Copy number analysis (GISTIC2)
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C11N7Z5D
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C11N7Z5D
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 191 tumor samples used in this analysis: 14 significant arm-level results, 6 significant focal amplifications, and 15 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 - 6 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
--- | --- | --- | --- | ---
11q23.3 | 2.3113e-09 | 2.3113e-09 | chr11:118341650-118354357 | 1
21q22.2 | 1.1836e-06 | 1.1836e-06 | chr21:39509205-42282190 | 20
1q43 | 0.0017345 | 0.0017345 | chr1:236900019-236902363 | 1
1p33 | 0.018357 | 0.018357 | chr1:47516423-47533836 | 2
20q11.21 | 0.13547 | 0.13547 | chr20:26197900-30867110 | 34
13q31.3 | 0.20147 | 0.20147 | chr13:90236534-92243193 | 12

Genes in Wide Peak

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

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

Genes
MLL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q22.2.

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

Genes
ERG
DSCAM
ETS2
HMGN1
KCNJ15
PCP4
SH3BGR
WRB
PSMG1
B3GALT5
BRWD1
DSCR8
C21orf88
LCA5L
IGSF5
BRWD1-IT2
DSCR10
LINC00114
DSCAM-AS1
MIR4760

Genes in Wide Peak

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

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

Genes
ACTN2

Genes in Wide Peak

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

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

Genes
CYP4Z1
CYP4X1

Genes in Wide Peak

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

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

Genes
hsa-mir-1825
hsa-mir-3193
BCL2L1
FOXS1
HCK
ID1
PLAGL2
KIF3B
TM9SF4
TPX2
POFUT1
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TSPY26P
MLLT10P1
C20orf160
LINC00028
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
PSIMCT-1
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q31.3.

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

Genes
hsa-mir-92a-1
hsa-mir-622
GPC5
LINC00410
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
MIR622

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 - 15 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
--- | --- | --- | --- | ---
5q31.2 | 1.0161e-07 | 1.0161e-07 | chr5:112352080-156187927 | 373
1q43 | 8.942e-07 | 8.942e-07 | chr1:236767073-236961354 | 1
17q11.2 | 0.00029245 | 0.00031184 | chr17:28936804-29722618 | 13
16q23.1 | 0.00051381 | 0.00051381 | chr16:66780177-82663437 | 187
7p12.1 | 0.00059838 | 0.00064841 | chr7:50632522-51084050 | 1
7q32.3 | 3.7128e-05 | 0.0012079 | chr7:126055410-159138663 | 309
12p13.2 | 0.0022726 | 0.0023129 | chr12:11415451-13714562 | 34
3p13 | 0.019726 | 0.019726 | chr3:64994325-77091215 | 42
18p11.21 | 0.020878 | 0.02096 | chr18:12273033-13621128 | 11
7q34 | 6.6571e-05 | 0.033649 | chr7:107526194-159138663 | 376
9p24.1 | 0.05089 | 0.048476 | chr9:8310705-12693402 | 1
12q21.33 | 0.094523 | 0.094139 | chr12:88430068-96052227 | 47
17p13.2 | 0.11781 | 0.11633 | chr17:1-7744654 | 218
20q13.13 | 0.15544 | 0.15863 | chr20:30824328-55848202 | 277
3q26.31 | 0.25169 | 0.26636 | chr3:1-198022430 | 1276
9q21.32 | 0.24078 | 0.26636 | chr9:1-141213431 | 983

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q31.2.

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

Genes
CD74
PDGFRB
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
ADRB2
ANXA6
ATOX1
ALDH7A1
CAMK2A
CAMLG
CD14
CDC25C
CDO1
CDX1
AP3S1
CSF1R
CSF2
CSNK1A1
CSNK1G3
CTNNA1
DMXL1
DIAPH1
DPYSL3
SLC26A2
HBEGF
EGR1
ETF1
FAT2
FBN2
FGF1
GDF9
GFRA3
GLRA1
GM2A
GPX3
GRIA1
NR3C1
HARS
HINT1
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL13
IRF1
KCNN2
LECT2
LMNB1
LOX
SMAD5
MCC
MFAP3
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
PURA
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC22A4
SLC22A5
SNX2
SPARC
SPINK1
SPOCK1
TAF7
TCF7
TCOF1
TGFBI
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
EIF4EBP3
PCDHGB4
CDC23
HDAC3
P4HA2
ATG12
CNOT8
HAND1
MYOT
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
PCDHGA8
PCDHA9
MATR3
KIAA0141
JAKMIP2
DDX46
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
SEC24A
C5orf4
FAM114A2
BRD8
TCERG1
HNRNPA0
SPINK5
KIF3A
SYNPO
ABLIM3
HMGXB3
ARHGAP26
FSTL4
SEPT8
ACSL6
PHF15
LARP1
HARS2
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
SNORD63
SNORA74A
PKD2L2
UQCRQ
AFF4
IL17B
SLC27A6
SNX24
MRPL22
PCDHB1
TMED7
ISOC1
SAR1B
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
LARS
CXXC5
RAPGEF6
KDM3B
PHAX
RBM27
PCDHB18
PCDHB17
ZCCHC10
WDR55
ANKHD1
TMCO6
TRIM36
GALNT10
RBM22
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
SIL1
ARAP3
YTHDC2
GRAMD3
PCYOX1L
SH3TC2
SAP30L
TXNDC15
NDFIP1
FBXO38
YIPF5
TIGD6
SPRY4
SLC4A9
SLC25A2
TSSK1B
PCDHB19P
PCBD2
PSD2
C5orf32
MEGF10
SPINK7
C5orf62
FCHSD1
LYRM7
CDKN2AIPNL
ZNF300
MYOZ3
PRDM6
FTMT
FNIP1
SLC35A4
MARCH3
LEAP2
SCGB3A2
PPARGC1B
PRRC1
ZNF474
AFAP1L1
GRPEL2
GPR151
ZNF300P1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
CEP120
SLC25A48
SRFBP1
LOC153469
ZMAT2
CCDC112
PRELID2
SH3RF2
PLAC8L1
ADAMTS19
SPATA24
DNAJC18
STK32A
AQPEP
SLC36A1
DTWD2
RELL2
SLC36A3
KIF4B
CHSY3
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
IRGM
CATSPER3
TICAM2
DND1
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR143
MIR145
SPINK14
C5orf56
IGIP
TIFAB
LOC553103
CTXN3
ECSCR
GRXCR2
SPINK9
LOC644100
FLJ33630
CCNI2
SNHG4
MIR143HG
LOC728342
LOC729080
VTRNA2-1
MIR874
MIR1289-2
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
MIR3141
MIR3655
MIR3936
MIR3661
LOC100505658
LOC100505841
MIR4633
MIR4461
MIR4460

