
CGA
CNR1
EPHA7
FOXO3
GABRR1
GABRR2
GPR6
GRIK2
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
SYNCRIP
SLC35A1
FUT9
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
DOPEY1
ZNF292
CDK19
MDN1
UFL1
ORC3
PNISR
IBTK
SENP6
FBXL4
SESN1
OSTM1
NDUFAF4
C6orf203
CDC40
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
FAM46A
RARS2
PDSS2
SMIM8
LYRM2
SNX14
HACE1
BEND3
RRAGD
BACH2
C6orf164
MICAL1
MANEA
GPR63
SPACA1
SH3BGRL2
ARMC2
MCHR2
FAXC
GJA10
USP45
SLC22A16
UBE3D
MRAP2
KLHL32
RIPPLY2
IRAK1BP1
PM20D2
SRSF12
C6orf165
PRSS35
LCA5
C6orf163
AK9
LACE1
MMS22L
CEP57L1
PPIL6
GJB7
LIN28B
MIR587
METTL24
MIR2113
MIR4464
MIR4643
MIR548AI

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q23.1.

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

Genes
ERCC3
snoU13|ENSG00000238662.1
RN7SKP152
RN7SL455P
RNA5SP111
RNA5SP110
SNORA70F
FIGN
RNA5SP109
GCA
snoU13|ENSG00000238570.1
TBR1
RN7SL423P
MIR4785
RMRPP3
MARCH7
snoZ5
RN7SL393P
RN7SKP281
GALNT5
snoU13|ENSG00000238481.1
snoU13|ENSG00000238543.1
RNA5SP107
SNORD56|ENSG00000200377.1
ARL5A
RN7SL124P
SNORA48|ENSG00000212181.1
RNA5SP106
snoU13|ENSG00000238860.1
snR65|ENSG00000253036.1
TEX41
RN7SL283P
SNORA72|ENSG00000206901.1
RN7SKP286
NXPH2
RNA5SP105
RN7SKP141
SNORA40|ENSG00000208308.1
snoU13|ENSG00000238337.1
MIR5590
RNA5SP104
RN7SKP93
RN7SKP154
RN7SKP103
RN7SL701P
MIR4784
CYP4F31P
SCARNA4|ENSG00000252829.2
CYP4F30P
CFC1
POTEI
CYP4F43P
snoU13|ENSG00000238546.1
RNA5SP103
RN7SL206P
RNY4P7
RNA5SP102
RN7SKP102
ACVR1
ACVR2A
BIN1
RND3
CACNB4
CCNT2
DARS
DPP4
FAP
GALNT3
GCG
GPD2
GPR17
GPR39
GRB14
GYPC
HNMT
ITGB6
KCNJ3
KIF5C
LCT
LY75
MCM6
MGAT5
MYO7B
NEB
NR4A2
ORC4
POLR2D
PROC
RBMS1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
TNFAIP6
TSN
CXCR4
PKP4
B3GALT1
KYNU
NMI
HS6ST1
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
MAP3K2
COBLL1
PLA2R1
RAB3GAP1
UBXN4
R3HDM1
EPC2
PTPN18
MMADHC
C2orf27A
BAZ2B
ARHGEF4
LRP1B
PLEKHB2
RIF1
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
RPRM
UGGT1
SLC4A10
ERMN
IFIH1
SAP130
GTDC1
TTC21B
CSRNP3
MZT2B
MAP3K19
THSD7B
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
SFT2D3
TANC1
KCNH7
CCDC74A
CCDC74B
DAPL1
IMP4
TUBA3E
TUBA3D
FMNL2
GALNT13
LYPD1
XIRP2
CNTNAP5
ACMSD
FAM168B
ACVR1C
LYPD6
LYPD6B
CCDC148
ARL6IP6
SLC38A11
WDSUB1
UPP2
AMER3
SPOPL
CYP27C1
NCKAP5
GPR148
RBM43
C2orf27B
POTEE
ANKRD30BL
CFC1B
POTEJ
MZT2A
POTEF
MIR663B
MIR3679
MIR4783

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p21.32.

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

Genes
PPP1R2P1
TAP2
HCG23
RNA5SP206
CYP21A1P
MIR1236
CFB
SNORD52
SNORD48
LY6G6E
MEGT1
MIR4646
LY6G5B
SNORA38|ENSG00000200816.1
SNORD84
SNORD117
MCCD1
HCP5
AGER
AIF1
ATP6V1G2
CFB
C2
C4A
C4B
CLIC1
ATF6B
CSNK2B
CYP21A2
DOM3Z
HSPA1A
HSPA1B
HSPA1L
LTA
LTB
MICB
MSH5
NEU1
NFKBIL1
NOTCH4
PBX2
PSMB8
PSMB9
BRD2
RNF5
SKIV2L
TAP1
TAP2
TNF
TNXB
VARS
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
NELFE
LST1
STK19
PPT2
AGPAT1
C6orf10
EHMT2
DDAH2
C6orf48
APOM
BTNL2
LSM2
C6orf47
LY6G6D
GPSM3
FKBPL
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRRT1
EGFL8
ZBTB12
NCR3
LY6G6F
SAPCD1
MICA
MIR3135B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.1.

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

Genes
RGS9
GNA13

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q33.3.

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

Genes
EBF1
SNORA68|ENSG00000252458.1
UBLCP1
RNF145

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

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

Genes
SETD2
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
RN7SL321P
MIR2115
RN7SL664P
MIR1226
CSPG5
RN7SL870P
snoU13|ENSG00000238350.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000251938.1
PRSS44
PRSS45
SNORD77|ENSG00000251967.1
LUZPP1
RTP3
RN7SL145P
LIMD1
U3|ENSG00000202268.1
ZDHHC3
MIR564
ZNF660
ZNF852
LINC00694
ABHD5
RN7SL517P
HIGD1A
RN7SL567P
ZBTB47
AMT
APEH
RHOA
SLC25A20
CAMP
CDC25A
CCR1
CCR3
CCR5
ACKR2
COL7A1
CYP8B1
DAG1
CELSR3
XCR1
GPX1
IMPDH2
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
NKTR
PFKFB4
PLXNB1
PRKAR2A
PTH1R
QARS
SMARCC1
TCTA
TDGF1
TGM4
CLEC3B
UBA7
USP4
UQCRC1
ZNF35
BSN
ACKR5
SEC22C
IP6K1
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
CXCR6
CCR9
USP19
WDR6
TREX1
DHX30
SACM1L
SCAP
EXOSC7
NBEAL2
KLHL18
LARS2
TMEM158
PTPN23
PRSS50
GMPPB
SS18L2
SHISA5
TMA7
ZNF589
IP6K2
NCKIPSD
LZTFL1
P4HTM
SLC6A20
ELP6
SNRK
QRICH1
ANO10
DALRD3
ZKSCAN7
KIF15
KIAA1143
HHATL
RNF123
KIF9
CDCP1
CCDC71
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
ATRIP
NICN1
MON1A
GTDC2
UCN2
ZNF502
ZNF501
KLHL40
TMEM42
CCDC12
CCDC13
KLHDC8B
ALS2CL
TMIE
FBXW12
TCAIM
CCDC36
PRSS42
ZNF445
TOPAZ1
AMIGO3
ZNF662
CDHR4
FAM212A
MIR191
MIR425
SPINK8
ARIH2OS
C3orf84
FAM198A
CCR2
PRSS46
MIR4271
KRBOX1
MIR4443

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q12.1.

