SNP6 Copy number analysis (GISTIC2)
Sarcoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1CZ3633
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1CZ3633
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.21 (Firehose task version: 127).

Summary

There were 257 tumor samples used in this analysis: 20 significant arm-level results, 25 significant focal amplifications, and 41 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 - 25 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
--- | --- | --- | --- | ---
12q15 | 4.6914e-75 | 4.6914e-75 | chr12:69178021-69244387 | 3
1q24.3 | 4.1505e-20 | 2.7978e-16 | chr1:171978841-172273155 | 4
1p32.1 | 1.1449e-12 | 1.1449e-12 | chr1:59209605-59471985 | 1
17p11.2 | 9.5719e-19 | 2.4607e-11 | chr17:17759832-18752581 | 29
3p12.1 | 5.054e-09 | 5.054e-09 | chr3:86917447-87350419 | 4
19q12 | 6.7567e-09 | 6.7567e-09 | chr19:30245403-30321189 | 1
6q25.1 | 7.472e-09 | 7.472e-09 | chr6:148810209-149693136 | 4
13q34 | 1.9026e-05 | 1.9026e-05 | chr13:113363456-114881111 | 22
5p15.33 | 2.7569e-05 | 2.7569e-05 | chr5:1019815-1300024 | 6
19p13.2 | 0.00033161 | 0.00033161 | chr19:6882410-7309686 | 8
17p12 | 1.1229e-16 | 0.0042825 | chr17:11702856-15565257 | 30
1q21.3 | 1.9664e-08 | 0.0094653 | chr1:149884928-154270184 | 167
17q24.3 | 0.03964 | 0.03964 | chr17:55680230-81195210 | 393
20q13.33 | 0.040367 | 0.040367 | chr20:51959332-63025520 | 138
6p21.1 | 0.04127 | 0.04127 | chr6:41687253-42194234 | 16
11q22.2 | 0.043732 | 0.043732 | chr11:101789694-102574603 | 11
Xq21.1 | 0.047784 | 0.047784 | chrX:81233210-82660744 | 1
15q26.3 | 0.062076 | 0.062076 | chr15:95392151-102531392 | 46
8p11.22 | 0.13101 | 0.13101 | chr8:37930951-38712612 | 12
4q12 | 0.15378 | 0.15378 | chr4:48068784-58112347 | 58
Xp21.2 | 0.15638 | 0.15638 | chrX:9424633-63680612 | 374
2p11.2 | 0.16643 | 0.16643 | chr2:82640170-97591130 | 110
8q24.21 | 0.16883 | 0.16883 | chr8:42932479-146364022 | 557
21q21.1 | 0.17714 | 0.17714 | chr21:16693634-17956275 | 6
7q31.2 | 0.19305 | 0.19305 | chr7:114122507-116100184 | 9

Genes in Wide Peak

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

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

Genes
MDM2
SLC35E3
CPM

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q24.3.

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

Genes
DNM3OS
DNM3
MIR199A2
MIR214

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p32.1.

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

Genes
JUN

Genes in Wide Peak

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

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

Genes
RN7SL627P
ZNF286B
TBC1D28
RN7SL639P
KRT16P1
KRT17P2
SMCR8
snoU13|ENSG00000238691.1
DRG2
FLII
LLGL1
PRPSAP2
SHMT1
TOP3A
FBXW10
TVP23B
MYO15A
ALKBH5
GID4
FAM106A
LRRC48
ATPAF2
SMCR7
TOM1L2
TRIM16L
USP32P2
CCDC144B
EVPLL
LGALS9C

Genes in Wide Peak

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

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

Genes
POU1F1
CHMP2B
VGLL3
MIR4795

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q25.1.

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

Genes
RN7SL234P
UST
TAB2
SASH1

Genes in Wide Peak

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

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

Genes
LINC00565
LINC00452
LINC00453
LINC00454
GRK1
DCUN1D2
ATP4B
F7
F10
GAS6
LAMP1
TFDP1
CUL4A
PROZ
RASA3
ATP11A
MCF2L
TMCO3
PCID2
GRTP1
ADPRHL1
TMEM255B

Genes in Wide Peak

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

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

Genes
MIR4635
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18

Genes in Wide Peak

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

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

Genes
EMR4P
EMR1
INSR
ZNF557
MBD3L2
MBD3L5
MBD3L4
MBD3L3

Genes in Wide Peak

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

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

Genes
MAP2K4
SNORA74|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
SNORA74|ENSG00000252305.1
MIR548H3
RN7SL550P
MIR744
RPL21P122
COX10
DNAH9
PMP22
ZNF18
ARHGAP44
HS3ST3A1
TRIM16
ELAC2
TEKT3
MYOCD
TVP23C
LINC00670
CDRT4
CDRT1
MIR1269B

Genes in Wide Peak

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

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

Genes
ARNT
TPM3
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
CTSK
CTSS
ECM1
ENSA
FLG
ILF2
IVL
LOR
MCL1
SMCP
NPR1
PI4KB
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
TCHH
TUFT1
PIP5K1A
ANXA9
SELENBP1
PRPF3
SETDB1
UBAP2L
SV2A
DENND4B
SF3B4
HAX1
SEMA6C
JTB
MTMR11
SLC27A3
TDRKH
VPS45
POGZ
RPRD2
SNAPIN
CA14
C1orf43
CHTOP
LCE2B
SLC39A1
TMOD4
CERS2
CRNN
APH1A
PLEKHO1
OAZ3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
FAM63A
CDC42SE1
PGLYRP4
S100A14
GATAD2B
CGN
ZNF687
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
LCE3D
NUP210L
PGLYRP3
GABPB2
TCHHL1
RPTN
S100A16
CREB3L4
C1orf51
LELP1
BNIPL
SPRR4
LCE4A
CRTC2
LCE5A
RIIAD1
THEM5
S100A7A
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LYSMD1
HRNR
FLG2
KPRP
LCE6A
PRR9
MIR190B
C1orf68
C2CD4D
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q24.3.