Genes in Wide Peak

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

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

Genes
ACTN2

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG
SH3GL1P2
CRLF3
ADAP2
TEFM
ATAD5
RNF135
SUZ12P
DPRXP4
MIR4733

Genes in Wide Peak

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

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

Genes
CBFB
CDH1
MAF
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
AARS
AP1G1
AGRP
ZFHX3
CA7
CALB2
CDH3
CDH16
CTRB1
CTRL
DHODH
NQO1
E2F4
GCSH
GLG1
HAS3
HP
HPR
HSD11B2
HSD17B2
HSF4
KARS
LCAT
CHST6
NFATC3
PLCG2
PSKH1
PSMB10
PSMD7
RRAD
ST3GAL2
SLC9A5
SLC12A4
SNTB2
TAT
TERF2
ZNF19
ZNF23
GAN
TRADD
CES2
NAE1
NOL3
SLC7A6
ATP6V0D1
BCAR1
DHX38
IST1
CLEC3A
CHST4
MPHOSPH6
NUTF2
CFDP1
CTCF
NFAT5
WWP2
DDX19B
GABARAPL2
MON1B
PHLPP2
ATMIN
SF3B3
CES3
ADAT1
CHST5
EDC4
PLA2G15
COG4
PLEKHG4
LRRC29
VPS4A
NOB1
TMEM208
FHOD1
ZDHHC1
PARD6A
NIP7
FAM96B
TPPP3
WWOX
BCMO1
TERF2IP
PRMT7
HYDIN
DUS2L
CHTF8
TXNL4B
PDPR
RFWD3
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
VAC14
FTSJD1
DDX28
TSNAXIP1
CENPN
C16orf61
THAP11
PDP2
RANBP10
VAT1L
PDF
DPEP2
DPEP3
ACD
FA2H
FAM65A
TMEM231
TMCO7
WDR59
ELMO3
ESRP2
CENPT
C16orf70
CYB5B
CMIP
GFOD2
PMFBP1
DYNLRB2
C16orf48
SLC7A6OS
COG8
B3GNT9
CIRH1A
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
SDR42E1
PKD1L2
EXOSC6
C16orf46
NRN1L
CDYL2
TMEM170A
ZFP90
RLTPR
KCTD19
IL34
TMED6
ZFP1
ADAMTS18
LDHD
FUK
MLKL
CCDC79
CES4A
EXOC3L1
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
ATXN1L
PKD1L3
CLEC18A
C16orf86
MIR140
CTRB2
MIR328
CLEC18B
KIAA0895L
SNORD71
SNORD111
LOC729513
SNORD111B
LOC100129617
LOC100130894
SYCE1L
MIR1538
MIR1972-1
SNORA70D
MIR1972-2
LOC100506083
LOC100506172
MIR4720
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p12.1.

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

Genes
GRB10

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q32.3.

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

Genes
BRAF
EZH2
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
CLEC5A
MKRN1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
CPA4
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

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

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
CDKN1B
CREBL2
EMP1
GPR19
LRP6
PRB1
PRB3
PRB4
GPRC5A
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
DUSP16
APOLD1
GSG1
HTR7P1
LOH12CR1
C12orf36
LOC338817
RPL13AP20
LOH12CR2
PRB2
MIR613
MIR614
MIR1244-1
MIR1244-3
MIR1244-2
LOC100506314

Genes in Wide Peak

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

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

Genes
MITF
FOXP1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
GPR27
CNTN3
TMF1
SUCLG2
UBA3
MAGI1
ARL6IP5
PDZRN3
FRMD4B
RYBP
LRIG1
EBLN2
SHQ1
LMOD3
PROK2
KBTBD8
SLC25A26
FAM19A4
PPP4R2
LOC201617
C3orf64
EIF4E3
LOC401074
FAM19A1
FLJ20518
FAM86DP
GXYLT2
ZNF717
FRG2C
MIR1284
MIR1324
MIR3136
MIR4272
MIR4273
MIR4444-1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.21.

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

Genes
PTPN2
SLMO1
AFG3L2
CEP192
SPIRE1
PSMG2
CEP76
SEH1L
TUBB6
LOC100288122
MIR4526

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DLD
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IFRD1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRCAM
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ZNF277
ABCB8
TFEC
LAMB4
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
NAA38
GPR85
TAS2R5
CHPF2
ING3
LRRN3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
TMEM168
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
IMMP2L
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
C7orf60
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
THAP5
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
C7orf53
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
LOC401397
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
EIF3IP1
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
MIR3666
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

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

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

Genes
PTPRD

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.33.

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

Genes
BTG1
hsa-mir-331
hsa-mir-492
ATP2B1
DCN
EPYC
DUSP6
LUM
KITLG
NR2C1
UBE2N
EEA1
GALNT4
CRADD
SOCS2
PLXNC1
METAP2
KERA
NUDT4
MRPL42
CCDC41
VEZT
FGD6
NDUFA12
TMCC3
CEP290
USP44
LOC144481
LOC144486
KRT19P2
TMTC3
C12orf12
LOC256021
POC1B
LOC338758
C12orf74
C12orf37
PLEKHG7
NUDT4P1
MIR331
CLLU1OS
CLLU1
MIR492
LOC643339
LOC728084
MIR3685
POC1B-GALNT4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.2.

