SNP6 Copy number analysis (GISTIC2) - Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C18914TF

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 539 tumor samples used in this analysis: 29 significant arm-level results, 51 significant focal amplifications, and 49 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 - 51 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
19q12	6.9225e-41	6.9225e-41	chr19:30304858-30358071	1
3q26.2	3.2756e-59	9.386e-36	chr3:168605367-168677467	0 [EGFEM1P]
8q24.21	2.2888e-43	3.2207e-24	chr8:129543557-129554481	0 [RN7SKP226]
17q12	2.2586e-34	2.5662e-20	chr17:37827871-37904210	5
8q24.21	1.9887e-39	6.5639e-16	chr8:128739772-128763161	1
1q22	1.571e-23	1.3982e-15	chr1:155848899-156017401	9
19p13.2	5.3465e-15	5.3465e-15	chr19:13178800-13458242	7
2q13	6.5355e-14	6.5355e-14	chr2:114050324-114109976	0 [PAX8]
10q22.2	7.2256e-14	7.2256e-14	chr10:77001334-77071885	0 [COMTD1]
1p22.3	7.6685e-15	6.7508e-13	chr1:85979933-86002734	1
8p11.21	3.4273e-11	1.4069e-09	chr8:41701319-42001905	3
3q26.2	1.781e-40	3.1136e-09	chr3:169267317-169509651	4
3p25.1	3.7439e-09	6.2042e-08	chr3:13713491-13726839	1
6p24.2	3.6149e-10	2.2924e-07	chr6:11230043-11466767	1
12q13.2	2.401e-09	1.4111e-06	chr12:56484785-56490664	1
17q25.1	1.7814e-11	1.7485e-06	chr17:73553929-73774242	9
1q21.3	7.3213e-22	6.5544e-06	chr1:150493148-150611099	8
5p15.33	1.3504e-05	1.3504e-05	chr5:1-1425066	25
4p16.3	3.571e-05	3.571e-05	chr4:1629690-1881446	8
11q13.2	2.0171e-06	8.456e-05	chr11:67294199-67775127	11
20q11.21	1.118e-08	0.00019953	chr20:30190878-30325712	4
9p24.2	0.00020615	0.00020615	chr9:3631009-3867341	1
2p24.3	0.00029454	0.00029454	chr2:15772866-16358714	4
16p11.2	0.00033377	0.00033377	chr16:30854953-30989870	8
20q13.12	2.5962e-07	0.00044792	chr20:45936286-46076395	2
18q11.2	0.00072581	0.00072581	chr18:23857484-24065368	3
6q25.1	0.0010426	0.0010426	chr6:151925378-152042501	2
22q12.2	0.0011907	0.0011907	chr22:30299754-31008866	19
11q14.1	8.456e-05	0.0036574	chr11:75936943-78134061	25
Xp11.23	0.0040075	0.0040075	chrX:46547716-47356397	17
20q13.33	6.0774e-06	0.0079914	chr20:60838713-61264514	10
1p34.2	0.00028641	0.008627	chr1:41319053-41507861	4
Xq28	0.010489	0.010489	chrX:153029080-153341059	17
18p11.31	0.020695	0.020695	chr18:3293976-3739936	5
12p12.1	0.027951	0.030554	chr12:24536838-25683946	9
1q44	6.7001e-05	0.04236	chr1:224086864-249250621	260
12q13.11	0.00018621	0.056453	chr12:48107006-48305012	5
9q34.3	0.063744	0.063744	chr9:139812578-139951370	14
13q34	0.078562	0.078562	chr13:109144777-114923884	47
3p14.1	0.0060265	0.085836	chr3:66724129-66740563	0 [LRIG1]
7q31.2	0.089736	0.089736	chr7:117179038-117381805	2
14q24.3	0.0096533	0.091786	chr14:77305985-77565636	5
1p35.2	0.0060265	0.10519	chr1:31354381-31376674	1
14q32.33	0.019592	0.10958	chr14:105592026-105654190	2
17q11.2	1.952e-06	0.11684	chr17:26704253-27113673	24
11p11.2	0.12484	0.12484	chr11:46300642-46786791	15
20p13	0.12484	0.12484	chr20:2661659-4359815	38
5q35.3	0.1439	0.1439	chr5:176744583-176890641	9
15q26.3	0.15279	0.15279	chr15:98000287-102531392	39
8p11.22	0.0011534	0.18505	chr8:38061530-38802675	10
6p22.3	9.3996e-05	0.20966	chr6:18469820-18521016	0 [RNF144B]

Genes in Wide Peak

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

Table S1. 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 17q12.