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

Genes
PLAG1
TCEA1
CHCHD7
LINC00966
RN7SKP135
RN7SL135P
NKAIN3
RN7SKP97
CA8
RNA5SP267
SNORA51|ENSG00000206853.1
snoU13|ENSG00000238433.1
LINC00588
RNA5SP266
LINC00968
SDR16C6P
SNORA3|ENSG00000221093.1
SNORD54
RPS20
RN7SL323P
RN7SL798P
SNORA1|ENSG00000199405.1
RNA5SP265
XKR4
RN7SL250P
RNU105C
RNU6ATAC32P
MRPL15
ASPH
CYP7A1
LYN
MOS
PENK
RAB2A
RP1
SDCBP
TTPA
NSMAF
RGS20
GGH
CYP7B1
TOX
LYPLA1
BHLHE22
IMPAD1
CHD7
SOX17
FAM110B
TGS1
TMEM68
UBXN2B
CLVS1
SDR16C5
YTHDF3
MIR4470

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.13.

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

Genes
CIITA

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.2.

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

Genes
ELAVL1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q33.

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

Genes
BRAF
EZH2
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
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
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1|ENSG00000271739.1
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
CPED1
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HPGD
ING2
IRF2
KLKB1
MTNR1A
NEK1
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
ANXA10
PALLD
FAM149A
FBXO8
SPOCK3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
DDX60
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
SH3RF1
SPCS3
TRAPPC11
MLF1IP
WWC2
CEP44
SNX25
CBR4
DDX60L
WDR17
ZFP42
SPATA4
ENPP6
ASB5
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR4276
MIR3945
MIR4455

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

Genes
LCK
MPL
MUTYH
PAX7
RPL22
SDHB
SFPQ
TAL1
ARID1A
TNFRSF14
THRAP3
PRDM16
MDS2
SKINTL
TRABD2B
LINC00853
CYP4A22
CYP4Z2P
KNCN
LINC00505
NSUN4
TMEM69
snoU13|ENSG00000238945.1
RNA5SP47
BTBD19
SNORD38B
SNORD38A
SNORD46|ENSG00000200913.1
SNORD55
MIR5584
RN7SL479P
RNA5SP46
RNA5SP45
RN7SL326P
MIR30C1
MIR30E
BMP8B
SNORA55
BMP8A
RNA5SP44
MYCBP
SNORA63|ENSG00000252448.1
snoU13|ENSG00000238871.1
MIR5581
MEAF6
RNA5SP43
SNORA63|ENSG00000201448.1
RN7SL131P
RN7SL281P
PSMB2
RNY5P1
SNORA62|ENSG00000201542.1
RN7SL503P
RN7SL136P
ZMYM6
SNORD112|ENSG00000252728.1
SMIM12
RNA5SP42
RN7SKP16
MIR3605
FKSG48
ZBTB8OS
ZBTB8B
RN7SL122P
MTMR9LP
MIR5585
MIR4254
FABP3
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
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
AK2
ALPL
RERE
ATP6V0B
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC20
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
PLK3
CNR2
COL8A2
COL9A2
COL16A1
CORT
CSF3R
CTPS1
CYP4A11
CYP4B1
DDOST
DFFB
DPH2
DVL1
E2F2
ECE1
EDN2
PHC2
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FAAH
FGR
FHL3
FOXE3
FOXD2
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
GRIK3
GUCA2A
GUCA2B
HCRTR1
HDAC1
ZBTB48
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
INPP5B
IPP
STMN1
MATN1
MFAP2
MTF1
MTHFR
MYCL
NASP
NBL1
NDUFS5
NFYC
NPPA
NPPB
YBX1
OPRD1
PAFAH2
PRDX1
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
POU3F1
PPP1R8
PPT1
PRKCZ
PTAFR
PTPRF
RAP1GAP
RBBP4
RHCE
RHD
RLF
RPA2
RPL11
RPS6KA1
RPS8
RSC1A1
SCNN1D
SRSF4
ST3GAL3
STIL
SKI
SLC2A1
SLC2A5
SLC6A9
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TIE1
TNFRSF1B
TP73
TNFRSF4
UQCRH
UROD
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
DNALI1
LAPTM5
PTP4A2
SNHG3
NR0B2
RAD54L
PIK3R3
MMP23B
KCNAB2
FCN3
YARS
MKNK1
PTCH2
ALDH4A1
EIF3I
EIF4G3
B4GALT2
TNFRSF25
PABPC4
TNFRSF18
PER3
EIF2B3
ARTN
MAP3K6
KCNQ4
ZMYM4
ZMYM6
DHRS3
VAMP3
SNRNP40
THEMIS2
H6PD
ISG15
PLCH2
IPO13
KDM4A
CROCC
PUM1
CEP104
RIMS3
EFCAB14
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
TSPAN1
CELA3A
PDZK1IP1
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
ZMPSTE24
UBE4B
AKR1A1
TESK2
PPIE
MAD2L2
PPIH
CAP1
LRRC41
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
SF3A3
EBNA1BP2
KIF2C
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
FOXJ3
SCMH1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
MAST2
NCDN
PLEKHM2
OTUD3
KAZN
CAMTA1
SZT2
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
MACF1
PADI4
TMEM50A
KPNA6
STX12
CLIC4
MMACHC
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HEYL
AGO1
TRAPPC3
HSPB7
ARHGEF16
AHDC1
TEKT2
SMPDL3B
SSU72
GNL2
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF691
MECR
UTP11L
SDF4
MRTO4
HPCAL4
YTHDF2
ZCCHC17
PADI3
CMPK1
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
TRIT1
PQLC2
CASZ1
RHBDL2
ADPRHL2
TRNAU1AP
C1orf109
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
BSDC1
XKR8
TMEM39B
CDCA8
ARHGEF10L
RNF220
VPS13D
EVA1B
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
POMGNT1
PNRC2
PIGV
NBPF1
MAP7D1
NECAP2
IQCC
DNAJC11
RCC2
DMAP1
AJAP1
TMEM234
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
ZSWIM5
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
HIVEP3
GPBP1L1
MIIP
CELA2A
GPATCH3
CLSPN
OXCT2
RRAGC
TINAGL1
LEPRE1
PLA2G2F
SMAP2
ATPAF1
S100PBP
EXO5
CEP85
NMNAT1
ELOVL1
VWA1
MRPS15
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
ZFP69B
PHACTR4
AUNIP
ERI3
C1orf50
CCDC28B
EFHD2
MMEL1
RSG1
NKAIN1
MUL1
TMEM53
AKIRIN1
HECTD3
YRDC
NOL9
PPCS
LIN28A
SH3D21
SNIP1
ZMYM1
LINC00115
MORN1
FAM110D
KIAA0319L
DHDDS
ZC3H12A
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
GJA9
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
HYI
SESN2
ESPN
ATAD3B
STK40
TMEM222
PLEKHN1
USP48
ZMYND12
NBPF3
LZIC
NT5C1A
TRIM63
FAM167B
C1orf170
HPDL
MFSD2A
SYTL1
IGSF21
LSM10
C1orf94
KIAA2013
THAP3
STPG1
SPOCD1
UBXN11
FBXO44
ATPIF1
MED8
ADC
TMEM54
TOE1
ERMAP
CSMD2
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
CCDC163P
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
DMBX1
TMCO2
ZNF684
GJB4
HMGB4
RNF19B
A3GALT2
C1orf122
OSCP1
C1orf216
KLHDC7A
VWA5B1
KLF17
TMEM125
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
MOB3C
DCDC2B
ZNF362
MANEAL
PDIK1L
CLDN19
WDR65
C1orf210
CCDC24
CCDC17
SLC2A7
CALML6
IFNLR1
CITED4
FAM43B
PAQR7
AGO3
AGO4
FAM76A
TMEM201
CYP4Z1
C1orf86
TXLNA
SLFNL1
ATAD3C
AKR7L
FNDC5
TTLL10
TMCO4
ZNF683
CYP4X1
NPHP4
BEST4
RSPO1
EPHA10
RIMKLA
SLC25A34
C1orf174
KLHL17
TMEM52
TFAP2E
C1orf228
ZFP69
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
TCTEX1D4
SERINC2
FAM131C
SPATA21
CCDC23
TEX38
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
FAM183A
ANKRD65
PRAMEF7
LURAP1
PEF1
MIR429
KIAA0754
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
ZBTB8A
PRAMEF22
PRAMEF15
PRAMEF16
MIR552
CCDC30
CDK11A
SLC35E2B
C1orf234
OR4F29
FAM229A
FOXO6
MIR4255
MIR4253
MIR1273D
MIR4252
MIR3659
MIR3917
MIR3675
ZMYM6NB
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 6q22.32.