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

Genes
TP53
USP6
hsa-mir-324
hsa-mir-497
hsa-mir-1253
hsa-mir-212
hsa-mir-22
hsa-mir-3183
ABR
ACADVL
ALOX12
ALOX12P2
ALOX15
ARRB2
ASGR1
ASGR2
ASPA
ATP1B2
ATP2A3
C1QBP
CD68
CHRNB1
CHRNE
CLDN7
CRK
CTNS
DLG4
DPH1
DVL2
EFNB3
EIF4A1
EIF5A
ENO3
FGF11
GP1BA
GPS2
HIC1
ITGAE
MNT
MYO1C
NUP88
OR1D2
OR3A1
OR3A2
P2RX1
P2RX5
PAFAH1B1
SERPINF1
PFN1
PITPNA
PLD2
SERPINF2
POLR2A
PSMB6
RPA1
SHBG
SLC2A4
SOX15
UBE2G1
TRPV1
YWHAE
ZNF232
OR1A1
OR1D5
OR1E1
OR1E2
OR1G1
OR3A3
SLC25A11
DOC2B
SCARF1
TNK1
TNFSF13
TNFSF12
TM4SF5
RABEP1
RPH3AL
FXR2
MPDU1
SPAG7
ACAP1
KIAA0753
SGSM2
CLEC10A
MYBBP1A
PRPF8
KIF1C
GABARAP
NLRP1
RAP1GAP2
CAMTA2
ZZEF1
KIAA0664
SMG6
WSCD1
CTDNEP1
C17orf81
SHPK
AIPL1
RNF167
SENP3
OR1A2
SNORA67
PELP1
TIMM22
TAX1BP3
MINK1
GEMIN4
MED31
DERL2
GLOD4
YBX2
ANKFY1
INPP5K
FAM64A
XAF1
GPR172B
WRAP53
RNMTL1
VPS53
C17orf85
TSR1
DHX33
PLSCR3
NLGN2
ZBTB4
CXCL16
SRR
NXN
MIS12
METTL16
PHF23
FAM57A
PITPNM3
TMEM93
RILP
TEKT1
GSG2
ZMYND15
CAMKK1
RPAIN
NEURL4
ZNF594
SPATA22
TXNDC17
MIR22HG
SAT2
SMYD4
RPL29P2
OVCA2
SLC43A2
CYB5D2
C17orf49
ZFP3
GGT6
SPNS2
WDR81
DNAH2
RTN4RL1
KCTD11
TRPV3
SLC16A11
FBXO39
SLC16A13
C17orf74
SPNS3
C17orf61
BCL6B
LOC284009
VMO1
SLC13A5
TMEM102
TUSC5
LOC339166
TMEM95
SMTNL2
ALOX15P1
FAM101B
SPEM1
GLTPD2
INCA1
SCIMP
C17orf100
OR3A4P
C17orf97
MED11
MIR132
MIR195
MIR212
MIR22
TNFSF12-TNFSF13
RNASEK
MIR324
MIR497
SLC35G6
SNORA48
SNORD10
OR1D4
SNORD91A
SNORD91B
BHLHA9
TLCD2
LOC728392
C17orf107
LOC100130950
DBIL5P
MIR1253
LOC100306951
MIR3183
LOC100506388
LOC100506713
MIR497HG
RNASEK-C17ORF49
C17orf61-PLSCR3
SENP3-EIF4A1
P2RX5-TAX1BP3
MIR4520A
MIR4520B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20q13.13.

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

Genes
TOP1
MAFB
ASXL1
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-1289-1
hsa-mir-499
hsa-mir-644
hsa-mir-1825
hsa-mir-3194
ADA
AHCY
ASIP
BMP7
BPI
CD40
CEBPB
CSE1L
CSTF1
CYP24A1
DNMT3B
E2F1
EPB41L1
EYA2
GGT7
GHRH
GSS
HNF4A
EIF6
KCNB1
KCNG1
KCNS1
LBP
MC3R
MMP9
MYBL2
NFATC2
NNAT
PFDN4
PI3
PLCG1
PLTP
CTSA
PTGIS
PTPN1
RBL1
RPN2
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SNTA1
SPAG4
SRC
STAU1
STK4
AURKA
TFAP2C
TGM2
TNNC2
UBE2V1
YWHAB
MKRN7P
ZNF217
GDF5
NCOA3
BCAS1
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
B4GALT5
KIF3B
RBM39
TTI1
SPATA2
ACOT8
ATP9A
SGK2
RBM12
MYL9
WFDC2
PROCR
ARFGEF2
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
UBE2C
PTPRT
PKIG
CEP250
PXMP4
RBPJL
DLGAP4
RALY
MAPRE1
ZHX3
NCOA6
SLC9A8
ADNP
ZMYND8
SAMHD1
C20orf4
L3MBTL1
PPP1R16B
TRPC4AP
SNORD12C
SNORA71B
SNORA71A
TP53TG5
MOCS3
SLC35C2
IFT52
PHF20
SCAND1
BPIFA1
C20orf43
C20orf111
PIGT
ERGIC3
CDK5RAP1
UQCC
BCAS4
DDX27
ZNF334
ZFP64
EDEM2
DOK5
DBNDD2
ACSS2
RNF114
SULF2
C20orf24
CTNNBL1
CASS4
SPINLW1
RALGAPB
JPH2
SALL4
ZNFX1
NDRG3
SLC12A5
PREX1
MYH7B
NCOA5
TP53INP2
RPRD1B
TGIF2
KCNK15
DHX35
MANBAL
ELMO2
ZNF335
PCIF1
NECAB3
CDH22
SLC13A3
LPIN3
GDAP1L1
LOC79015
TTPAL
ACTR5
DSN1
FER1L4
PABPC1L
BPIFB2
SLC2A10
FAM83D
DYNLRB1
ITCH
SLA2
CHD6
MAP1LC3A
PARD6B
ZNF341
TOX2
KIAA1755
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
BPIFB1
TP53RK
DNTTIP1
FAM210B
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
SLC32A1
BPIFA2
WFDC3
GCNT7
C20orf112
CBLN4
C20orf132
KIAA0889
C20orf118
RIMS4
SUN5
ROMO1
NEURL2
ZSWIM3
WFDC10A
WFDC6
C20orf173
FAM65C
C20orf152
R3HDML
ADIG
GTSF1L
WFDC5
LOC149950
COMMD7
BPIFB4
WFDC13
ACTL10
FAM209A
WFDC11
WFDC9
WFDC10B
LINC00494
LOC284751
C20orf203
BPIFA4P
LOC339568
ARHGAP40
BPIFB3
TMEM189
TMEM189-UBE2V1
LOC388796
FAM209B
SPINT4
SUMO1P1
ZNFX1-AS1
MIR499A
LOC647979
SNORA39
SNORA60
SNORA71C
SNORA71D
SNORD12
MIR644A
MIR645
SYS1-DBNDD2
SNORD12B
ZNF663
LOC100131496
LOC100287792
MIR3194
MIR3646
MIR3616
LOC100505783
LOC100505826
SPINLW1-WFDC6
TGIF2-C20ORF24
MIR499B
MIR4756
MIR4755