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

Genes
BRIP1
CD79B
CLTC
DDX5
PRKAR1A
ASPSCR1
MSI2
CANT1
MIR4525
RAB40B
snoU13|ENSG00000238403.1
snoU13|ENSG00000238947.1
DUS1L
PCYT2
SLC25A10
LINC00482
MIR1250
MIR657
MIR4730
CBX8
snoU13|ENSG00000239173.1
ENGASE
DDC8
RN7SL454P
SNORA30|ENSG00000200063.1
RN7SL236P
FLJ45079
LINC00338
LINC00868
MIR636
SNORD1B
SNHG16
PRCD
snoU13|ENSG00000238418.1
MYO15B
RN7SL573P
MIR3615
CD300LD
GPRC5C
RNA5SP448
LINC00469
SSTR2
SCARNA24|ENSG00000252274.1
RN7SKP180
LINC00511
MAP2K6
SNORA40|ENSG00000252352.1
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
RN7SL622P
SNORA38B
MIR548D2
RN7SL756P
snoU13|ENSG00000238612.1
PSMD12
SNORA8|ENSG00000207410.1
RNA5SP447
RNA5SP446
MIR634
RNA5SP445
RN7SL735P
RNA5SP444
SLC16A6P1
RN7SL404P
RN7SL409P
PLEKHM1P
SMURF2
MIR5047
MIR3064
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
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
CSH1
CSH2
CSHL1
CSNK1D
SLC25A10
CYB561
ACE
ERN1
EVPL
BPTF
FASN
FDXR
FOXJ1
GAA
GALK1
GCGR
GH1
GH2
UTS2R
GPS1
GRB2
GRIN2C
H3F3B
ICAM2
ICT1
FOXK2
ITGB4
KCNJ2
KCNJ16
KPNA2
LGALS3BP
LLGL2
LPO
MAFG
MAP3K3
MPO
TRIM37
NPTX1
P4HB
PDE6G
SEPT4
PRKCA
PRPSAP1
PSMC5
PYCR1
RAC3
RAD51C
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
SUPT4H1
TBCD
TBX2
TIMP2
TK1
EPX
AXIN2
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
MTMR4
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
BZRAP1
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
POLG2
CD300A
TMC6
DDX42
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
OR4D1
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
PTRH2
SDK2
BCAS3
TMEM104
RNF43
MKS1
C17orf80
CCDC40
WIPI1
SMG8
NPLOC4
ST6GALNAC1
TEX2
TEX14
WDR45B
CCDC47
MIF4GD
INTS2
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
SLC25A19
UBE2O
HEATR6
FN3K
DNAI2
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
DHX40
FN3KRP
OGFOD3
ZNF750
NUP85
C17orf70
LIMD2
KCNH6
VMP1
TSPAN10
QRICH2
CBX2
FAM104A
FBF1
UNK
CEP95
TRIM47
STRADA
C17orf72
OTOP2
TTYH2
CYGB
RNF157
C1QTNF1
PPP1R27
FTSJ3
METTL23
HSF5
OR4D2
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
MGAT5B
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
EFCAB3
NOTUM
TMC8
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MYADML2
NPB
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
C17orf47
SLC26A11
ENDOV
GDPD1
C17orf89
TMEM105
METRNL
RAB37
METTL2A
ENPP7
OXLD1
CCDC137
ARL16
CD300E
NACA2
OTOP3
SKA2
FAM195B
GPR142
ZACN
LRRC37A3
YPEL2
C17orf82
BTBD17
TEX19
CUEDC1
MIR142
MIR21
MXRA7
CPSF4L
SMIM5
MIR633
SMIM6
TEN1
C17orf99
MIR4316
MIR338
MIR3186
MIR3678
MIR3615
MIR4739
MIR4737
MIR4736
MIR4738
MIR4740
MIR4524B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
GNAS
SS18L1
NPBWR2
MIR647
MIR1914
C20ORF135
SLC2A4RG
MIR4326
MIR3196
HAR1A
HAR1B
LINC00029
GID8
LINC00659
LINC00686
MIR133A2
MIR4758
ATP5E
MGC4294
ANKRD60
RAE1
RN7SL170P
U3|ENSG00000252536.1
FAM209A
GCNT7
snoU13|ENSG00000238294.1
RNA5SP487
RNU4ATAC7P
BMP7
CDH4
CHRNA4
COL9A3
CSTF1
CTSZ
CYP24A1
EDN3
EEF1A2
KCNQ2
LAMA5
MC3R
MYT1
NTSR1
OPRL1
PCK1
PFDN4
PPP1R3D
PSMA7
PTK6
RPS21
SRMS
AURKA
TAF4
TCEA2
TFAP2C
TPD52L2
ZNF217
BCAS1
STX16
TNFRSF6B
VAPB
OSBPL2
ARFRP1
RGS19
SYCP2
TCFL5
ADRM1
OGFR
DIDO1
HRH3
SPO11
PRPF6
MTG2
GMEB2
SLCO4A1
STMN3
SLMO2
NELFCD
RTFDC1
RTEL1
SOX18
YTHDF1
LIME1
UCKL1
PCMTD2
MRGBP
PPP4R1L
RBM38
ARFGAP1
DOK5
PMEPA1
CASS4
RAB22A
ZNF512B
COL20A1
CDH26
SLC17A9
FAM217B
C20orf195
PPDPF
BIRC7
NPEPL1
DNAJC5
TUBB1
ZBP1
CABLES2
ZGPAT
HELZ2
FAM210B
PHACTR3
BHLHE23
NKAIN4
TSHZ2
C20orf85
ZNF831
C20orf166
GATA5
ZBTB46
CBLN4
CTCFL
SAMD10
ABHD16B
RBBP8NL
LSM14B
APCDD1L
C20orf201
LINC00176
C20orf197
FAM209B
MIR296
MIR646
MIR298
MIR1257
MIR4325
MTRNR2L3
MIR4756
MIR4532
MIR4533
MIR548AG2

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
GUCA1B
SNORA8|ENSG00000206977.1
TOMM6
BYSL
GUCA1A
PGC
MED20
FRS3
USP49
PRICKLE4
MRPS10
TRERF1
TAF8
C6orf132

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.2.

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

Genes
BIRC3
snoU13|ENSG00000239154.1
snoU13|ENSG00000252679.1
BIRC2
MMP7
MMP20
YAP1
KIAA1377
MMP27
C11orf70
TMEM123

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq21.1.

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

Genes
SNORA4|ENSG00000202183.1

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.22.

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

Genes
FGFR1
WHSC1L1
RPS20P22
STAR
TACC1
ASH2L
BAG4
DDHD2
LSM1
PPAPDC1B
LETM2
C8orf86

Genes in Wide Peak

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

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

Genes
KDR
KIT
PDGFRA
CHIC2
FIP1L1
snoU13|ENSG00000238541.1
snoU13|ENSG00000238579.1
NOA1
RN7SL357P
RN7SL492P
ARL9
SRP72
RNA5SP162
KIAA1211
RNA5SP161
RN7SKP30
RN7SL822P
RN7SL424P
snoU13|ENSG00000238753.1
GSX2
SNORA26|ENSG00000212490.1
SNORA26|ENSG00000212588.1
DANCR
snoU13|ENSG00000239068.1
IGFBP7
POLR2B
PPAT
REST
SGCB
SPINK2
TEC
TXK
CLOCK
CEP135
PAICS
NMU
DCUN1D4
OCIAD1
EXOC1
TMEM165
SLAIN2
USP46
RASL11B
SRD5A3
CWH43
HOPX
LNX1
OCIAD2
SPATA18
AASDH
PDCL2
SCFD2
SLC10A4
FRYL
ZAR1
LRRC66
THEGL
MIR4449

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp21.2.