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

Genes
PRDM1
MYB
ROS1
TNFAIP3
GOPC
MIR3145
HEBP2
SNORD112|ENSG00000252476.1
SNORA27|ENSG00000201807.1
RNA5SP219
7SK|ENSG00000271765.1
COX5BP2
LINC00271
RNA5SP218
snoU13|ENSG00000238631.1
RN7SL408P
SLC2A12
TBPL1
LINC00326
SNORA33|ENSG00000200534.1
SNORD100
SNORD101
RPS12
TAAR3
STX7
RN7SKP245
snoU13|ENSG00000238938.1
KIAA0408
SOGA3
RNA5SP217
RSPO3
PRELID1P1
RNA5SP216
RN7SKP56
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13|ENSG00000238563.1
U3|ENSG00000253091.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13|ENSG00000238775.1
SNORA40|ENSG00000212587.1
RN7SL617P
snoU13|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13|ENSG00000238974.1
SNORA73|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33|ENSG00000202283.1
snoU13|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
AIM1
AMD1
ARG1
CCNC
COL10A1
CTGF
EPB41L2
EYA4
FABP7
FOXO3
FYN
GJA1
GPR6
GRIK2
HDAC2
HSF2
IFNGR1
KPNA5
LAMA2
LAMA4
MARCKS
MAN1A1
MAP3K5
ENPP1
ENPP3
PEX7
PLN
POU3F2
PREP
PKIB
PTPRK
REV3L
SGK1
SIM1
SMPD2
TCF21
NR2E1
TPD52L1
DDO
SNX3
CD164
WISP3
VNN2
VNN1
WASF1
TAAR5
MAP7
TAAR2
MED23
FHL5
AKAP7
ATG5
BCLAF1
ZBTB24
FIG4
TRDN
FUT9
TRAF3IP2
HBS1L
SMPDL3A
ASCC3
BVES
SEC63
CDK19
TSPYL4
UFL1
HEY2
ASF1A
CCDC28A
PNISR
MOXD1
FBXL4
PDE7B
SESN1
OSTM1
NDUFAF4
DSE
HDDC2
TUBE1
C6orf203
CDC40
RWDD1
HECA
COQ3
IL20RA
AHI1
SOBP
QRSL1
VNN3
ECHDC1
PDSS2
KIAA1244
NHSL1
SERINC1
HACE1
BEND3
ABRACL
PBOV1
TRMT11
PERP
ALDH8A1
MICAL1
OR2A4
FAM184A
MANEA
GPR63
RNF146
TAAR8
ARMC2
L3MBTL3
MCHR2
FAXC
USP45
REPS1
SLC22A16
ARHGAP18
GTF3C6
MTFR2
KLHL32
TMEM200A
NUS1
IL22RA2
SLC18B1
SLC16A10
TAAR9
TAAR1
NCOA7
HINT3
SAMD3
RNF217
NKAIN2
OLIG3
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
TMEM244
MMS22L
MCM9
CEP57L1
PPIL6
DCBLD1
TAAR6
SLC35D3
RSPH4A
ECT2L
C6orf58
CENPW
SOGA3
CEP85L
THEMIS
LIN28B
FAM26F
RFPL4B
FAM229B
CTAGE9
MIR548A2
MIR587
MIR588
METTL24
TRAPPC3L
MIR2113
MIR3144
SMLR1
MIR548AJ1
MIR548AI
MIR548H5

Genes in Wide Peak

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

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

Genes
CIC
SNORD112|ENSG00000252356.1
ERF
GSK3A
POU2F2
ZNF574
ZNF526
DEDD2
MIR4323

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

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

Genes
CCND2
ETV6
KDM5A
ZNF384
C12orf39
PYROXD1
LST3
AEBP2
RN7SL67P
RN7SL459P
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
C1R
SCARNA12
DSTNP2
RPL13P5
RN7SL380P
SCARNA11|ENSG00000251898.1
SCARNA10
MRPL51
RN7SL391P
RN7SL69P
NDUFA9
C12orf5
FKBP4
CBX3P4
CACNA1C
LINC00940
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
A2M
APOBEC1
ARHGDIB
C1S
C3AR1
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FOXM1
GAPDH
GNB3
GPR19
GUCY2C
GYS2
IAPP
KCNA1
KCNA5
KCNA6
KCNJ8
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LDHB
LRP6
LTBR
M6PR
MGP
MGST1
NINJ2
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PRB1
PRB3
PRB4
PRH1
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
RECQL
SCNN1A
ST8SIA1
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
KLRC4
YBX3
DYRK4
CD163
GDF3
CLSTN3
NCAPD2
ABCC9
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
AKAP3
SLCO1B1
RAD51AP1
KLRAP1
TSPAN9
STRAP
PRR4
PHB2
KLRK1
ERC1
GABARAPL1
IFFO1
NECAP1
CLEC4E
GALNT8
GPR162
SLCO1B3
COPS7A
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
HEBP1
GOLT1B
DERA
ING4
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
FAM90A1
PLEKHG6
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
CMAS
PRMT8
PARP11
ANO2
C12orf4
LPAR5
AICDA
RIMKLB
KIAA1467
CLEC7A
WNK1
BCL2L14
ADIPOR2
RERGL
NANOG
WNT5B
APOLD1
GSG1
CDCA3
RHNO1
NRIP2
RBP5
CCDC77
ACRBP
SPSB2
EFCAB4B
RERG
PLCZ1
CACNA2D4
CAPZA3
CLEC6A
C12orf57
LOH12CR1
TMEM52B
HIST4H4
SLC2A14
A2ML1
FBXL14
CLEC12A
CLECL1
CLEC4C
PIANP
DCP1B
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CD163L1
B4GALNT3
CLEC9A
C12orf36
CLEC4D
SLCO1B7
ACSM4
TAS2R42
DPPA3
NANOGNB
CLEC2A
CLEC12B
LINC00937
MIR141
MIR200C
IQSEC3
ZNF705A
SMCO3
PRB2
LRTM2
MIR614
SLC15A5
MIR3649