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

Genes
ERBB2
MIR4728
GRB7
MIEN1
PGAP3

Genes in Wide Peak

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

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

Genes
MYC

Genes in Wide Peak

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

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

Genes
SCARNA4\|ENSG00000252808.1
SNORA42\|ENSG00000207475.1
RIT1
SSR2
ARHGEF2
KIAA0907
SYT11
UBQLN4
RXFP4

Genes in Wide Peak

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

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

Genes
LYL1
CACNA1A
NFIX
STX10
IER2
TRMT1
NACC1

Genes in Wide Peak

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

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

Genes
DDAH1

Genes in Wide Peak

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

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

Genes
SNORD112\|ENSG00000238966.1
ANK1
KAT6A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
TERC
MECOM
MYNN
ACTRT3

Genes in Wide Peak

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

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

Genes
LINC00620

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.2.

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

Genes
NEDD9

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.2.

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

Genes
ERBB3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
MYO15B
GALK1
H3F3B
ITGB4
LLGL2
RECQL5
SAP30BP
SMIM5
SMIM6

Genes in Wide Peak

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

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

Genes
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
ENSA
MCL1
ADAMTSL4
MIR4257

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
RN7SL671P
LETM1
SLBP
TACC3
TMEM129
FAM53A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
FAM86C2P
DOC2GP
C11orf72
RN7SL59P
ALDH3B2
GSTP1
NDUFV1
UNC93B1
ACY3
NUDT8
TBX10

Genes in Wide Peak

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

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

Genes
BCL2L1
ID1
COX4I2
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.2.

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

Genes
GLIS3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.3.

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

Genes
MYCN
RN7SL104P
MYCNOS
snoU13\|ENSG00000238371.1

Genes in Wide Peak

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

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

Genes
MIR4519
MIR4519
BCL7C
CTF1
SETD1A
FBXL19
ORAI3
MIR762

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.12.

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

Genes
RN7SL243P
ZMYND8

Genes in Wide Peak

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

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

Genes
U3\|ENSG00000252921.1
TAF4B
KCTD1

Genes in Wide Peak

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

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

Genes
ESR1
CCDC170

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q12.2.

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

Genes
SEC14L6
KIAA1658
MGC20647
LIF
OSM
TCN2
MTMR3
GAL3ST1
SF3A1
PES1
SEC14L2
MTFP1
TBC1D10A
HORMAD2
RNF215
SEC14L3
SEC14L4
CCDC157
GATSL3

Genes in Wide Peak

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

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

Genes
DKFZP434E1119
ACER3
GUCY2EP
CAPN5
CLNS1A
LRRC32
MYO7A
NDUFC2
OMP
PAK1
PRKRIR
THRSP
GAB2
TSKU
AAMDC
RSF1
C11orf30
USP35
KCTD14
ALG8
INTS4
B3GNT6
GDPD4
AQP11
KCTD21

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.23.

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

Genes
CXorf24
SNORA11C
ZNF157
RN7SL785P
snoU13\|ENSG00000238729.1
INE1
SLC9A7
CDK16
RP2
UBA1
ZNF41
USP11
RBM10
RGN
PHF16
NDUFB11
CXorf31

Genes in Wide Peak

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

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

Genes
MIR133A2
MIR4758
LAMA5
RPS21
OSBPL2
ADRM1
CABLES2
C20orf166
GATA5
RBBP8NL

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
CTPS1
SCMH1
CITED4
SLFNL1

Genes in Wide Peak

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

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

Genes
NAA10
LCA10
SNORD36\|ENSG00000251846.1
ARHGAP4
AVPR2
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
PLXNB3
RENBP
SSR4
TMEM187
SRPK3
PDZD4
MIR718

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238445.1
RN7SL39P
snoU13\|ENSG00000238863.1
TGIF1
DLGAP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
RN7SL38P
BCAT1
LRMP
CASC1
LINC00477
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

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

Table S32. 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
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
CHML
LYST
EPHX1
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
LBR
LGALS8
MTR
NID1
NVL
PSEN2
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
LEFTY2
GPR137B
TSNAX
ZNF124
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
AKT3
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
COG2
RBM34
FBXO28
ABCB10
OPN3
AHCTF1
OR2M4
OR2L2
OR2T1
TAF5L
DISC1
CNIH4
PYCR2
DESI2
SCCPDH
TRIM17
ARID4B
EGLN1
MAP10
KIF26B
HEATR1
ZNF692
ENAH
NUP133
ERO1LB
FMN2
ADCK3
ZNF695
GJC2
SIPA1L2
RHOU
TFB2M
GREM2
ACBD3
SMYD3
ARV1
JMJD4
C1orf35
TTC13
PGBD5
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
SPRTN
OBSCN
EFCAB2
MLK4
ZNF496
C1orf198
WNT3A
HIST3H2A
NLRP3
COX20
SNAP47
CCSAP
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
GCSAML
CNIH3
EXOC8
SDE2
CNST
PLD5
C1orf100
IBA57
OR2T6
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
TRIM67
MAP1LC3C
OR13G1
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.11.