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

Genes
GATA1
SSX1
SSX2
SSX4
TFE3
KDM6A
WAS
KDM5C
RN7SL799P
SPIN3
SNORD112|ENSG00000252961.1
APEX2
SNORA11|ENSG00000221750.1
SNORA11|ENSG00000221716.1
GNL3L
U3|ENSG00000252175.1
RNA5SP505
MIRLET7F2
MIR98
SPANXN5
RNA5SP504
XAGE2
SNORA11D
SNORA11E
CENPVP1
DGKK
MIR502
MIR660
MIR500B
MIR501
MIR362
MIR500A
MIR188
MIR532
GAGE1
MAGIX
RN7SL262P
GPKOW
WDR45
RN7SL139P
ERAS
GLOD5
RBM3
snoU13|ENSG00000239017.1
RNA5SP503
snoU13|ENSG00000238473.1
CXXC1P1
CXorf24
SNORA11C
ZNF157
RN7SL785P
snoU13|ENSG00000238729.1
INE1
SLC9A7
SNORD77|ENSG00000212347.2
RN7SL291P
EFHC2
MAOA
RN7SL144P
RN7SL406P
RN7SL15P
RNA5SP502
CXorf38
snoU13|ENSG00000238920.1
MIR1587
RN7SL732P
SNORA31|ENSG00000252050.1
TM4SF2
CXorf30
snoU13|ENSG00000238969.1
MIR548F5
MIR3915
RNA5SP501
NR0B1
MIR4666B
RNA5SP500
SNORD74|ENSG00000201666.1
IL1RAPL1
DCAF8L2
VENTXP1
RN7SL91P
SCARNA23
SNORA68|ENSG00000201407.1
EIF2S3
snoU13|ENSG00000238327.1
PTCHD1
RN7SL436P
RN7SKP183
MIR23C
RN7SL48P
MIR4768
snoU13|ENSG00000238764.1
SNORA16|ENSG00000201467.1
SYAP1
MIR548AM
RN7SL658P
GRPR
SNORA7|ENSG00000200620.1
CA5BP1
RAB9A
TCEANC
RN7SKP20
7SK|ENSG00000271814.1
MIR548AX
ALAS2
AMELX
SHROOM2
ARAF
ARHGAP6
BMX
CACNA1F
S100G
CLCN4
CLCN5
CYBB
DDX3X
DMD
EIF1AX
ELK1
FANCB
FGD1
FIGF
GAGE2C
GK
GLRA2
GPM6B
GPR34
HSD17B10
HCCS
KCND1
PRICKLE3
MAGEB1
MAGEB2
MAGEB3
MAGEB4
MAOB
MID1
NDP
NHS
GPR143
TBC1D25
OTC
CDK16
PDHA1
PDK3
CFP
PFKFB1
PHEX
PHKA2
PIGA
PLP2
POLA1
PPEF1
PRPS2
PRRG1
RBBP7
RP2
RPGR
RPS6KA3
RS1
SAT1
SCML1
TRAPPC2
SMS
SSX5
CDKL5
SUV39H1
SYN1
SYP
TBL1X
DYNLT3
TIMP1
TSPAN7
TMSB4X
TRO
UBA1
SLC35A2
XK
ZFX
ZNF182
ZNF41
ZXDA
ZRSR2
USP11
USP9X
RBM10
SMC1A
SRPX
UXT
OFD1
PIR
CASK
PAGE1
AKAP4
AP1S2
RGN
REPS2
BMP15
MED14
PCYT1B
MAGED1
XAGE2B
XAGE1D
PAGE4
FRMPD4
PHF16
HDAC6
HUWE1
PQBP1
GPR64
ATP6AP2
SSX3
TIMM17B
RRAGB
SCML2
PRDX4
EBP
RAI2
MAGED2
MSL3
PIM2
WDR45
PRAF2
CA5B
KLF8
CNKSR2
IQSEC2
PHF8
ARHGEF9
ACOT9
SMPX
GSPT2
FTSJ1
CXorf27
EGFL6
GAGE12I
GAGE2E
GPR82
PCSK1N
CCDC22
MAGEH1
FAM156A
UBQLN2
SH3KBP1
FOXP3
TLR7
TLR8
MBTPS2
FTHL17
GPR173
SPIN2A
NDUFB11
BCOR
FAM120C
GEMIN8
NUDT11
OTUD5
MTMR8
KRBOX4
TXLNG
WWC3
CTPS2
CHST7
GRIPAP1
ZNF630
TMEM27
SHROOM4
MID1IP1
ACE2
NYX
DUSP21
TSPYL2
WDR13
PORCN
WNK3
APOO
CXorf36
CXorf21
KLHL15
MAGED4B
TMEM47
CCNB3
PPP1R3F
CCDC120
TSR2
FAM104B
PAGE5
ATXN3L
SLC38A5
SYTL5
BEND2
AMER1
FUNDC1
MAGEB10
DCAF8L1
MAGEB16
FOXR2
PAGE3
SPIN4
ASB11
ASB9
ASB12
ZNF645
FAAH2
ZXDB
FAM47A
MOSPD2
RIBC1
MAGEB6
USP51
DDX53
FAM47B
CXorf22
ARX
XAGE3
XAGE5
NUDT10
FAM9C
PAGE2
CXorf58
CXorf23
MAP7D2
KLHL34
TAB3
SSX6
SSX7
SSX9
CHDC2
MAGEB18
CXorf67
ZNF81
ITIH6
LANCL3
MAGEB5
MAP3K15
SPACA5
USP27X
PAGE2B
YY2
MIR221
MIR222
FAM47C
SPIN2B
SSX4B
ZNF674
GAGE10
GAGE2B
GAGE13
GAGE12G
MAGEB17
XAGE1C
XAGE1E
XAGE1A
XAGE1B
CXorf31
SSX2B
FAM156B
MAGED4
SPACA5B
GAGE12J
GAGE2D
GAGE12C
GAGE12B
GAGE12E
GAGE12H
GAGE2A
GAGE12F
GAGE12D
MIR1468
MTRNR2L10
MIR3937
MIR4769
MIR1587
MIR548AJ2

Genes in Wide Peak

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

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

Genes
CNNM3
MIR3127
FER1L5
CIAO1
TMEM127
FAHD2CP
RN7SL210P
ANKRD36C
LINC00342
FLJ14082
RN7SL575P
ANKRD20A8P
SLC9B1P2
RNA5SP100
IGKJ1
IGKJ2
IGKJ3
IGKJ4
IGKJ5
IGKC
ANKRD36BP2
FOXI3
snoU13|ENSG00000239049.1
RNY4P15
snoU13|ENSG00000238979.1
RGPD2
PLGLB2
PLGLB1
SNORA19|ENSG00000251974.1
U8|ENSG00000202537.1
MIR4779
SNORD94
RN7SKP83
ATOH8
C2orf68
RNF181
RN7SL126P
RN7SL830P
RN7SL251P
RN7SL113P
SNORD112|ENSG00000252298.1
ADRA2B
CAPG
CD8A
CD8B
DNAH6
DUSP2
FABP1
GGCX
MAL
MAT2A
SFTPB
ZNF2
RNF103
VAMP8
SUCLG1
ST3GAL5
TMSB10
EIF2AK3
GNLY
TGOLN2
USP39
VAMP5
ARID5A
IMMT
RPIA
SNRNP200
NCAPH
POLR1A
CNNM4
KCNIP3
FAHD2A
ANKRD39
FAM178B
KRCC1
MRPL35
RETSAT
SEMA4C
PTCD3
THNSL2
KANSL3
KDM3A
KCMF1
STARD7
RMND5A
MRPS5
REEP1
LMAN2L
TCF7L1
ELMOD3
ZNF514
NEURL3
LINC00152
TRABD2A
TMEM150A
TRIM43
TEKT4
SMYD1
PROM2
GPAT2
ITPRIPL1
TEX37
ANKRD23
SH2D6
FUNDC2P2
RGPD1
ASTL
CHMP3
MIR4436A
MIR4780