Genes in Wide Peak

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

Table S35. 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 8p23.2.

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

Genes
PCM1
WRN
RNA5SP263
RNA5SP262
RNA5SP261
UBXN8
TUBBP1
FAM183CP
LINC00589
RN7SL781P
RNA5SP260
RNA5SP259
MIR4287
snoU13|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13|ENSG00000238466.1
U3|ENSG00000251944.1
SNORA62|ENSG00000201157.1
RNA5SP256
MIR548V
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
LINC00529
MIR598
SNORD112|ENSG00000252565.1
SOX7
RNA5SP252
PRSS51
snoU13|ENSG00000238496.1
snoU13|ENSG00000239065.1
MIR597
U3|ENSG00000252543.1
SNORA70|ENSG00000207244.1
RN7SL178P
SGK223
ALG1L13P
FAM86B3P
LRLE1
FAM85B
FAM90A24P
FAM66E
DEFB105A
DEFB105B
DEFB103B
ZNF705G
FAM66B
XKR5
MIR4659A
AGPAT5
RN7SKP159
RN7SL318P
SNORA70|ENSG00000206661.1
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
DMTN
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
GSR
GTF2E2
NRG1
LOXL2
LPL
MSR1
MSRA
NEFM
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
DOK2
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
FBXO25
ADAMDEC1
CNOT7
PURG
SCARA3
TMEM66
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
HMBOX1
MCPH1
PPP1R3B
DOCK5
REEP4
STMN4
SOX7
FAM167A
SLC35G5
FUT10
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
SGCZ
DEFB104A
PEBP4
CDCA2
ESCO2
FBXO16
TDRP
ERICH1
TDH
C8orf48
ZNF596
R3HCC1
PRSS55
C8orf74
LGI3
DEFB106A
DEFB107A
DEFB130|ENSG00000232948.1
NEIL2
XKR6
MICU3
SCARA5
USP17L2
NUGGC
LINC00599
MIR320A
DEFB103A
DEFB107B
DEFB104B
DEFB106B
C8orf58
DEFB135
DEFB136
MBOAT4
SPAG11A
MIR596
DEFA1B
ZNF705D
ZNF705B
DEFB4B
MIR548I3
MIR548H4
MIR3148
MIR4288
MIR4286
MIR3622B
SMIM18
MIR4660
MIR5692A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