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

Genes
VDR
ENDOU
RAPGEF3
HDAC7
SLC48A1

Genes in Wide Peak

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

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

Genes
CLIC3
C9orf141
ABCA2
C8G
ENTPD2
FUT7
PTGDS
TRAF2
FBXW5
NPDC1
LCN12
C9orf142
LCNL1
C9orf139

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
CFTR
CTTNBP2

Genes in Wide Peak

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

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

Genes
RN7SL356P
RN7SKP17
IRF2BPL
KIAA1737
C14orf166B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p35.2.

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

Genes
SDC3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.33.

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

Genes
JAG2
NUDT14

Genes in Wide Peak

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

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

Genes
NEK8
SNORD4B
SNORD42A
SNORD4A
SNORD42B
RPL23A
SGK494
TMEM199
ALDOC
SDF2
SUPT6H
FOXN1
SLC13A2
UNC119
TRAF4
KIAA0100
SPAG5
SARM1
FAM222B
RAB34
PIGS
SLC46A1
TLCD1
PROCA1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p11.2.

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

Genes
CREB3L1
SNORD67\|ENSG00000212135.1
SNORD67\|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
ARHGAP1
CHRM4
F2
MDK
DGKZ
ATG13
CKAP5
AMBRA1
ZNF408

Genes in Wide Peak

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

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

Genes
MIR103A2
MAVS
U3\|ENSG00000201346.1
RN7SL839P
RN7SL555P
TMEM239
ADRA1D
AVP
CDC25B
CENPB
GNRH2
ITPA
OXT
PTPRA
SIGLEC1
ATRN
LZTS3
RNF24
UBOX5
SPEF1
C20orf194
SMOX
C20orf27
AP5S1
CPXM1
EBF4
FASTKD5
GFRA4
VPS16
PCED1A
MRPS26
DDRGK1
PANK2
ADAM33
SLC4A11
HSPA12B
C20orf141
TMEM239

Genes in Wide Peak

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

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

Genes
RN7SL562P
DBN1
F12
GRK6
SLC34A1
RGS14
LMAN2
PRR7
PFN3

Genes in Wide Peak

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

Table S44. 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
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
VIMP
TTC23
LRRK1
TM2D3
ARRDC4
LINC00923
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
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 S45. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR1
WHSC1L1
PLEKHA2
RPS20P22
TACC1
BAG4
DDHD2
PPAPDC1B
LETM2
C8orf86