Genes in Wide Peak

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

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

Genes
EXT1
COX6C
MYC
PLAG1
TCEA1
RECQL4
NCOA2
CHCHD7
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
SNORD112|ENSG00000252559.1
TMEM74
RNA5SP275
snoU13|ENSG00000238687.1
RIMS2
MIR3151
RNU6ATAC8P
snoU13|ENSG00000238533.1
snoU13|ENSG00000238372.1
RN7SL563P
NACAP1
RN7SKP249
RN7SL685P
RNU6ATAC41P
MIR1273A
SNORD77|ENSG00000212414.1
RN7SL350P
RN7SKP85
KCNS2
NIPAL2
SNORA72|ENSG00000207067.1
LAPTM4B
U3|ENSG00000207215.1
PTDSS1
snoU13|ENSG00000238791.1
FSBP
RNA5SP274
LINC00535
RN7SKP231
snoU13|ENSG00000239134.1
MIR4661
RN7SL777P
RNA5SP273
LINC00534
RNA5SP272
MMP16
REXO1L10P|ENSG00000255940.1
REXO1L11P
REXO1L10P|ENSG00000270416.1
snoU13|ENSG00000238566.1
SLC10A5
IMPA1P
RN7SL308P
RN7SL107P
SNORA20|ENSG00000206649.1
RN7SL41P
snoU13|ENSG00000238595.1
CASC9
RNA5SP271
U8|ENSG00000200191.1
RN7SL19P
snoU13|ENSG00000238450.1
RNA5SP270
RN7SL675P
RN7SKP29
RNA5SP269
PREX2
RNA5SP268
SNORD87
LINC00967
PDE7A
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
NPBWR1
SNORA7|ENSG00000201316.1
RN7SKP294
UBE2V2
CEBPD
RN7SKP32
LINC00293
RN7SKP41
U3|ENSG00000201329.1
POTEA
ADCY8
ANGPT1
ANXA13
ASPH
ATP6V1C1
BAI1
OSGIN2
CA1
CA2
CA3
CALB1
RUNX1T1
CDH17
CRH
CYC1
CYP7A1
CYP11B1
CYP11B2
DECR1
DPYS
E2F5
EEF1D
EYA1
FABP4
FABP5
FNTA
GEM
GLI4
GML
GPR20
GPT
GRINA
HNF4G
HSF1
IL7
IMPA1
EIF3E
KCNQ3
LY6E
LY6H
LYN
MATN2
MCM4
MOS
MYBL1
NBN
NDUFB9
TONSL
NOV
ODF1
TNFRSF11B
OPRK1
ENPP2
PENK
PLEC
PMP2
POLR2K
PKIA
PRKDC
PTK2
PEX2
RAB2A
RAD21
RP1
RPL7
RPL8
RPL30
SDC2
SDCBP
ST3GAL1
SLA
SNAI2
SNTB1
SPAG1
SQLE
STK3
TAF2
TCEB1
TERF1
TG
KLF10
TPD52
TRHR
TRPS1
TSTA3
TTPA
COL14A1
UQCRB
YWHAZ
ZNF7
ZNF16
PSCA
FZD6
NSMAF
LY6D
RGS20
GPAA1
RIPK2
GGH
CPNE3
FOXH1
TRPA1
CCNE2
EBAG9
MSC
KCNB2
CYP7B1
MTFR1
LRRC14
EMC2
ST18
TOX
MTSS1
RB1CC1
ZNF623
KIAA0196
HHLA1
TRIB1
HRSP12
NDRG1
CPQ
LYPLA1
ARFGEF1
KHDRBS3
POP1
COPS5
WWP1
STMN2
ZHX1
PUF60
ZHX2
DENND3
ZC3H3
EFR3A
RRS1
SULF1
BOP1
ZFPM2
HEY1
TRAM1
SCRIB
SPIDR
LRRC6
LY96
SGK3
RAD54B
DCAF13
RNF19A
KIAA1429
RGS22
FBXL6
OPLAH
PABPC1
KCNV1
STAU2
MTBP
AGO2
BHLHE22
MRPS28
COMMD5
MRPL13
ATAD2
CPSF1
LRP12
RRM2B
CYHR1
ASAP1
MTERFD1
PI15
FAM135B
ZC2HC1A
PHF20L1
LACTB2
RMDN1
ZNF706
VPS28
FAM203A
KCNK9
THEM6
UBR5
FAM49B
AZIN1
ATP6V1H
OTUD6B
CHRAC1
SNTG1
GDAP1
EXOSC4
PDP1
CNGB3
ESRP1
IMPAD1
TMEM70
TRMT12
OXR1
WDYHV1
ARMC1
UBE2W
TMEM55A
SLC39A4
CHD7
SYBU
INTS8
PAG1
GSDMC
C8orf44
JPH1
ENY2
CPA6
SLURP1
SLC45A4
ZFAT
ZNF250
PRDM14
SNX16
NECAB1
SOX17
DEPTOR
PYCRL
C8orf33
ZBTB10
LYNX1
DSCC1
DERL1
SLC52A2
EFCAB1
PLEKHF2
ZFAND1
ZFHX4
GSDMD
CSPP1
BAALC
GRHL2
VCPIP1
ARHGAP39
ZNF34
SLC25A32
DCSTAMP
SLCO5A1
SHARPIN
SCRT1
CRISPLD1
TRAPPC9
TATDN1
NCALD
SGK196
MAF1
UTP23
TRIM55
PARP10
C8orf76
TIGD5
NUDCD1
FAM83A
PPP1R16A
LRRCC1
TSPYL5
DNAJC5B
PSKH2
FAM110B
MED30
ZNF251
KIFC2
TMEM67
MTDH
CHMP4C
PKHD1L1
NAPRT1
TBC1D31
TP53INP1
TGS1
MFSD3
MAL2
CSMD3
RHPN1
FBXO32
SLC26A7
PCMTD1
CTHRC1
OSR2
C8orf34
TOP1MT
ZNF572
FAM92A1
NDUFAF6
TMEM68
ABRA
LYPD2
TMEM71
ADHFE1
UBXN2B
PXDNL
DCAF4L2
RALYL
HGSNAT
RDH10
C8orf56
ANKRD46
FAM84B
C8orf37
VPS13B
SLC7A13
FAM91A1
MCMDC2
CLVS1
SBSPON
CNBD1
SLC30A8
COL22A1
SNX31
TMEM64
SDR16C5
ADCK5
TSNARE1
C8orf47
MAPK15
ATP6V0D2
YTHDF3
C8orf46
REXO1L1
NSMCE2
ZNF707
FAM83H
C8orf31
ZFP41
TRIQK
DPY19L4
FBXO43
PPP1R42
GPIHBP1
KLHL38
NRBP2
ZNF517
KIAA1875
TMEM249
RSPO2
SPATC1
CA13
FAM150A
XKR9
C8orf87
RBM12B
MROH5
MAFA
GDF6
C8orf59
SAMD12
MIR30B
MIR30D
LRRC24
C8orf22
ZNF704
SNHG6
MROH6
FABP9
FABP12
FER1L6
MIR548A3
MIR599
MROH1
FAM203B
OC90
MIR875
TCF24
LRRC69
MIR1205
MIR1207
PVT1
MIR2053
MIR1208
MIR3686
MIR548AA1
MIR3150B
MIR3610
MIR378D2
MIR4662B
MIR4663
MIR4664
MIR4471
MIR4470
MIR5680
MIR5194
MIR5708
MIR5681A

Genes in Wide Peak

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

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

Genes
SNORD74|ENSG00000201025.1
snoU13|ENSG00000238591.1
USP25
LINC00478
MIRLET7C
MIR99A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q31.2.