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

Genes
BRIP1
RARA
BRCA1
CD79B
CLTC
COL1A1
ERBB2
ETV4
HLF
LASP1
MLLT6
NF1
PER1
MAP2K4
TP53
TAF15
GAS7
USP6
SUZ12
MSI2
SNORD104
SNORA76|ENSG00000266402.2
TCAM1P
RN7SL805P
ACE
TLK2
TBC1D3P2
RN7SL800P
snoU13|ENSG00000238799.1
RN7SL448P
RN7SL606P
PPM1D
RPL12P38
SCARNA20|ENSG00000252577.1
USP32
MIR4729
PRR11
MIR301A
MIR454
RN7SL716P
PPM1E
U3|ENSG00000212195.1
DYNLL2
SRSF1
VEZF1
MRPS23
RN7SKP94
RN7SL449P
RN7SL437P
RNF126P1
RN7SKP14
snoZ178
RN7SL699P
snoU13|ENSG00000238815.1
snoU13|ENSG00000239135.1
HILS1
NXPH3
ZNF652
snoU13|ENSG00000238804.1
SNF8
SNORA68|ENSG00000212565.1
RN7SL125P
HOXB4
HOXB3
HOXB2
HOXB1
U3|ENSG00000200538.1
MIR1203
MIR152
PNPO
KPNB1
MRPL45P2
ITGB3
snoU13|ENSG00000252088.1
RN7SL270P
LRRC37A17P
RNU6ATAC3P
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
ZNF385C
TTC25
RN7SL871P
RN7SL399P
RNA5SP442
EIF1
KRT42P
LINC00974
KRT223P
KRT222
KRT222
RNA5SP441
GJD3
RNY4P8
SNORD124
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
ARL5C
LINC00672
SNORA21|ENSG00000199293.1
SNORA21|ENSG00000252699.1
RPL23
RNA5SP440
CISD3
MIR4726
RN7SL102P
RN7SL458P
SOCS7
HMGB1P24
MIR2909
RNA5SP439
CCL4L2
RN7SL301P
CCL4
CCL18
RN7SKP274
SNORD7
SLFN12L
SLFN5
Vault|ENSG00000252328.1
snoU13|ENSG00000238858.1
RNA5SP438
C17orf75
SH3GL1P1
RNA5SP437
UTP6
RNU6ATAC7P
RN7SL45P
RN7SL79P
EVI2A
RN7SL138P
TEFM
SUZ12P
RN7SL316P
LRRC37BP1
SMURF2P1
SNORD63|ENSG00000252112.1
MIR423
MIR3184
RNY4P13
RNY4P13
snoU13|ENSG00000239129.1
SNORA70|ENSG00000252657.1
MIR4523
TIAF1
NEK8
SNORD4B
SNORD42A
SNORD4A
SNORD42B
RPL23A
SGK494
VTN
SEBOX
MIR4723
TMEM199
Vault|ENSG00000252283.1
SNORA70|ENSG00000202389.1
SCARNA20|ENSG00000251818.1
RN7SL576P
LGALS9
KSR1
TBC1D3P5
MTND1P15
UBBP4
RN7SL426P
TMEM11
KRT16P3
NOS2P3
USP32P3
UPF3AP2
RN7SL17P
U6|ENSG00000266839.2
CCDC144CP
SNORA31|ENSG00000252349.1
SNORA59B
MIR1180
SNORD3C
SNORD3A
GRAPL
SNORD3D
GRAP
FAM83G
RN7SL627P
ZNF286B
TBC1D28
RN7SL639P
KRT16P1
KRT17P2
SMCR8
snoU13|ENSG00000238691.1
MIR33B
SMCR5
SMCR2
RN7SL775P
TBC1D27
KRT17P1
KRT16P2
USP32P1
RN7SL620P
ZNF287
MIR1288
RN7SL442P
RNA5SP436
ZNF286A
SNORA74|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
SNORA74|ENSG00000252305.1
MIR548H3
RN7SL550P
MIR744
RPL21P122
RN7SL601P
LINC00675
MAGOH2
ADPRM
RCVRN
GLP2R
STX8
RN7SL129P
SNORA69|ENSG00000212206.1
CTC1
MIR3676
SNORD118
TMEM107
snoU13|ENSG00000238676.1
SCARNA21|ENSG00000252835.1
RPL29P2
snoU13|ENSG00000251860.1
SNORD10
SNORA48|ENSG00000209582.1
SNORA67|ENSG00000264772.2
SLC35G6
GABARAP
ALOX12P2
TEKT1
C17orf100
RNA5SP435
DERL2
RN7SL784P
RN7SL171P
SPNS2
RN7SL774P
snoU13|ENSG00000238807.1
RNA5SP434
C17orf85
SHPK
ASPA
OR1E1
OR1D4
RN7SL605P
MIR1253
RN7SL608P
snoU13|ENSG00000239024.1
RN7SL33P
SNORD91A
SNORD91B
RN7SL624P
TLCD2
snoU13|ENSG00000238946.1
RN7SL105P
BHLHA9
MIR3183
TIMM22
DBIL5P
DOC2B
ABR
ACACA
ACADVL
ASIC2
ACLY
ADORA2B
AP2B1
ALDH3A1
ALDH3A2
ALDOC
ALOX12
ALOX12B
ALOX15
ALOX15B
AOC2
ARL4D
ARRB2
ASGR1
ASGR2
ATP1B2
ATP2A3
ATP5G1
ATP6V0A1
BLMH
C1QBP
FMNL1
CA4
CACNB1
CD68
CDC6
CDC27
CHAD
CHD3
CHRNB1
CHRNE
CCR7
CNP
COX10
COX11
CPD
CLDN7
CRHR1
CRK
CRYBA1
CSF3
CSH1
CSH2
CSHL1
CTNS
CYB561
ACE
DHX8
DLG4
DLX3
DLX4
DNAH9
DPH1
DRG2
DUSP3
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
ERN1
EVI2B
EZH1
FGF11
FLII
FLOT2
GAST
KAT2A
GFAP
GH1
GH2
GIP
GNGT2
GP1BA
GPS2
GRB7
GRN
GUCY2D
HCRT
HIC1
HOXB5
HOXB6
HOXB7
HOXB8
HOXB9
ICAM2
IFI35
IGFBP4
ITGA2B
ITGA3
ITGAE
ITGB3
JUP
KCNJ12
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LHX1
LIG3
LLGL1
LPO
NBR1
MAPT
ADAM11
MAP3K3
MEOX1
MFAP4
MNT
MPO
MPP2
MPP3
TRIM37
MYH1
MYH2
MYH3
MYH4
MYH8
MYH10
MYL4
MYO1C
MYO1D
NAGLU
NFE2L1
NGFR
NME1
NMT1
NOS2
NSF
NUP88
OMG
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
PDK2
SERPINF1
PEX12
PFAS
PFN1
PHB
PITPNA
PLD2
SERPINF2
PMP22
SEPT4
POLR2A
MED1
PPY
MAPK7
MAP2K3
PRPSAP2
PSMB3
PSMB6
PYY
PSMC5
PSMD3
PSMD11
RAB5C
RAD51C
RAD51D
RPA1
RPL19
RPL26
RPL27
RPS6KB1
SCN4A
SCO1
CCL1
CCL2
CCL3
CCL3L1
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL23
SDF2
SGCA
SHBG
SHMT1
SLC2A4
SLC4A1
SLC6A4
SMARCD2
SMARCE1
SOX15