Genes in Wide Peak

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

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

Genes
BCL6
FOXL2
CBLB
CTNNB1
EIF4A2
ETV5
FANCD2
FHIT
GATA2
LPP
MITF
MLF1
MLH1
MYD88
PIK3CA
PPARG
RAF1
RPN1
SOX2
TFRC
VHL
XPC
BAP1
GMPS
SRGAP3
TFG
FOXP1
SETD2
PBRM1
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
AADAC
ACAA1
ACPP
ACTL6A
ACVR2B
ACY1
ADCY5
ADPRH
AGTR1
AHSG
ALAS1
ALCAM
AMT
APEH
APOD
ARF4
RHOA
ATP1B3
ATP2B2
ATP6V1A
ATR
BCHE
BDH1
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CASR
CAV3
CCK
CD80
CD86
ENTPD3
CD47
CDC25A
CISH
AP2M1
CLCN2
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CP
CPA3
CPB1
CPN2
CPOX
CRYGS
CSTA
CX3CR1
CYP8B1
DAG1
DGKG
DAZL
DLG1
DNASE1L3
DOCK3
DRD3
DUSP7
DVL3
ECT2
CELSR3
EHHADH
EIF4G1
EPHA3
EPHB1
EPHB3
MECOM
FBLN2
FGF12
FLNB
GAP43
GBE1
GHSR
GLB1
GNAI2
GNAT1
GOLGA4
GOLGB1
GP5
GP9
XCR1
GPR15
GPR27
GPX1
GRM2
GRM7
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRH1
HRG
HES1
HTR1F
HYAL1
IL1RAP
IL5RA
IL12A
IMPDH2
IRAK2
ITGA9
ITGB5
ITIH1
ITIH3
ITIH4
ITPR1
KNG1
KPNA1
KPNA4
LAMB2
RPSA
LSAMP
LTF
TM4SF1
MAP4
MBNL1
MCM2
MFI2
MME
MOBP
CD200
MST1
MST1R
MUC4
MYL3
MYLK
NCK1
NDUFB4
NDUFB5
NKTR
OGG1
OPA1
CLDN11
OXTR
P2RY1
PAK2
CNTN3
PCCB
PCYT1A
PDHB
PFKFB4
PFN2
SERPINI1
SERPINI2
PIK3CB
PLCD1
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
PLXNB1
POLR2H
POU1F1
PPP1R2
PPP2R3A
PRKAR2A
PRKCD
PRKCI
PROS1
MASP1
PSMD2
PTH1R
PTPRG
PTX3
QARS
RAB5A
RAP2B
RARB
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
SNORA62
ROBO1
ROBO2
RPL15
RPL24
RPL29
RPL32
RPL35A
RYK
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC6A1
SLC6A6
SLC6A11
SLC15A2
SLCO2A1
HLTF
SMARCC1
SSR3
SST
STAC
NEK4
SYN2
TCTA
TDGF1
TERC
TF
TFDP2
TGM4
TGFBR2
THPO
THRB
TIMP4
TKT
SEC62
TM4SF4
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
TRH
TRPC1
UBA7
UBE2E1
UBE2E2
UBP1
UPK1B
UMPS
USP4
UQCRC1
CLRN1
VIPR1
WNT5A
WNT7A
ZIC1
CNBP
ZNF35
ZNF80
ZNF148
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
RAB7A
KCNAB1
FXR1
COLQ
ACOX2
EOMES
HYAL3
SOX14
BFSP2
CAMK1
CGGBP1
BHLHE40
RUVBL1
CADPS
TP63
CHRD
HYAL2
B4GALT4
B3GALNT1
SNX4
TNFSF10
SUCLG2
HESX1
KAT2B
NR1I2
EIF2B5
BSN
MBD4
H1FX
USP13
LIMD1
KALRN
CCRL2
UBA3
RPL14
CLDN1
SEC22C
RRP9
MAP3K13
SLC33A1
LRRFIP2
MAGI1
CACNA2D2
COPB2
ADIPOQ
SLC22A14
SLC22A13
CHST2
SH3BP5
SLC4A7
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
VGLL4
EDEM1
KIAA0226
ECE2
VPRBP
TBC1D5
TATDN2
IP6K1
TSC22D2
EPM2AIP1
PSMD6
TOMM70A
TRANK1
IQSEC1
P2RY14
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
SMC4
ABCC5
COX17
ARPC4
ZNF197
RBM6
RBM5
TNK2
ALG3
NME6
CTDSPL
CD96
KCNMB2
STAG1
EIF1B
TRAIP
ST3GAL6
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
IGF2BP2
CXCR6
CSPG5
CLDN16
POLQ
CHL1
ARPP21
CCR9
ALDH1L1
USP19
PDIA5
SLC38A3
CYB561D2
TMEM115
TOPBP1
RPP14
HHLA2
FSTL1
FAM107A
WDR6
RASSF1
NISCH
MRPL3
PDCD10
FILIP1L
TREX1
SCN11A
TUSC2
RNF13
MGLL
TWF2
MRAS
COPG
SLITRK3
NLGN1
TRAK1
DHX30
SACM1L
NCBP2
SCAP
LAMB2P1
MYH15
PLCH1
EXOSC7
TMCC1
PDZRN3
TNIK
CAND2
MCF2L2
CLASP2
PLXND1
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
ATP11B
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
DNAJC13
U2SURP
VPS8
LARS2
RYBP
C3orf27
CAPN7
ACAP2
MKRN2
NAT6
FBXL2
ANAPC13
ARMC8
ABHD14A
C3orf17
POC1A
ABI3BP
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
WWTR1
PVRL3
TIPARP
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
UBXN7
ERC2
APPL1
HACL1
ARHGEF26
ZBTB20
TTLL3
OR5K1
OR5H1
GNL3
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
ZBTB11
MORC1
SERP1
CNTN6
LSM3
RBMS3
GOLIM4
NKIRAS1
SPCS1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
PRSS50
RBM15B
GPR171
GMPPB
SEC61A1
LINC00312
SCHIP1
LMCD1
PIK3R4
PODXL2
ARHGEF3
TRAT1
VILL
IMPG2
C3orf32
NMD3
TRNT1
ABHD5
COMMD2
DYNC1LI1
A4GNT
C3orf18
DBR1
CRBN
SS18L2
ZNF639
CLDN18
C3orf19
SHISA5
TIMMDC1
ZDHHC3
RSRC1
ZMYND10
PLA1A
TEX264
CCDC72
ZNF589
HEMK1
AMOTL2
IP6K2
SFMBT1
NCKIPSD
PHF7
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
GHRL
P2RY13
IL20RB
GPR87
TLR9
DCUN1D1
SEMA5B
XRN1
WDR5B
LZTFL1
PARP14
P4HTM
SLC6A20
IL17RD
GRAMD1C
ROPN1
KLHL24
SIDT1
C3orf75
SNRK
QRICH1
PXK
CMTM6
RG9MTD1
SLC41A3
PIGX
SLC25A38
ULK4
OXSM
SLC35A5
TMEM45A
FEZF2
IFT57
EBLN2
ANO10
DALRD3
SHQ1
MSL2
TBCCD1
FAIM
SLC25A36
ARL8B
SETD5
DPPA4
LEPREL1
TMEM39A
ZNF654
TMEM40
ABCF3
LSG1
ABHD10
CHDH
PARL
IL17RB
CDV3
MFN1
YEATS2
IFT122
NGLY1
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
TMEM111
EAF2
BRK1
ZNF167
MYNN
LMOD3
EIF5A2
CLDND1
MUC13
SUCNR1
RAD18
SEMA3G
MCCC1
LXN
C3orf37
MRPS22
NIT2
POGLUT1
BBX
KIF15
ADAMTS9
CCNL1
PLSCR2
PCBP4
PLSCR4
PCNP
HRASLS
MRPL47