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

Genes
snoZ185
SNORA25|ENSG00000202377.1
MIR3666
RNA5SP238
CAV2
TFEC
TES
MDFIC
FOXP2

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 - 41 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
--- | --- | --- | --- | ---
13q14.2 | 5.9267e-61 | 5.9267e-61 | chr13:48875329-49064807 | 2
17p13.1 | 2.9271e-52 | 2.9271e-52 | chr17:7549751-7593565 | 2
9p21.3 | 5.805e-31 | 7.4836e-27 | chr9:21931610-22448737 | 3
10p15.3 | 1.2765e-16 | 1.2765e-16 | chr10:1-857150 | 8
Xq21.1 | 1.678e-16 | 1.9012e-15 | chrX:76710176-77102528 | 1
2q37.3 | 5.8918e-33 | 1.9848e-14 | chr2:242162274-243199373 | 16
4q35.1 | 2.8599e-14 | 2.8599e-14 | chr4:179280062-191154276 | 66
19q13.43 | 7.9191e-13 | 7.9191e-13 | chr19:58264000-59128983 | 39
11q24.2 | 2.3575e-11 | 2.3575e-11 | chr11:118301786-135006516 | 172
1p36.32 | 2.7944e-11 | 2.7944e-11 | chr1:1-5923787 | 93
19p13.3 | 1.0246e-09 | 1.0246e-09 | chr19:1-390340 | 6
11p15.5 | 4.9182e-09 | 4.9182e-09 | chr11:1-496996 | 18
17q11.2 | 2.7634e-10 | 7.2037e-09 | chr17:29326736-29794469 | 6
8p23.3 | 5.4468e-08 | 5.6899e-08 | chr8:1-4251018 | 14
1q44 | 1.1094e-07 | 1.1097e-07 | chr1:208416154-249250621 | 354
2q37.3 | 3.1172e-24 | 1.5863e-06 | chr2:233877222-243199373 | 97
7q36.3 | 2.2379e-06 | 2.2998e-06 | chr7:157210222-159138663 | 8
10q23.31 | 1.0175e-07 | 4.7325e-06 | chr10:89617158-89755074 | 3
2p25.3 | 8.3954e-06 | 8.3954e-06 | chr2:1-1917603 | 8
17q25.3 | 2.5422e-07 | 3.7808e-05 | chr17:80443432-80617015 | 3
12p13.1 | 0.00020169 | 0.00030646 | chr12:10962282-13525906 | 41
9q34.3 | 0.00032708 | 0.00032849 | chr9:134952380-141213431 | 163
14q24.1 | 0.00095189 | 0.00095499 | chr14:65562996-84218136 | 162
3p21.31 | 0.0038047 | 0.0038047 | chr3:43774427-66121046 | 299
21q22.3 | 0.00084328 | 0.0039236 | chr21:47427840-48129895 | 11
16q11.2 | 0.0011401 | 0.004628 | chr16:31804435-55329012 | 83
6q14.1 | 0.0049587 | 0.0049983 | chr6:66417081-104031403 | 147
22q13.32 | 0.011226 | 0.01125 | chr22:45095899-51304566 | 73
16q23.1 | 0.0061298 | 0.012553 | chr16:78098006-79299841 | 3
6p25.3 | 0.015554 | 0.015538 | chr6:1-25758514 | 150
10q26.3 | 7.0458e-05 | 0.017347 | chr10:135190263-135534747 | 6
18q23 | 0.020265 | 0.020483 | chr18:75573485-78077248 | 13
12q12 | 0.019606 | 0.026285 | chr12:33514047-39688977 | 7
Xp21.1 | 0.027781 | 0.027781 | chrX:30870233-34644819 | 7
Xq22.3 | 0.0070761 | 0.045745 | chrX:107382193-108617052 | 3
3q29 | 0.0056695 | 0.057996 | chr3:165509351-198022430 | 249
5p15.33 | 0.058927 | 0.060252 | chr5:1-5129938 | 35
3q13.31 | 0.031908 | 0.11944 | chr3:115440285-118620828 | 7
9p24.3 | 3.4711e-05 | 0.1874 | chr9:1-3826080 | 18
21q11.2 | 0.12448 | 0.19934 | chr21:1-23095995 | 36
12q24.33 | 0.20754 | 0.20754 | chr12:132611527-133851895 | 23

Genes in Wide Peak

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

Table S26. 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 17p13.1.

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

Genes
TP53
ATP1B2

Genes in Wide Peak

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

Table S28. 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 10p15.3.

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

Genes
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ZMYND11
DIP2C
PRR26

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.1.

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

Genes
ATRX

Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
BOK
DTYMK
HDLBP
SEPT2
PDCD1
FARP2
STK25
ATG4B
THAP4
GAL3ST2
ING5
NEU4
D2HGDH

Genes in Wide Peak

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

Table S32. 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
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
ING2
IRF2
KLKB1
MTNR1A
SORBS2
FAM149A
CLDN22
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
ZFP42
ENPP6
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR3945
MIR4455

Genes in Wide Peak

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

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

Genes
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
ZNF417
ZNF814
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF256
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF586
ZNF446
ZSCAN18
RPL23AP79
ZNF329
ZNF552
ZNF606
ZBTB45
ZNF587
ZNF837
C19orf18
ZNF418
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
ZNF587B
MIR4754

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.2.

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

Genes
DDX6
CBL
FLI1
ARHGEF12
snoU13|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
ACRV1
APLP2
ARCN1
CHEK1
DPAGT1
ETS1
SLC37A4
GRIK4
H2AFX
HMBS
HSPA8
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NFRKB
NRGN
OPCML
PVRL1
ST3GAL4
SORL1
SRPR
ST14
TECTA
UPK2
ZNF202
BARX2
USP2
EI24
FEZ1
ARHGAP32
HYOU1
ADAMTS8
TREH
IGSF9B
PHLDB1
NCAPD3
VSIG2
TRIM29
POU2F3
OR8B8
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
TRAPPC4
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
VPS11
CRTAM
IFT46
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
JAM3
KIRREL3
TMEM25
RPUSD4
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
TMEM45B
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
SPATA19
HEPACAM
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
HEPN1
PATE3
MIR4697
MIR4493
MIR4492

Genes in Wide Peak

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

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

Genes
TNFRSF14
PRDM16
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
CDK11B
DFFB
DVL1
GABRD
GNB1
PEX10
PRKCZ
SCNN1D
SKI
TP73
TNFRSF4
MMP23B
TNFRSF18
ISG15
PLCH2
CEP104
SLC35E2
RER1
NOC2L
ARHGEF16
SSU72
WRAP73
SDF4
MXRA8
CPSF3L
C1orf159
AURKAIP1
MRPL20
ATAD3A
PANK4
AJAP1
LRRC47
HES4
VWA1
NADK
MMEL1
LINC00115
MORN1
GLTPD1
OR4F16
CCNL2
ATAD3B
PLEKHN1
C1orf170
ACAP3
UBE2J2
PUSL1
B3GALT6
TPRG1L
FAM213B
ACTRT2
MIB2
SAMD11
CCDC27
CALML6
C1orf86
ATAD3C
TTLL10
C1orf174
KLHL17
TMEM52
AGRN
FAM132A
HES5
SMIM1
MIR200A
MIR200B
ANKRD65
MIR429
TMEM88B
C1orf233
CDK11A
SLC35E2B
OR4F29
MIR4689
MIR4417