SP2
SREBF1
STAT3
STAT5A
STAT5B
SUPT4H1
SUPT6H
VAMP2
TADA2A
TBX2
HNF1B
MLX
THRA
TNFAIP1
TOP2A
TOP3A
DNAJC7
TUBG1
UBB
UBE2G1
UBTF
TRPV1
WNT3
WNT9B
YWHAE
ZNF18
PCGF2
TRIM25
RNF112
ZNF207
ZNF232
RND2
COIL
AKAP1
EPX
OR1A1
OR1D5
OR1E2
OR1G1
OR3A3
PIP4K2B
SLC25A11
SPOP
FOXN1
CNTNAP1
DGKE
COPS3
SCARF1
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
TNK1
ABCC3
MYH13
TNFSF13
CDK5R1
CACNA1G
HAP1
TM4SF5
SPAG9
SLC13A2
UNC119
MTMR4
RABEP1
KCNAB3
AURKB
NOG
BZRAP1
ZNHIT3
EFTUD2
NTN1
PIGL
TBX4
RPH3AL
FXR2
NPEPPS
MPDU1
GOSR1
SPAG7
CCL4L1
GOSR2
NR1D1
NCOR1
TRAF4
KIAA0100
ULK2
CCDC144A
ACAP1
TBKBP1
PLEKHM1
KIAA0753
MED24
LRRC37A
MRC2
SGSM2
ARHGAP44
HS3ST3A1
MED13
HDAC5
TOM1L1
GJC1
TOB1
PSME3
NBR2
SLC35B1
DCAF7
CALCOCO2
RAMP2
PEMT
CLEC10A
HOXB13
VAT1
APPBP2
MYBBP1A
FBXW10
PRPF8
LEPREL4
HEXIM1
SPAG5
TRIM16
IGF2BP1
CCT6B
RAI1
KIF1C
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
KAT7
AKAP10
SYNRG
DDX42
CASC3
NLRP1
ARHGEF15
EPN2
SARM1
RAP1GAP2
CAMTA2
KDM6B
ZZEF1
MPRIP
CLUH
SMG6
WSCD1
USP22
CTDNEP1
KCNH4
TNFRSF13B
MMD
PIK3R5
ELP5
FAM215A
PPY2
PYY2
SHPK
AIPL1
DHRS7B
KRT23
RNF167
TMEM98
POLDIP2
TBC1D29
TANC2
WSB1
SENP3
OR1A2
ERAL1
AATF
OR4D1
PELP1
B9D1
TUBG2
TMEM97
NKIRAS2
COA3
GIT1
RANGRF
PSMC3IP
SNX11
TBX21
TAX1BP3
MINK1
GEMIN4
SOST
MED31
TVP23B
GLOD4
YBX2
UTP18
RNFT1
MYO15A
TUBD1
RAPGEFL1
TACO1
ABI3
COPZ2
MRPL27
PIPOX
ARL17A
CRLF3
TRPV2
ANKFY1
SLC25A39
PTRH2
RASD1
NLK
LUC7L3
HIGD1B
CDK12
INPP5K
KRT20
NLE1
FAM64A
XAF1
FNDC8
C17orf59
MBTD1
BCAS3
CWC25
ALKBH5
RNF43
TTC19
MKS1
LINC00483
EPN3
SLC52A1
MED9
SLFN12
WRAP53
KLHL11
RNMTL1
SMG8
SLC47A1
TMEM100
VPS53
RHOT1
RSAD1
COPRS
LRRC59
TSR1
FAM222B
ADAP2
GSDMB
TEX14
DHX33
CA10
NT5M
ATXN7L3
CCDC47
PLSCR3
PLXDC1
LYZL6
ZNF286A
INTS2
NUFIP2
ZNF624
TAOK1
NLGN2
ARHGAP23
PHF12
ZBTB4
CXCL16
TRAPPC1
PCTP
SCPEP1
ALOXE3
ELAC2
FKBP10
SRR
HEATR6
XYLT2
NXN
TEKT3
SPATA20
UBE2Z
WNK4
C17orf53
MIS12
GID4
METTL16
TMUB2
DHX58
PHF23
MMP28
DHRS11
PRR15L
DHX40
ACBD4
FAM57A
DCAKD
GGNBP2
ATAD5
MRM1
PLEKHH3
FAM106A
DBF4B
MYO19
ACSF2
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
LIMD2
KCNH6
FAM117A
NDEL1
VMP1
ACKR6
LRRC48
EMC6
RILP
RAB34
GSG2
MYCBPAP
NSRP1
PPP1R1B
TBC1D3F
ZMYND15
CAMKK1
RPAIN
RNF135
MIEN1
MRPL45
VPS25
LSMD1
TMEM101
PRAC
RAB11FIP4
NEURL4
GHDC
ZNF594
KIF2B
HES7
PPP1R9B
SPATA22
TXNDC17
CORO6
TNS4
FBXL20
SSH2
TP53I13
IFT20
LRRC46
SCRN2
ANKRD40
ZNF830
SLFN11
RASL10B
ATPAF2
TMEM88
STRADA
C17orf72
SPECC1
G6PC3
ASB16
PGAP3
MYOCD
PIGS
HSPB9
ORMDL3
SAT2
PLCD3
SLC46A1
TMEM106A
LRRC37B
SMYD4
OSBPL7
NT5C3B
ABHD15
TLCD1
CNTROB
FTSJ3
RFFL
HSF5
OR4D2
ZPBP2
CYB5D1
OVCA2
USP43
KRBA2
C17orf64
SPATA32
HEXIM2
LSM12
CCDC43
TMEM132E
WFIKKN2
B4GALNT2
SPACA3
SEZ6
ANKRD13B
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
EFCAB13
MRPL10
WDR81
KRT40
ZSWIM7
SMCR7
SLC5A10
TOM1L2
DNAH2
RTN4RL1
EFCAB3
SLC47A2
WDR16
CCDC42
PIK3R6
ODF4
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
EME1
PROCA1
DHRS13
KCTD11
TRIM16L
WIPF2
KRT25
TMEM99
ANKFN1
MARCH10
MFSD6L
NAGS
FAM134C
TMEM92
PHOSPHO1
RHBDL3
TRPV3
SLC16A11
FBXO39
SPPL2C
KRT28
KRT24
DHRS7C
TVP23C
CENPV
FLCN
PLD6
ARHGAP27
SAMD14
LYRM9
SLC16A13
C17orf74
RDM1
SPNS3
USP32P2
GAS2L2
STH
STXBP4
TMEM256
TAC4
BCL6B
CDRT15L2
C17orf103
C17orf66
VMO1
LINC00324
LINC00670
CDRT4
CCDC144B
KANSL1
FAM171A2
C17orf104
TTLL6
C17orf47
KRT18P55
PIGW
C17orf78
GSDMA
SLC13A5
TMEM102
PTRF
FAM27L
GDPD1
LGALS9B
TUSC5
KLHL10
TMEM95
METTL2A
CCDC144NL
C17orf67
C17orf51
MSL1
SMTNL2
NACA2
KRT27
SLFN14
LRRC37A11P
STAC2
SKA2
TBC1D26
KRT26
FAM101B
CDRT1
SPEM1
EFCAB5
GLTPD2
INCA1
SCIMP
SPDYE4
TMEM220
SHISA6
FAM211A
TMIGD1
C17orf98
LINC00671
RPRML
YPEL2
C17orf82
OR3A4P
KRT39
SLC25A35
MYO18A
C17orf97
MED11
C17orf102
CUEDC1
MIR10A
MIR132
MIR142
MIR193A
MIR196A1
MIR21
MIR212
MIR22HG
TNFSF12
TBC1D3B
TBC1D3C
CCL3L3
RNASEK
GPR179
MIR324
LRRC37A2
FBXO47
MIR497HG
RNF222
PIRT
EVPLL
TBC1D3G
LGALS9C
NME2
MIR632
MIR633
TBC1D3
TBC1D3H
MIR365B
C17orf107
C17orf96
MIR2117
MIR3185
MIR4314
MTRNR2L1
MIR3614
LRRC3C
ARL17B
C17orf112
MIR4523
MIR4734
MIR4737
MIR4736
MIR4724
MIR4733
MIR4522
MIR4732
MIR4520B
MIR4727
MIR4725
MIR1269B
MIR5089
PTGES3L

Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
LINC00229
SCUBE1
RNU12
RN7SKP80
RRP7B
RRP7A
snoU13|ENSG00000238498.1
LINC00634
SHISA8
MIR33A
RNU6ATAC22P
ACR
ACO2
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
NAGA
NDUFA6
NHP2L1
PMM1
PPARA
MAPK11
RANGAP1
MAPK12
SBF1
SREBF2
TCF20
TEF
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
TOB2
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
ZC3H7B
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
CSDC2
MCAT
DESI1
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
MIOX
PRR5
TRMU
SEPT3
PANX2
PARVG
CERK
EFCAB6
CENPM
CRELD2
C22orf46
CCDC134
ADM2
TRABD
PNPLA3
HDAC10
LDOC1L
POLDIP3
PHF5A
KIAA1644
SHANK3
TUBGCP6
LMF2
SMDT1
SERHL
PHF21B
KLHDC7B
TNFRSF13C
MEI1
FAM109B
NFAM1
PNPLA5
WBP2NL
POLR3H
SERHL2
ATP5L2
C22orf34
LINC00207
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR378I
MIR4535

Genes in Wide Peak

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

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

Genes
ATRX
ELF4
GPC3
MSN
MTCP1
NONO
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
MIR452
MIR224
U3|ENSG00000253009.1
LINC00894
LINC00893
RN7SKP267
CXorf51A
CXorf51B
RNA5SP517
SPANXN1
RN7SKP189
RN7SKP149
RN7SKP81
snoU13|ENSG00000239188.1
RNA5SP516
SPANXD
SPANXA2
SPANXA1
RN7SL727P
MIR505
SNORA18|ENSG00000252719.1
RNU6ATAC23P
snoU13|ENSG00000238485.1
MIR504
RN7SKP31
RN7SL325P
SNORD61|ENSG00000206979.1
MIR934
snoU13|ENSG00000239080.1
RNA5SP515
LINC00086
LINC00633
LINC00087
SMIM10
LINC00629
GPC4
SNORA8|ENSG00000207100.1
RNA5SP514
RN7SL191P
FAM45B
RNA5SP513
DCAF12L2
snoU13|ENSG00000238626.1
SNORA40|ENSG00000252693.1
snoU13|ENSG00000239058.1
RN7SL29P
U3|ENSG00000212321.1
CT47A12
MCTS1
snoU13|ENSG00000272179.1
RHOXF2B
NDUFA1
SNORA69|ENSG00000206622.1
MIR766
RN7SL118P
SNORA35|ENSG00000239182.1
MIR1277
RN7SL712P
SNORA64|ENSG00000252441.1
SNORA35|ENSG00000271907.1
MIR448
MIR1911
SNORA35|ENSG00000208839.1
SNORD30
RN7SL93P
U3|ENSG00000201674.1
snoU13|ENSG00000238811.1
RN7SL266P
MIR4329
ZCCHC16
TRPC5OS
RNA5SP512
RN7SL661P
LINC00890
TDGF1P3
GNG5P2
SNORD96B
MIR3978
MIR652
MID2
NCBP2L
RBM41
MIR548AN
ZCCHC18
RNA5SP511
LINC00630
NXF4
TCP11X1
TCP11X3P
TCEAL6
SNORA9|ENSG00000202231.1
TSPAN6
SNORA25|ENSG00000252296.1
RN7SL74P
RN7SKP194
RN7SL379P
RNA5SP510
ACA64|ENSG00000252016.1
SNORD45|ENSG00000200422.1
MIR361
APOOL
UBE2DNL
RPS6KA6
SNORA4|ENSG00000202183.1
ACA64|ENSG00000239008.1
CYSLTR1
COX7B
RN7SL460P
FGF16
RNA5SP509
RNA5SP508
RN7SL641P
RN7SL790P
RN7SL648P
FTX
JPX
XIST
TSIX
MAP2K4P1
CDX4
LINC00684
FAM226A
U3|ENSG00000202482.1
RPS4X
RN7SL264P
RN7SL388P
CXorf49B
CXorf49
INGX
snoU13|ENSG00000252525.1
CXorf65
RN7SL746P
U3|ENSG00000199769.1
RNY4P23
RNA5SP507
RN7SL581P
MIR676
U3|ENSG00000212434.1
LINC00269
RN7SL799P
ABCB7
AGTR2
ABCD1
SLC25A5
XIAP
AR
ARHGAP4
ARR3
ATP2B3
ATP6AP1
ATP7A
AVPR2
BGN
BRS3
BTK
CAPN6
CD40LG
CDR1
CHM
CLIC2
CNGA2
COL4A5
COL4A6
CSTF2
CTAG1B
TEX28
CYLC1
DCX
TIMM8A
DIAPH2
DKC1
DLG3
DNASE1L1
DRP2
TSC22D3
DUSP9
EDA
EFNB1
EMD
F8
F9
ACSL4
FGF13
FHL1
FLNA
FMR1
AFF2
CENPI
G6PD
GABRA3
GABRE
GDI1
GJB1
GLA
GLUD2
CXCR3
LPAR4
GRIA3
GUCY2F
HCFC1
HMGB3
HNRNPH2
HPRT1
HTR2C
IDH3G
IDS
IGBP1
IGSF1
IL2RG
IL9R|ENSG00000124334.12
IL13RA1
IL13RA2
IRAK1
L1CAM
LAMP2
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
FOXO4
MPP1
CITED1
MTM1
NAP1L2
NAP1L3
OCRL
OPHN1
P2RY4
PAK3
PGK1
PHKA1
PIN4
PLP1
PLS3
PLXNB3
POU3F4
PRPS1
PSMD10
OPN1LW
RENBP
RPL10
RPL39
RPL36A
SH3BGRL
SLC6A8
SLC16A2
SMARCA1
SOX3
SSR4
VAMP7|ENSG00000124333.10
TAF1
TAZ
SERPINA7
TRPC5
UBE2A
VBP1
XPNPEP2
ZIC3
ZNF711
ZNF75D
RNF113A
ZNF185
ZXDA
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
CUL4B
IRS4
OGT
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
CLDN2
FAM50A
AIFM1
TMEM257
ZMYM3
GPR50
TCEAL1
RAB33A
ITM2A
ARHGEF6
MORF4L2
GPRASP1
STARD8
ARMCX2
HEPH
MAGEC1
AMMECR1
MED12
ZBTB33
MAMLD1
BCAP31
TENM1
SPRY3|ENSG00000168939.6
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
PGRMC1
TMSB15A
TREX2
SLC6A14
VSIG4
SEPT6
ARHGEF9
ATP1B4
KCNE1L
LDOC1
KIF4A
FAM127B
IL1RAPL2
ITGB1BP2
SRPK3
NGFRAP1
NOX1
FAM155B
SRPX2
RBMX
PCDH11X
P2RY10
HTATSF1
C1GALT1C1
SNX12
RPA4
PNMA3
CTAG2
NSDHL
TBX22
ZDHHC9
RLIM
WBP5
RAB9B
LUZP4
PDZD11
PBDC1
TFDP3
ARMCX1
MAGEC2
VGLL1
ARMCX3
TAF9B
RBMX2
MST4
CPXCR1
CHIC1
NLGN3
SASH3
TAF7L
ARMCX6
WDR44
ERCC6L
NUP62CL
GDPD2
TBC1D8B
CXorf48
TMEM255A
CXorf57
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MTMR8
MBNL3
BEX1
HDAC8
ZC4H2
NXT2
NKRF
NXF5
NXF3
NXF2
KLHL4
TEX13B
TEX13A
TEX11
MOSPD1
BEX4
TCEAL7
THOC2
KIAA1210
PCDH19
RGAG1
PDZD4
LRCH2
MAGEE1
RAP2C
TMEM35
FAM3A
EDA2R
BCORL1
CXorf56
DMRTC1
TNMD
PJA1
SPANXC
ARMCX5
UPF3B
PRRG3
BRCC3
HMGN5
NKAP
RNF128
MAP7D3
MORC4
LONRF3
ALG13
TCEAL4