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
ISY1
HHATL
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
WDR48
LRRN1
KIAA1524
SLC7A14
SRPRB
SELK
SENP2
GNB4
BPESC1
PROK2
EEFSEC
RNF123
NSUN3
CIDEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZFYVE20
KIF9
NFKBIZ
AZI2
ZMAT3
MTMR14
ATG3
MRPS25
CSRNP1
GORASP1
MFSD1
CCDC14
FNDC3B
P2RY12
CDCP1
CCDC71
NT5DC2
SLC26A6
TMEM108
CRELD1
CAMKV
TMEM43
OR5H6
OR5H2
ZXDC
ZBED2
LRRC2
FYCO1
ATP13A3
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC51
TBL1XR1
ZBBX
ZNF385D
LRRC31
CCDC48
NEK11
UBA5
HDAC11
MAP6D1
PHC3
C3orf36
ARL14
THOC7
NAA50
PIGZ
CEP63
CEP70
ABTB1
WDR82
TMEM22
TSEN2
GRIP2
OR5AC2
RTP3
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
C3orf20
ID2B
ARL6
ZIC4
ATRIP
ACAD11
IQCG
ATP13A4
FYTTD1
NICN1
CHCHD6
MON1A
C3orf26
HPS3
ARPM1
JAGN1
KBTBD8
SLC12A8
GHRLOS2
RETNLB
CCDC54
MGC2889
IL17RC
ABHD14B
LRCH3
MINA
GPR128
C3orf39
DIRC2
CEP19
EAF1
DCLK3
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
UCN2
LOC90246
C3orf25
TMEM41A
ZNF502
BOC
FAM55C
RFT1
OXNAD1
SPSB4
ACPL2
ZBTB47
TMEM44
EGFEM1P
ACTR8
CAMK2N2
CMTM7
TXNRD3
OSBPL10
OSBPL11
SLC25A26
ZNF501
C3orf24
LRRC58
LRRC3B
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
GALNTL2
GPR62
CPNE4
CCDC58
KCNH8
DNAJC19
OTOL1
FAM3D
ZPLD1
LYZL4
KBTBD5
TRIM71
FAM131A
CD200R1
CHCHD4
ZDHHC19
DCBLD2
LRRC15
FAM43A
TPRA1
TMEM42
UROC1
FAM194A
NUDT16
COL6A6
GRK7
FAM172BP
TMEM207
METTL6
TAMM41
IL17RE
RTP1
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
RPL32P3
H1FOO
PISRT1
ASB14
TTC14
DTX3L
FAM19A4
SGOL1
PP2D1
EFHB
LOC151658
PPM1L
WDR49
LRRC34
CPNE9
DPPA2
CCDC80
BTLA
CCDC12
MB21D2
PPP4R2
XXYLT1
ROPN1B
LOC152024
C3orf22
C3orf55
ZCWPW2
CMC1
NEK10
C3orf79
CCDC50
PYDC2
SPICE1
CMTM8
NUDT16P1
CCDC13
LOC152217
LOC152225
FGD5
CIDECP
CNTN4
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
XIRP1
RNF168
CHST13
PRICKLE2
KBTBD12
DHX36
HTR3C
DZIP1L
TTC21A
ALG1L
C3orf67
KCTD6
LIPH
ARL13B
DHFRL1
HTR3D
RPL22L1
OSTalpha
FBXO45
KLHDC8B
MUC20
GABRR3
PTPLB
STT3B
LOC201617
DNAH12
PDE12
FAM116A
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
CADM2
LOC253573
ZNF620
NAALADL2
ZDHHC23
LOC255025
NUP210P1
TCTEX1D2
C3orf43
SDHAP1
COL6A5
GK5
PLCXD2
GCET2
UTS2D
ALS2CL
TMIE
LSAMP-AS3
SLC9A9
C3orf64
LOC285205
EPHA6
DNAJB8-AS1
FBXW12
C3orf38
HTR3E
ENTPD3-AS1
ZNF619
ZNF621
RABL3
IGSF10
C3orf33
LOC285326
CCDC66
SLC9A10
C3orf23
ZNF660
FLJ39534
LOC285359
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
C3orf70
TPRG1
LOC285401
ILDR1
TRIM59
TRIM42
EIF4E3
RAB43
CCDC39
CCDC36
KY
LOC339862
LOC339874
C3orf35
LOC339894
GADL1
PRSS42
LOC339926
LPP-AS2
H1FX-AS1
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
ZNF860
TMPRSS7
CD200R1L
PAQR9
COL6A4P1
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
LNP1
CCDC37
NPHP3-AS1
TPRXL
ANKRD18DP
NMNAT3
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
LRRC33
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
VENTXP7
LOC401052
IQCF3
LOC401074
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR15B
MIR16-2
MIR191
MIR198
MIR26A1
FAM19A1
STX19
LOC440944
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
ARGFX
SNORA6
SNORA7A
SNORD2
SNORA4
TMPPE
TMEM30C
LOC644714
ALG1L2
LOC644990
LOC645206
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
SPINK8
C3orf71
LOC646498
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
FLJ20518
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
SNORA81
SNORD19
FAM86DP
SNORD66
SNORD69
MIR548A2
MIR548A3
MIR551B
MIR563
MIR564
MIR567
MIR568
MIR569
MIR570
GXYLT2
SDHAP2
FAM157A
FAM198A
CCR2
FAM86HP
PRR23A
LOC730091
ESRG
LOC100009676
SNORD19B
LOC100125556
MIR922
MIR885
MIR944
EGOT
GHRLOS
LOC100128023
WWTR1-AS1
LOC100128164
C3orf74
LOC100128640
NRADDP
LOC100129480
LOC100129550
ZBTB20-AS1
LOC100131551
LOC100131635
ZNF717
LOC100132146
LOC100132526
BSN-AS2
SNAR-I
MIR1224
TIPARP-AS1
PRSS46
LOC100287879
LOC100288428
FRG2C
LOC100289361
MIR1284
MIR1248
MIR1280
MIR548I1
MIR1324
MIR1226
LOC100302640
MIR548H2
MIR711
MIR548G
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
LOC100498859
MIR3919
MIR3921
MIR3938
MIR3714
IQCJ-SCHIP1
FGD5-AS1
LOC100505687
LOC100505696
KRBOX1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
IQCF4
LOC100506994
LOC100507032
MFI2-AS1
LOC100507062
LOC100507086
ADAMTS9-AS2
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
LOC100507582
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
NPHP3-ACAD11
ISY1-RAB43
TM4SF19-TCTEX1D2
MIR4793
MIR4787
MIR4795
MIR4796
MIR4797
MIR4788
MIR4791
MIR4790
MIR548AC
MIR4444-1
MIR4789
MIR4443
MIR4792
MIR4446
MIR4442
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.32.