Genes in Wide Peak

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

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

Genes
OR4F17
FAM138F
WASH5P
PPAP2C
THEG
MIER2

Genes in Wide Peak

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

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

Genes
RN7SL838P
ODF3
PSMD13
IFITM1
IFITM3
IFITM2
PKP3
SIRT3
BET1L
SIGIRR
RIC8A
ATHL1
PTDSS2
SCGB1C1
NLRP6
ANO9
B4GALNT4
IFITM5

Genes in Wide Peak

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

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

Genes
NF1
RN7SL79P
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

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

Genes
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
TDRP
ERICH1
ZNF596
MIR596

Genes in Wide Peak

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

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

Genes
FH
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
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
HSD11B1
IRF6
ITPKB
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
ZNF124
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
INTS7
AHCTF1
NSL1
OR2M4
OR2L2
OR2T1
RPS6KC1
DIEXF
TAF5L
DISC1
FLVCR1
CNIH4
PYCR2
NENF
G0S2
RRP15
DESI2
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
ZNF692
IARS2
HHAT
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
SPRTN
OBSCN
EFCAB2
MLK4
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
NLRP3
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
B3GALNT2
GCSAML
CNIH3
EXOC8
C1orf227
FAM71A
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
SYT14
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
TRIM67
MAP1LC3C
OR13G1
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
RN7SL204P
MSL3P1
DNAJB3
UGT1A3
SCARNA6|ENSG00000251791.1
SCARNA5
RN7SL32P
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
NDUFA10
SEPT2
NEU2
PDCD1
PPP1R7
SAG
SPP2
DGKD
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
CAPN10
PASK
ATG4B
SH3BP4
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
ATG16L1
USP40
HJURP
HES6
ACKR3
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
ILKAP
ING5
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
DUSP28
MROH2A
ESPNL
AQP12A
KLHL30
OR6B2
ASB18
PRR21
AQP12B
D2HGDH
MIR4269
MIR4786

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
LINC00689
MIR595
PTPRN2
VIPR2
NCAPG2
WDR60
ESYT2
MIR5707

Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
KLLN

Genes in Wide Peak

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

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

Genes
TMEM18
FAM110C
ACP1
TPO
PXDN
SH3YL1
SNTG2
FAM150B

Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000238403.1
FOXK2
WDR45B

Genes in Wide Peak

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

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

Genes
ETV6
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
CDKN1B
CREBL2
EMP1
GPR19
LRP6
PRB1
PRB3
PRB4
PRH1
PRR4
TAS2R13
TAS2R10
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
APOLD1
GSG1
LOH12CR1
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
TAS2R42
PRB2
MIR614

Genes in Wide Peak

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

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

Genes
NOTCH1
RALGDS
TSC1
BRD3
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
ABCA2
C8G
CACNA1B
ENTPD2
CEL
COL5A1
DBH
SARDH
FCN1
FCN2
FUT7
GRIN1
LCN1
PAEP
PTGDS
RPL7A
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
GTF3C5
ADAMTSL2
PPP1R26
SEC16A
TUBB4B
UBAC1
OLFM1
AGPAT2
SDCCAG3
NOXA1
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
MAN1B1
SETX
PMPCA
NELFB
NSMF
GPSM1
GBGT1
NDOR1
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
FBXW5
TOR4A
EXD3
RABL6
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
DDX31
EHMT1
NTNG2
KIAA1984
TMEM141
C9orf37
SAPCD2
C9orf69
UAP1L1
ARRDC1
DPH7
TMEM203
ZMYND19
NACC2
C9orf116
LCN8
SLC34A3
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LCN12
C9orf142
TPRN
GLT6D1
PNPLA7
C9orf169
ENTPD8
C9orf171
LCN15
LRRC26
TMEM8C
LCN9
LCNL1
C9orf139
FAM166A
SOHLH1
C9orf173
NRARP
MIR602
RNF208
CARD9
MIR3689A
MIR3689B
MIR3689D1
MIR3689F
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR548AW

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.1.

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

Genes
TSHR
GPHN
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
ACTN1
ACYP1
ARG2
ZFP36L1
DIO2
DLST
EIF2S1
ESRRB
FOS
FUT8
GSTZ1
GTF2A1
LTBP2
MAP3K9
ALDH6A1
PGF
PIGH
PSEN1
ABCD4
RAD51B
SEL1L
SRSF5
SLC8A3
DPF3
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
SPTLC2
RGS6
KIAA0247
AREL1
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
VASH1
SNW1
PCNX
TTLL5
ANGEL1
ZFYVE26
TTC9
SIPA1L1
DCAF4
PLEK2
MLH3
POMT2
COQ6
FCF1
RDH11
COX16
ZFYVE1
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
YLPM1
ADCK1
TMEM63C
GALNT16
PLEKHH1
ZNF410
NGB
RBM25
VIPAS39
SMOC1
IRF2BPL
MPP5
ZC2HC1C
CCDC176
SLIRP
DNAL1
RPS6KL1
STON2
KIAA1737
PAPLN
ELMSAN1
NEK9
IFT43
NOXRED1
JDP2
RDH12
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
FAM71D
TMEM229B
PROX2
ZDHHC22
C14orf178
VSX2
HEATR4
PLEKHD1
LINC00238
ACOT1
ACOT6
SYNDIG1L
MIR625
MIR1260A
MIR4505
MIR4708
MIR5694

Genes in Wide Peak

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

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

Genes
FHIT
BAP1
SETD2
PBRM1
U3|ENSG00000200222.1
SNTN
RNA5SP134
LINC00698
RN7SL863P
PTPRG
U3|ENSG00000212211.1
NPCDR1
RPP14
RNU6ATAC26P
PDE12
snoU13|ENSG00000238905.1
HESX1
RNA5SP133
RN7SKP45
MIR3938
ESRG
CHDH
SNORD63|ENSG00000251987.1
SNORA26|ENSG00000212608.1
SNORD38|ENSG00000207109.1
RN7SL821P
snoU13|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19|ENSG00000222345.1
SNORD19B|ENSG00000238862.1
SNORD19|ENSG00000212493.1
SNORD19B|ENSG00000252787.1
RNU6ATAC16P
SMIM4
MIRLET7G
TLR9
LINC00696
ACY1
RN7SL504P
IQCF6
RNA5SP132
RNU6ATAC29P
VPRBP
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
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
ALAS1
AMT
APEH
ARF4
RHOA
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
ATXN7
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TGM4
TKT
CLEC3B
TNNC1
UBA7
USP4
UQCRC1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SLMAP
MANF
ACOX2
HYAL3
CADPS
HYAL2
BSN
ACKR5
RRP9
MAGI1
CACNA2D2
IP6K1
PSMD6
PARP3
ZNF197
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CCR9
USP19
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
EXOSC7
RAD54L2
STAB1
NBEAL2
FAM208A
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
PTPN23
DNAH1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
ELP6
QRICH1
PXK
FEZF2
DALRD3
IL17RB
CACNA2D3
DCP1A
GLT8D1
ZKSCAN7
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
SELK
RNF123
KIF9
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
ATRIP
NICN1
MON1A
ABHD14B
UCN2
ZNF502
RFT1
ACTR8
ZNF501
GPR62
FAM3D
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SYNPR
LSMEM2
ASB14
CCDC12
PRICKLE2
C3orf67
KCTD6
KLHDC8B
DNAH12
DENND6A
ALS2CL
TMIE
FBXW12
CCDC66
TCAIM
CCDC36
PRSS42
ZNF445
SPATA12
TOPAZ1
TMEM110
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
IQCF3
MIR135A1
MIR191
MIR425
SPINK8
ARIH2OS
C3orf84
CCR2
PRSS46
MIR4271
MIR4787
MIR4443