TRMT2B
POF1B
ESX1
BHLHB9
LAS1L
GPR101
CD99L2
H2AFB3
USP26
MAGT1
TMEM164
PHF6
FRMPD3
ZMAT1
RHOXF2
TMEM185A
SLITRK2
GPR174
BEX2
SLC7A3
TCEAL3
FATE1
HS6ST2
FRMD7
KLHL13
TGIF2LX
TCEAL8
CHRDL1
CXorf40A
FAM58A
RIPPLY1
MMGT1
ACRC
SYTL4
PNMA5
GPRASP2
ATG4A
RAB39B
DACH2
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
PIH1D3
MUM1L1
FAM199X
AMER1
HDX
GPR112
OTUD6A
UPRT
MAGEE2
GAB3
PNCK
ZFP92
ACTRT1
GPR119
RBMXL3
DOCK11
SPIN4
TCEAL2
PABPC5
RAB40A
ASB12
AMOT
CSAG1
FMR1NB
ARHGAP36
AKAP14
RHOXF1
NKAPP1
AWAT1
AWAT2
ZDHHC15
H2BFWT
FAM122B
FAM122C
FAM46D
ZCCHC12
CXorf61
SLC25A43
ZCCHC5
NRK
DDX26B
ZNF449
VMA21
TMEM31
CTAG1A
BRWD3
CT47A11
RAB40AL
ATP11C
LINC00632
H2BFM
YIPF6
FAM133A
TMSB15B
RGAG4
NHSL2
PABPC1L2A
KIAA2022
BEX5
TCEAL5
VSIG1
ZC3H12B
SATL1
LHFPL1
SOWAHD
OR13H1
CCDC160
CXorf66
DGAT2L6
RAB41
ZCCHC13
UBE2NL
ARL13A
SLC25A53
XKRX
MIR106A
MIR19B2
MIR223
MIR92A2
GLRA4
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
PGAM4
MIR325
MIR374A
H2AFB2
H2AFB1
SPANXN2
MIR503HG
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR450A2
MIR503
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR510
MIR514A1
MIR514A2
MIR514A3
CT47B1
PABPC1L2B
NAP1L6
CT47A7
MIR545
MIR542
MIR421
CT47A10
CT47A9
CT47A8
CT47A6
CT47A5
CT47A4
CT47A3
CT47A2
CT47A1
MAGEA9B
NXF2B
OPN1MW2
DMRTC1B
SPANXB1
CT45A2
MIR767
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR374B
MIR891A
MIR892A
LINC00892
HSFX2
CXorf64
ARMCX4
SMIM9
SPANXB2
CMC4
PNMA6C
MIR513C
MIR1468
MIR1912
MIR1298
MIR320D2
MIR548I4
MIR548M
MIR718
MIR513B
MIR764
MIR2114
MIR514B
MIR4330
MIR3672
HSFX1
TCP11X2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 12 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 | 0.02 | -1.18 | 0.951 | 0.09 | 0.486 | 0.984
1q | 1195 | 0.13 | 1.47 | 0.244 | 0.02 | -1.21 | 0.984
2p | 624 | 0.13 | 0.709 | 0.458 | 0.05 | -1.12 | 0.984
2q | 967 | 0.13 | 1.17 | 0.357 | 0.05 | -0.832 | 0.984
3p | 644 | 0.23 | 2.96 | 0.00902 | 0.13 | 0.691 | 0.984
3q | 733 | 0.28 | 4.16 | 0.000132 | 0.14 | 0.922 | 0.984
4p | 289 | 0.00 | -2.42 | 0.992 | 0.06 | -1.14 | 0.984
4q | 670 | 0.00 | -2.17 | 0.992 | 0.08 | -0.32 | 0.984
5p | 183 | 0.15 | 0.612 | 0.482 | 0.02 | -1.88 | 0.984
5q | 905 | 0.13 | 1.02 | 0.394 | 0.02 | -1.44 | 0.984
6p | 710 | 0.13 | 0.816 | 0.431 | 0.05 | -1.05 | 0.984
6q | 556 | 0.07 | -0.571 | 0.913 | 0.18 | 1.67 | 0.65
7p | 389 | 0.33 | 4.67 | 3.02e-05 | 0.06 | -0.91 | 0.984
7q | 783 | 0.28 | 4.49 | 4.94e-05 | 0.06 | -0.708 | 0.984
8p | 338 | 0.15 | 0.814 | 0.431 | 0.21 | 2.08 | 0.608
8q | 551 | 0.18 | 1.73 | 0.155 | 0.10 | -0.0544 | 0.984
9p | 301 | 0.15 | 0.806 | 0.431 | 0.05 | -1.32 | 0.984
9q | 700 | 0.15 | 1.24 | 0.337 | 0.02 | -1.55 | 0.984
10p | 253 | 0.09 | -0.627 | 0.913 | 0.05 | -1.47 | 0.984
10q | 738 | 0.09 | -0.159 | 0.855 | 0.05 | -1.1 | 0.984
11p | 509 | 0.19 | 1.88 | 0.124 | 0.00 | -2.13 | 0.984
11q | 975 | 0.28 | 4.83 | 2.82e-05 | 0.03 | -1.16 | 0.984
12p | 339 | 0.15 | 0.849 | 0.431 | 0.05 | -1.29 | 0.984
12q | 904 | 0.19 | 2.58 | 0.0253 | 0.03 | -1.34 | 0.984
13q | 560 | 0.11 | 0.198 | 0.691 | 0.07 | -0.702 | 0.984
14q | 938 | 0.04 | -0.998 | 0.951 | 0.04 | -0.998 | 0.984
15q | 810 | 0.05 | -0.93 | 0.951 | 0.15 | 1.46 | 0.739
16p | 559 | 0.13 | 0.689 | 0.458 | 0.07 | -0.659 | 0.984
16q | 455 | 0.16 | 1.11 | 0.362 | 0.10 | -0.198 | 0.984
17p | 415 | 0.05 | -1.16 | 0.951 | 0.20 | 1.89 | 0.608
17q | 972 | 0.07 | -0.352 | 0.901 | 0.09 | 0.148 | 0.984
18p | 104 | 0.29 | 3.19 | 0.00485 | 0.17 | 0.784 | 0.984
18q | 275 | 0.32 | 4.2 | 0.000132 | 0.12 | 0.0374 | 0.984
19p | 681 | 0.06 | -0.758 | 0.936 | 0.02 | -1.69 | 0.984
19q | 935 | 0.06 | -0.549 | 0.913 | 0.00 | -2.04 | 0.984
20p | 234 | 0.11 | -0.237 | 0.869 | 0.02 | -1.92 | 0.984
20q | 448 | 0.09 | -0.495 | 0.913 | 0.02 | -1.81 | 0.984
21q | 258 | 0.21 | 2.06 | 0.0897 | 0.03 | -1.73 | 0.984
22q | 564 | 0.02 | -1.77 | 0.992 | 0.06 | -0.865 | 0.984
Xp | 418 | 0.12 | 0.212 | 0.691 | 0.14 | 0.646 | 0.984
Xq | 668 | 0.10 | -0.0408 | 0.814 | 0.14 | 0.88 | 0.984

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/DLBC-TP/14517216/GDAC_MergeDataFiles_12183790/DLBC-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 48 Input Tumor Samples.

Tumor Sample Names
TCGA-FA-8693-01A-11D-2389-01
TCGA-FA-A4BB-01A-11D-A31W-01
TCGA-FA-A4XK-01A-11D-A31W-01
TCGA-FA-A6HN-01A-11D-A31W-01
TCGA-FA-A6HO-01A-11D-A31W-01
TCGA-FA-A7DS-01A-11D-A381-01
TCGA-FA-A7Q1-01A-11D-A381-01
TCGA-FA-A82F-01A-11D-A381-01
TCGA-FA-A86F-01A-11D-A381-01
TCGA-FF-8041-01A-11D-2209-01

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.

- 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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