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

Genes
ABL1
FANCC
FANCG
GNAQ
JAK2
MLLT3
NFIB
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
CD274
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
hsa-mir-455
hsa-mir-32
hsa-mir-1302-8
hsa-mir-24-1
hsa-mir-2278
hsa-let-7d
hsa-mir-4291
hsa-mir-4290
hsa-mir-3153
hsa-mir-4289
hsa-mir-7-1
hsa-mir-204
hsa-mir-1299
hsa-mir-873
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
ABCA1
ABCA2
ABO
ACO1
PLIN2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
ANXA2P2
NUDT2
APBA1
AQP3
AQP7
ASS1
AUH
BAAT
BAG1
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
TNFSF8
ENTPD2
CD72
CDK9
CDKN2A
CDKN2B
CEL
CELP
CKS2
CLTA
CNTFR
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL1
CTSL2
CTSL1P8
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
DMRT1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ELAVL2
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXD4
FOXE1
MLANA
FPGS
FXN
NR5A1
FUT7
GALT
GAS1
NR6A1
GCNT1
GGTA1P
B4GALT1
GLDC
GLE1
GNG10
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
DNAJA1
HSPA5
TNC
IARS
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
IL11RA
INSL4
LCN1
LCN2
LMX1B
MTAP
MUSK
NCBP1
NDUFA8
NDUFB6
NFIL3
NFX1
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PRSS3
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
PTPRD
RAD23B
RFX3
RGS3
RLN1
RLN2
RMRP
RORB
RPL7A
RPL12
RPS6
RXRA
CCL19
CCL21
SH3GL2
SHB
SLC1A1
SMARCA2
SNAPC3
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TEK
TESK1
TGFBR1
TLE1
TLE4
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
TYRP1
UGCG
VAV2
VCP
VLDLR
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
MPDZ
FBP2
DPM2
FUBP3
CLIC3
PRPF4
KLF4
GTF3C5
GTF3C4
CER1
LHX2
PLAA
GRHPR
FAM189A2
TJP2
MED27
PTGES
ATP6V1G1
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
RGP1
TRIM14
MELK
RUSC2
PPP1R26
SEC16A
ZBTB5
KIAA0020
TNFSF15
PTBP3
GNE
SH2D3C
RCL1
TOPORS
RABEPK
SIGMAR1
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
DMRT2
RRAGA
ZBTB6
NEK6
SDCCAG3
NOXA1
CCL27
USP20
ACTL7B
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
PSIP1
INSL6
SLC2A6
PTENP1
AKAP2
RPL35
MAN1B1
DCTN3
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
KDM4C
ZBTB43
SMC5
KANK1
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
FKBP15
KIAA1045
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
DDX58
RABGAP1
TMEM2
C9orf5
C9orf4
SLC24A2
CIZ1
DNAJB5
DCAF12
DFNB31
COBRA1
NIPSNAP3A
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
ZNF658
FAM75A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
RANBP6
TRUB2
DNAI1
ST6GALNAC4
INVS
NDOR1
SIT1
SPINK4
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
STOML2
DEC1
PCA3
AK3
EXOSC3
FAM108B1
MRPS2
COQ4
CERCAM
EGFL7
C9orf53
UBAP1
GOLM1
PRRX2
C9orf114
CHMP5
C9orf156
RAB14
TMEM8B
C9orf78
SHC3
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
C9orf11
TBC1D13
FAM22F
DIRAS2
BNC2
HAUS6
ASPN
BSPRY
APTX
C9orf167
CNTLN
TEX10
LPPR1
KIAA1797
UBE2R2
EXD3
FAM206A
C9orf95
STX17
NOL8
C9orf68
C9orf40
TMEM38B
SMU1
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
CDC37L1
DENND4C
C9orf86
CDK5RAP2
UBAP2
C9orf46
CBWD1
KLHL9
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
IFNK
SH3GLB2
REXO4
DOLPP1
KIAA1161
KCNT1
KIAA1432
BDAG1
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
LINC00474
C9orf80
ZNF462
DMRT3
PRDM12
NAA35
DMRTA1
SLC28A3
CARD9
SUSD1
POLR1E
IPPK
DDX31
FAM129B
LRRC19
MRPL41
NOL6
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
MOB3B
C9orf82
CNTNAP3
ERMP1
SVEP1
RMI1
TRPM3
PTGES2
IFT74
FAM214B
GKAP1
PDCD1LG2
AKNA
MIR600HG
URM1
ISCA1
DOCK8