Genes in Wide Peak

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

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

Genes
S100B
COL6A2
PRMT2
LSS
PCNT
MCM3AP
FTCD
DIP2A
C21orf58
YBEY
SPATC1L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q11.2.

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

Genes
CYLD
RN7SL841P
CRNDE
FTO
RNA5SP427
snoU13|ENSG00000238645.1
CASC16
LINC00919
RN7SKP142
HNRNPA1P48
RNA5SP426
NKD1
SNORD112|ENSG00000252077.1
snoU13|ENSG00000238544.1
SNORA70|ENSG00000252526.1
RNY4P3
snoU13|ENSG00000239038.1
snoU13|ENSG00000239013.1
RN7SL54P
LONP2
RNA5SP425
RNA5SP424
ITFG1
snoU13|ENSG00000238834.1
MYLK3
VPS35
ANKRD26P1
RNA5SP423
RNA5SP422
RNA5SP421
RNA5SP420
RNA5SP419
RNA5SP418
RNA5SP417
RNA5SP416
RNA5SP415
RNA5SP413
RNA5SP410
RNA5SP409
RNA5SP408
RNA5SP407
RNA5SP406
LINC00273
ARHGAP23P1
HERC2P8
HERC2P5
TP53TG3
TP53TG3D
HERC2P4
ADCY7
CBLN1
PHKB
RBL2
SALL1
SIAH1
N4BP1
IRX5
DNAJA2
ZNF267
ZNF423
RPGRIP1L
ORC6
TOX3
BRD7
HEATR3
NOD2
PAPD5
AKTIP
IRX3
SHCBP1
CHD9
NETO2
GPT2
ABCC11
ABCC12
C16orf78
SNX20
CNEP1R1
SLC6A10P
C16orf87
C16orf97
TP53TG3C
TP53TG3B

Genes in Wide Peak

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

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

Genes
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
U3|ENSG00000221332.1
MB21D1
snoU13|ENSG00000238464.1
OOEP
OGFRL1
U3|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65|ENSG00000212229.1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL12A1
COX7A2
EEF1A1
EPHA7
GABRR1
GABRR2
GRIK2
HTR1E
IMPG1
ME1
MYO6
NT5E
PGM3
POU3F2
SIM1
ELOVL4
MAP3K7
TPBG
TTK
RNGTT
TBX18
HMGN3
FHL5
SNAP91
SYNCRIP
SLC35A1
FUT9
PNRC1
ASCC3
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
MDN1
UFL1
ORC3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
FILIP1
NDUFAF4
UBE2J1
COQ3
PHIP
AKIRIN2
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
SMIM8
LYRM2
SNX14
FAM135A
RRAGD
BACH2
SMAP1
C6orf164
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
MCHR2
FAXC
GJA10
USP45
UBE3D
MRAP2
KLHL32
RIPPLY2
IRAK1BP1
CD109
PM20D2
SRSF12
KHDC3L
C6orf165
PRSS35
LCA5
C6orf163
MMS22L
DPPA5
GJB7
MIR30A
MIR30C2
KHDC1L
MIR2113
MIR4282
MIR4464
MIR4643
MIR548AI
MIR4463

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

Table S53. 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
ACR
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
MIOX
TRMU
PANX2
CERK
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
PHF21B
KLHDC7B
C22orf34
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535

Genes in Wide Peak

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

Table S54. 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 6p25.3.

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

Genes
IRF4
DEK
snoU13|ENSG00000238322.1
RNY5P5
CMAHP
RN7SL334P
C6orf62
SNORD46|ENSG00000251830.1
RN7SKP240
LINC00340
RN7SL128P
MBOAT1
ID4
RNA5SP205
snoU13|ENSG00000238458.1
RNA5SP204
STMND1
U3|ENSG00000251793.1
MIR4639
RN7SL332P
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
GPLD1
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
ALDH5A1
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
FAM65B
KIAA0319
NUP153
RANBP9
ECI2
CAP2
SCGN
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
GMNN
TBC1D7
NRN1
FAM8A1
DCDC2
TMEM14C
TDP2
GFOD1
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
BLOC1S5
MCUR1
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
NRSN1
SNRNP48
HDGFL1
HIST1H2AA
KDM1B
RBM24
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
RNF144B
HIST1H2BA
CAGE1
MYLK4
TUBB2B
KAAG1
NHLRC1
PSMG4
C6orf201
PPP1R3G
MIR548A1
TMEM170B
MIR4645
MIR5689
MIR5683

Genes in Wide Peak

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

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

Genes
CYP2E1
MTG1
SYCE1
PAOX
FRG2B
SPRN

Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
NFATC1
CTDP1
TXNL4A
ADNP2
KCNG2
PQLC1
PARD6G
ATP9B
HSBP1L1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q12.

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

Genes
ALG10B
RNA5SP359
RNA5SP358
ALG10
SYT10
SNORD112|ENSG00000251863.1
CPNE8

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
snoU13|ENSG00000238969.1
MIR548F5
MIR3915
RNA5SP501
DMD
FTHL17
FAM47A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
COL4A5
COL4A6
IRS4