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 - 49 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
19p13.3	2.4315e-47	1.6537e-46	chr19:3054758-3143282	1
5q12.1	5.5376e-32	5.5376e-32	chr5:58998410-59780946	2
4q34.3	5.4845e-33	3.1964e-26	chr4:179280062-182757119	4
10q23.31	6.8601e-23	6.8601e-23	chr10:89617158-89755074	3
22q13.32	7.0855e-20	7.0855e-20	chr22:48668761-51304566	42
Xp21.1	1.7528e-18	1.6081e-18	chrX:32117084-32611359	2
2q22.1	1.6081e-18	2.6982e-17	chr2:140708948-143637838	2
16q23.1	2.8253e-17	3.7966e-13	chr16:78098006-79299841	3
1p36.11	2.7419e-18	7.8853e-11	chr1:26900639-27570286	16
6q26	2.1501e-09	2.2085e-09	chr6:161693099-163153207	1
3q13.31	1.8448e-08	1.8419e-08	chr3:116426639-118620828	3
3p14.2	8.5171e-08	8.0502e-08	chr3:59034763-61547330	3
11p15.5	2.3896e-07	2.3782e-07	chr11:1-1084361	48
12q23.1	2.0116e-08	1.1686e-06	chr12:99119269-100107912	2
8p21.2	8.1184e-10	3.9047e-06	chr8:22111872-28177087	59
15q15.1	2.4086e-08	8.2605e-06	chr15:28096454-45507739	211
13q14.2	2.665e-06	6.2437e-05	chr13:48875329-49152025	3
7p22.3	8.0337e-05	8.0337e-05	chr7:1-1303032	15
20p12.1	8.4521e-05	8.676e-05	chr20:14301156-16252980	2
16p13.3	9.5885e-05	9.7495e-05	chr16:3764793-4004422	1
17q11.2	5.5849e-08	9.7495e-05	chr17:29326736-29722618	5
11q25	1.1614e-06	0.00011393	chr11:121061987-135006516	123
18q23	1.0899e-06	0.00011393	chr18:64271112-78077248	48
1p36.21	1.6595e-12	0.00020615	chr1:1-22596599	346
9p23	0.00037056	0.00035722	chr9:7887952-12687261	3
8p23.2	3.398e-10	0.00079069	chr8:1-4251018	14
4p15.2	0.00016287	0.00099067	chr4:19182220-22351071	4
11q14.1	0.00025028	0.00099794	chr11:82995735-85348794	2
17q21.31	4.3447e-06	0.0015371	chr17:38441512-45196143	199
19q13.43	0.002189	0.0021322	chr19:58485722-59128983	30
17p11.2	0.00032675	0.005426	chr17:9693062-25270516	158
14q13.1	0.005765	0.0057821	chr14:33297556-34394000	1
7q31.1	4.249e-05	0.013136	chr7:108535383-111366370	4
2q37.3	0.00037462	0.020965	chr2:232367824-243199373	127
17p13.3	0.0015371	0.02751	chr17:1-1201203	15
4q22.1	0.00023517	0.028877	chr4:90844993-94741521	4
9q34.2	0.014215	0.028877	chr9:135114366-139381924	84
12q24.33	0.00031706	0.034059	chr12:121102942-133851895	132
16q21	6.4257e-06	0.049303	chr16:31804435-70260738	273
4p16.3	0.0023249	0.086367	chr4:1-1511830	30
15q23	0.00021571	0.10898	chr15:71342247-72094855	2
16q22.3	8.7695e-12	0.10898	chr16:72209520-73126458	1
7q36.1	0.00020553	0.1163	chr7:120389649-159138663	345
18q21.2	0.0088985	0.1163	chr18:43261427-65175647	124
19p12	1.0011e-05	0.1163	chr19:23939307-29422400	5
9q21.2	0.068054	0.13477	chr9:38619152-107861723	288
2p25.3	0.16979	0.16987	chr2:1-27196298	161
13q11	0.0024494	0.17786	chr13:1-24042353	49
7q11.22	0.0030547	0.18742	chr7:69000716-70601215	2

Genes in Wide Peak

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

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

Genes
GNA11

Genes in Wide Peak

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

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

Genes
FKSG52
MIR582

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

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

Genes
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173

Genes in Wide Peak

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

Table S49. 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 22q13.32.

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
ACR
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
IL17REL
PIM3
ODF3B
SYCE3
MIR3201
MIR3667
MIR4535

Genes in Wide Peak

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

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

Genes
MIR3915
RNA5SP501

Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B

Genes in Wide Peak

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

Table S53. 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 1p36.11.

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

Genes
ARID1A
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
RN7SL679P
SFN
SLC9A1
NR0B2
NUDC
PIGV
GPATCH3
FAM46B
C1orf172
TRNP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
LINC00901
TUSC7
MIR4447

Genes in Wide Peak

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

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

Genes
FHIT
U3\|ENSG00000212211.1
NPCDR1

Genes in Wide Peak

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

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

Genes
HRAS
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
CD151
DRD4
IRF7
MUC6
POLR2L
PSMD13
RNH1
TALDO1
TSPAN4
RASSF7
IFITM1
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
BET1L
CEND1
CDHR5
PIDD
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
LRRC56
SCGB1C1
NLRP6
C11orf35
EFCAB4A
ANO9
B4GALNT4
PDDC1
IFITM5
MIR210

Genes in Wide Peak

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

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

Genes
RNA5SP366
FAM71C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

Genes
MIR4287
snoU13\|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67\|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
ADRA1A
BNIP3L
CHRNA2
CLU
DPYSL2
EGR3
EPHX2
PTK2B
GNRH1
LOXL2
NEFM
PPP2R2A
PPP3CC
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
ENTPD4
SORBS3
PNMA2
ADAM28
TRIM35
RHOBTB2
SLC39A14
ADAMDEC1
SCARA3
KCTD9
PIWIL2
ELP3
CCDC25
PBK
BIN3
KIAA1967
PDLIM2
EBF2
DOCK5
STMN4
CHMP7
PEBP4
CDCA2
ESCO2
R3HCC1
SCARA5
NUGGC
C8orf58
MIR548H4
MIR3622B