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
C9orf125
NTNG2
HIATL1
HINT2
C9orf24
PIGO
PRRC2B
PPAPDC3
GLIS3-AS1
ZDHHC12
FAM73B
C9orf100
C9orf3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
COL27A1
ALG2
FGD3
FAM125B
TPD52L3
WDR34
SAPCD2
C9orf69
LRSAM1
IL33
C9orf123
C9orf30
UAP1L1
MCART1
MRRF
RBM18
ARRDC1
WDR85
ADAMTSL1
FP588
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
UHRF2
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
FAM69B
PTRH1
PIP5KL1
TAF1L
PTPDC1
ANKRD19P
ARID3C
C9orf23
C9orf131
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
ASB6
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf66
LINC00032
LINGO2
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC39B
FAM201A
RG9MTD3
TTC16
LOC158257
FAM120AOS
FAM154A
LINC00475
FREM1
KIAA2026
LOC158376
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
LOC158434
LOC158435
PRUNE2
C9orf96
KCNV2
OLFML2A
C9orf71
QSOX2
GLIS3
ZNF883
ZNF169
C9orf21
ZNF367
C9orf91
C9orf72
C9orf93
NAIF1
C9orf25
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
LOC253039
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
FAM205A
LINC00094
CRB2
SCAI
C9orf117
C9orf47
C9orf79
LOC286238
LCN12
C9orf142
TPRN
LOC286297
TUSC1
LINC00256A
FAM78A
LURAP1L
LOC286359
OR13C9
OR13D1
LOC286367
LOC286370
FOXD4L3
IFNE
ZDHHC21
ACER2
LOC340508
LOC340515
GPR144
FAM75D5
QRFP
OR1J1
OR1B1
KIF24
IGFBPL1
MURC
FOXD4L4
GLT6D1
ENHO
AQP7P1
PTAR1
C9orf102
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
KGFLP1
LOC389705
FAM205B
FAM75A6
MGC21881
FAM75D4
FAM75D3
FAM75D1
LOC389765
C9orf153
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
C9orf128
OR13J1
CTSL3
LOC392364
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
FLJ35024
FLJ41200
PTPLAD2
LOC401497
TMEM215
TOMM5
FAM74A1
FAM74A4
ZNF658B
C9orf170
CENPP
C9orf152
SNX30
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
PPAPDC2
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR101-2
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR204
MIR219-2
MIR23B
MIR24-1
MIR27B
MIR31
MIR32
MIR7-1
C9orf106
C9orf103
LCN10
LOC415056
LOC440173
LOC440896
FLJ35282
SUGT1P1
ANKRD20A3
ANKRD20A2
AQP7P3
FAM75C1
LOC441454
LOC441455
FAM22G
ANKRD18B
LOC441461
C9orf173
NRARP
LOC442421
FOXB2
CBWD3
C9orf129
PALM2-AKAP2
LOC494127
LOC494558
FAM27A
DNAJC25
DNAJC25-GNG10
MIR31HG
LOC572558
MIR491
PGM5P2
MIR455
NRON
LOC642236
FAM75A2
FAM75A4
LOC642929
FAM163B
FLJ40292
TUBBP5
RNF224
LOC643648
CBWD6
FAM75C2
HRCT1
FAM75A1
C9orf29
FAM74A2
RPSAP9
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM138C
SCARNA8
SNORA17
SNORA43
SNORD62B
MSMP
SNORD90
MIR600
MIR601
MIR602
RNF208
FAM75A3
FAM75A5
DNLZ
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
CDKN2B-AS1
SNORD121A
SNORD121B
C9orf146
SNORA84
SNORA70C
MIR876
MIR873
LOC100128076
LOC100128361
LINC00256B
LOC100128505
LOC100128593
LINC00476
LOC100129034
UNQ6494
LOC100129250
LOC100129316
LOC100129722
LOC100130954
LOC100131193
LOC100132077
LOC100132352
FAM157B
LOC100132781
FAM27C
FAM95B1
FAM27B
LOC100133920
RNU6ATAC
LINC00092
LOC100272217
LOC100286938
WASH1
LOC100288842
LOC100289019
LOC100289341
MIR548H3
MIR2278
MIR548Q
MIR181A2HG
MIR3074
MIR4292
MIR3152
MIR3154
MIR2861
MIR4291
MIR3153
MIR4290
MIR3134
MIR4289
C9orf174
LOC100499484
MIR3621
MIR3910-1
MIR3689A
MIR3911
MIR3910-2
MIR3689B
MIR3651
LOC100505478
LOC100506100
LOC100506190
LOC100506422
LOC100506599
LOC100506710
LOC100507244
LOC100507299
LOC100507346
C9orf30-TMEFF1
MIR4668
MIR3689D1
MIR3689F
MIR4667
MIR4473
MIR4669
MIR4673
MIR3960
MIR4540
MIR4665
MIR4475
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4670
MIR4672
MIR4474
MIR4476
MIR3689E
MIR4479