Genes in Wide Peak

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

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

Genes
PIK3CA
BCL6
EIF4A2
ETV5
LPP
SOX2
TFRC
FAM157A
FYTTD1
snoU13|ENSG00000238491.1
MIR4797
U4|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
RN7SL36P
MIR3137
LINC00884
LINC00887
RN7SL215P
RN7SL447P
snoU13|ENSG00000238902.1
RN7SKP222
RN7SKP296
RN7SL486P
MIR944
MIR28
snoU13|ENSG00000239093.1
RTP4
SNORA4|ENSG00000263776.1
SNORA63|ENSG00000200320.1
SNORA81|ENSG00000221420.2
SNORA63|ENSG00000200418.1
SNORD2|ENSG00000238942.1
KNG1
CRYGS
RN7SL637P
TRA2B
MIR548AQ
SENP2
snoU13|ENSG00000239146.1
SNORD66|ENSG00000212158.1
MIR1224
CYP2AB1P
SNORA4|ENSG00000251730.1
SNORA63|ENSG00000199363.1
SNORA81|ENSG00000253092.1
SNORA63|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
RN7SL229P
U8|ENSG00000201810.1
RNA5SP149
snoU13|ENSG00000239096.1
GNB4
SNORA25|ENSG00000201957.1
RNA5SP148
SNORA18|ENSG00000200288.1
RN7SKP52
LINC00578
LINC00501
RNA5SP147
snoU13|ENSG00000271842.1
MIR4789
RN7SKP40
RN7SKP234
snoU13|ENSG00000239141.1
SNORA72|ENSG00000200355.1
RN7SL141P
PP13439
snoU13|ENSG00000238359.1
MIR569
RNY5P3
CLDN11
TERC
EGFEM1P
RN7SKP298
ACTL6A
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
RPL35A
ST6GAL1
SKIL
SLC2A2
SST
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
ACTRT3
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
SLC51A
FBXO45
MUC20
SENP5
NAALADL2
TCTEX1D2
SMCO1
UTS2B
HTR3E
C3orf70
TPRG1
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
WDR53
ANKRD18DP
NRROS
TMEM212
LINC00885
C3orf65
GMNC
MIR551B
MIR570
MIR922
MIR4448

Genes in Wide Peak

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

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

Genes
RN7SKP73
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
IRX4
CEP72
AHRR
MRPL36
BRD9
IRX1
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
C5orf38
IRX2
SLC6A19
SLC6A18
MIR4277
MIR4457
MIR4456

Genes in Wide Peak

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

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

Genes
LINC00901
TUSC7
RN7SL582P
LINC00903
RN7SL815P
LSAMP
MIR4447

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.3.

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

Genes
CARM1P1
RN7SL592P
RNA5SP279
RN7SL412P
FAM138C
DMRT1
FOXD4
RFX3
SMARCA2
VLDLR
KIAA0020
DMRT2
KANK1
CBWD1
DMRT3
DOCK8
C9orf66
KCNV2

Genes in Wide Peak

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

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

Genes
LINC00320
RN7SKP147
RN7SL163P
SNORD74|ENSG00000201025.1
snoU13|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
C21orf91
SAMSN1
CHODL
LIPI
ABCC13
POTED
LINC00478
MIRLET7C
MIR125B2
MIR99A
MIR548X
MIR3687
C21orf37

Genes in Wide Peak

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

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

Genes
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
GOLGA3
POLE
PXMP2
ZNF10
ZNF26
ZNF84
ZNF268
P2RX2
ANKLE2
GALNT9
CHFR
FBRSL1
NOC4L
PGAM5
DDX51
ZNF605

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 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 | 0.23 | 0.344 | 1 | 0.18 | -1.47 | 1
1q | 1195 | 0.21 | -0.752 | 1 | 0.21 | -0.624 | 1
2p | 624 | 0.12 | -4.32 | 1 | 0.38 | 3.89 | 0.000219
2q | 967 | 0.11 | -4.29 | 1 | 0.31 | 2.27 | 0.0421
3p | 644 | 0.17 | -2.94 | 1 | 0.27 | 0.242 | 0.735
3q | 733 | 0.17 | -2.87 | 1 | 0.22 | -1.31 | 1
4p | 289 | 0.29 | -0.124 | 1 | 0.26 | -1.02 | 1
4q | 670 | 0.21 | -1.67 | 1 | 0.26 | -0.253 | 0.949
5p | 183 | 0.41 | 3.73 | 0.0038 | 0.15 | -3.99 | 1
5q | 905 | 0.31 | 2 | 0.152 | 0.21 | -1.39 | 1
6p | 710 | 0.25 | -0.46 | 1 | 0.30 | 1.3 | 0.259
6q | 556 | 0.24 | -1.11 | 1 | 0.26 | -0.298 | 0.949
7p | 389 | 0.35 | 2.29 | 0.113 | 0.20 | -2.45 | 1
7q | 783 | 0.30 | 1.42 | 0.402 | 0.19 | -2.17 | 1
8p | 338 | 0.25 | -1.21 | 1 | 0.32 | 1.03 | 0.359
8q | 551 | 0.29 | 0.712 | 0.794 | 0.26 | -0.552 | 1
9p | 301 | 0.29 | 0.0396 | 1 | 0.44 | 4.8 | 4.47e-06
9q | 700 | 0.34 | 2.33 | 0.113 | 0.30 | 1.17 | 0.302
10p | 253 | 0.13 | -4.1 | 1 | 0.53 | 7.91 | 1.33e-14
10q | 738 | 0.08 | -4.55 | 1 | 0.54 | 9.97 | 0
11p | 509 | 0.14 | -3.98 | 1 | 0.40 | 4.42 | 2.49e-05
11q | 975 | 0.13 | -3.49 | 1 | 0.39 | 5.21 | 6.2e-07
12p | 339 | 0.21 | -2.41 | 1 | 0.32 | 0.965 | 0.36
12q | 904 | 0.15 | -3.07 | 1 | 0.25 | 0.117 | 0.783
13q | 560 | 0.12 | -3.82 | 1 | 0.55 | 9.56 | 0
14q | 938 | 0.29 | 1.32 | 0.418 | 0.31 | 2.04 | 0.0643
15q | 810 | 0.30 | 1.4 | 0.402 | 0.23 | -0.742 | 1
16p | 559 | 0.21 | -1.84 | 1 | 0.35 | 2.64 | 0.0164
16q | 455 | 0.15 | -3.42 | 1 | 0.53 | 8.61 | 0
17p | 415 | 0.28 | 0.052 | 1 | 0.31 | 0.949 | 0.36
17q | 972 | 0.25 | 0.353 | 1 | 0.26 | 0.475 | 0.635
18p | 104 | 0.26 | -1.28 | 1 | 0.31 | 0.351 | 0.691
18q | 275 | 0.17 | -3.52 | 1 | 0.34 | 1.64 | 0.145
19p | 681 | 0.33 | 2.2 | 0.113 | 0.19 | -2.27 | 1
19q | 935 | 0.28 | 1.02 | 0.557 | 0.22 | -0.801 | 1
20p | 234 | 0.29 | -0.0339 | 1 | 0.30 | 0.076 | 0.783
20q | 448 | 0.35 | 2.25 | 0.113 | 0.16 | -3.47 | 1
21q | 258 | 0.27 | -0.606 | 1 | 0.26 | -1.05 | 1
22q | 564 | 0.31 | 1.2 | 0.46 | 0.34 | 2.11 | 0.0586
Xq | 668 | 0.16 | -2.99 | 1 | 0.45 | 6.43 | 5.09e-10

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/SARC-TP/11449060/GDAC_MergeDataFiles_11451561/SARC-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 257 Input Tumor Samples.

Tumor Sample Names
TCGA-3B-A9HI-01A-11D-A386-01
TCGA-3B-A9HJ-01A-11D-A386-01
TCGA-3B-A9HL-01A-11D-A386-01
TCGA-3B-A9HO-01A-11D-A386-01
TCGA-3B-A9HP-01A-11D-A386-01
TCGA-3B-A9HQ-01A-11D-A386-01
TCGA-3B-A9HR-01A-11D-A386-01
TCGA-3B-A9HS-01A-11D-A38Y-01
TCGA-3B-A9HT-01A-11D-A38Y-01
TCGA-3B-A9HU-01A-11D-A38Y-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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