Arm-level results

Table 3. Get Full Table Arm-level significance table - 14 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 | 2121 | 0.02 | 0.363 | 0.948 | 0.00 | -1.56 | 0.948
1q | 1955 | 0.01 | -0.293 | 0.948 | 0.00 | -1.57 | 0.948
2p | 924 | 0.01 | -0.36 | 0.948 | 0.00 | -1.61 | 0.948
2q | 1556 | 0.01 | -0.956 | 0.948 | 0.00 | -1.59 | 0.948
3p | 1062 | 0.01 | -0.963 | 0.948 | 0.02 | 0.287 | 0.948
3q | 1139 | 0.01 | -0.959 | 0.948 | 0.02 | 0.293 | 0.948
4p | 489 | 0.02 | 0.877 | 0.692 | 0.01 | -0.358 | 0.948
4q | 1049 | 0.02 | 0.928 | 0.692 | 0.01 | -0.322 | 0.948
5p | 270 | 0.01 | -1.01 | 0.948 | 0.01 | -0.394 | 0.948
5q | 1427 | 0.00 | -1.57 | 0.948 | 0.03 | 2.21 | 0.0903
6p | 1173 | 0.01 | -0.975 | 0.948 | 0.00 | -1.6 | 0.948
6q | 839 | 0.01 | -0.992 | 0.948 | 0.00 | -1.61 | 0.948
7p | 641 | 0.01 | -0.898 | 0.948 | 0.09 | 9.01 | 0
7q | 1277 | 0.00 | -1.52 | 0.948 | 0.10 | 11 | 0
8p | 580 | 0.12 | 12.1 | 0 | 0.01 | -0.869 | 0.948
8q | 859 | 0.12 | 12.8 | 0 | 0.00 | -1.52 | 0.948
9p | 422 | 0.01 | -1 | 0.948 | 0.01 | -0.385 | 0.948
9q | 1113 | 0.01 | -0.967 | 0.948 | 0.01 | -0.341 | 0.948
10p | 409 | 0.01 | -0.386 | 0.948 | 0.01 | -1 | 0.948
10q | 1268 | 0.02 | 0.303 | 0.948 | 0.01 | -0.953 | 0.948
11p | 862 | 0.02 | 0.911 | 0.692 | 0.01 | -0.334 | 0.948
11q | 1515 | 0.03 | 2.24 | 0.0765 | 0.01 | -0.922 | 0.948
12p | 575 | 0.00 | -1.61 | 0.948 | 0.02 | 0.863 | 0.607
12q | 1447 | 0.00 | -1.59 | 0.948 | 0.01 | -0.961 | 0.948
13q | 654 | 0.03 | 2.13 | 0.0826 | 0.01 | -0.966 | 0.948
14q | 1341 | 0.01 | -0.334 | 0.948 | 0.00 | -1.59 | 0.948
15q | 1355 | 0.00 | -1.58 | 0.948 | 0.02 | 0.934 | 0.607
16p | 872 | 0.00 | -1.61 | 0.948 | 0.01 | -0.364 | 0.948
16q | 702 | 0.00 | -1.61 | 0.948 | 0.02 | 0.874 | 0.607
17p | 683 | 0.00 | -1.57 | 0.948 | 0.07 | 6.49 | 5.72e-10
17q | 1592 | 0.02 | 0.385 | 0.948 | 0.04 | 2.92 | 0.0178
18p | 143 | 0.00 | -1.62 | 0.948 | 0.03 | 1.44 | 0.427
18q | 446 | 0.00 | -1.62 | 0.948 | 0.02 | 0.851 | 0.607
19p | 995 | 0.03 | 2.22 | 0.0765 | 0.02 | 0.967 | 0.607
19q | 1709 | 0.03 | 2.3 | 0.0765 | 0.02 | 1.03 | 0.607
20p | 355 | 0.01 | -0.397 | 0.948 | 0.00 | -1.63 | 0.948
20q | 753 | 0.01 | -0.991 | 0.948 | 0.01 | -0.991 | 0.948
21q | 509 | 0.04 | 3.38 | 0.00364 | 0.01 | -0.325 | 0.948
22q | 921 | 0.05 | 4.07 | 0.000314 | 0.01 | -0.292 | 0.948
Xq | 1312 | 0.01 | -0.29 | 0.948 | 0.03 | 2.22 | 0.0903

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

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

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

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

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LAML-TB/3349070/GDAC_MergeDataFiles_3125797/LAML-TB.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 191 Input Tumor Samples.

Tumor Sample Names
TCGA-AB-2803-03A-01D-0756-21
TCGA-AB-2804-03A-01D-0756-21
TCGA-AB-2805-03A-01D-0756-21
TCGA-AB-2806-03A-01D-0756-21
TCGA-AB-2807-03A-01D-0756-21
TCGA-AB-2808-03A-01D-0756-21
TCGA-AB-2809-03A-01D-0756-21
TCGA-AB-2810-03A-01D-0756-21
TCGA-AB-2811-03A-01D-0756-21
TCGA-AB-2812-03A-01D-0756-21

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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