Genes in Wide Peak

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

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

Genes
BUB1B
SNORA11\|ENSG00000261709.2
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13\|ENSG00000238494.1
snoU13\|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13\|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13\|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13\|ENSG00000238564.1
THBS1
FAM98B
U3\|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18\|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77\|ENSG00000212415.1
snoU13\|ENSG00000238342.1
RN7SL286P
RN7SL539P
GOLGA8O
U8\|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18\|ENSG00000206849.1
MIR211
RN7SL82P
U8\|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8\|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8\|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8\|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
ACTC1
APBA2
CAPN3
CHRM5
CKMT1B
EPB42
GANC
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
PLCB2
RAD51
RYR3
SCG5
SPINT1
SRP14
TJP1
TP53BP1
TYRO3
EIF3J
SNAP23
HERC2
TGM5
PPIP5K1
AQR
ARHGAP11A
LCMT2
RASGRP1
GPR176
CHP1
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
FAM189A1
SERF2
TMEM87A
RPAP1
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
RMDN3
DNAJC17
NOP10
NDNL2
EMC7
PAK6
CASC5
AVEN
STARD9
VPS18
ZNF106
CHAC1
KATNBL1
WDR76
TMEM62
SPG11
ELL3
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
NUTM1
PLA2G4D
GOLGA8G
FMN1
C15orf52
C15orf53
C15orf54
DUOXA2
HERC2P9
GOLGA8B
EIF2AK4
CKMT1A
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4510

Genes in Wide Peak

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

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

Genes
RB1
RCBTB2
LPAR6

Genes in Wide Peak

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

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

Genes
UNCX
MIR339
COX19
FAM20C
GPER
PDGFA
PRKAR1B
ADAP1
SUN1
GET4
CYP2W1
HEATR2
C7orf50
ZFAND2A
GPR146

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
RNA5SP475
FLRT3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

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

Genes
CREBBP

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

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

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

Genes
FLI1
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
ACRV1
APLP2
CHEK1
ETS1
HSPA8
STT3A
KCNJ1
VWA5A
NFRKB
NRGN
OPCML
ST3GAL4
SORL1
SRPR
ST14
ZNF202
BARX2
EI24
FEZ1
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
VSIG2
OR8B8
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
CRTAM
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ROBO3
FAM118B
MSANTD2
CLMP
C11orf63
CCDC15
PUS3
JAM3
KIRREL3
RPUSD4
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
PANX3
TMEM45B
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
SPATA19
HEPACAM
OR8D1
OR8D2
OR8B4
C11orf44
TMEM225
OR8D4
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
HEPN1
PATE3
MIR4697
MIR4493

Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25\|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
CYB5A
MBP
NFATC1
ZNF236
CTDP1
SOCS6
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
PQLC1
NETO1
PARD6G
CNDP1
DSEL
FAM69C
CBLN2
FBXO15
GTSCR1
DOK6
LINC00908
ATP9B
LINC00909
HSBP1L1
C18orf63
MIR5011

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13\|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13\|ENSG00000239020.1
PADI6
MIR3972
U1\|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1\|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13\|ENSG00000238818.1
DDI2
AGMAT
SCARNA21\|ENSG00000251866.1
C1orf195
SCARNA11\|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13\|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70\|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13\|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16\|ENSG00000252404.1
RN7SL451P
SNORA77\|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13\|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
CA6
CAPZB
CASP9
TNFRSF8
CDA
CDK11B
CDC42
CLCN6
CLCNKA
CLCNKB
CORT
DDOST
DFFB
DVL1
ECE1
EPHA2
ENO1
MTOR
GABRD
GNB1
ZBTB48
HSPG2
HTR6
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TNFRSF1B
TP73
TNFRSF4
ZBTB17
PRDM2
MMP23B
KCNAB2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
MFN2
CELA3A
ANGPTL7
UBE4B
MAD2L2
PDPN
MASP2
UTS2
RER1
PADI2
PARK7
CTRC
ACOT7
CLSTN1
SPEN
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
CHD5
SZRD1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
ARHGEF10L
VPS13D
ATAD3A
PANK4
CAMK2N1
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
AGTRAP
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
MIIP
CELA2A
PLA2G2F
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
EFHD2
MMEL1
RSG1
MUL1
NOL9
LINC00115
MORN1
SPSB1
GLTPD1
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
ATAD3B
PLEKHN1
USP48
NBPF3
LZIC
C1orf170
IGSF21
KIAA2013
THAP3
FBXO44
FHAD1
RBP7
ACAP3
UBE2J2
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
SLC2A7
CALML6
FAM43B
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
OR4F29
MIR1273D
MIR4252
MIR3675
APITD1
MIR4689
MIR4418
MIR4417
MIR5697

Genes in Wide Peak

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

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

Genes
RN7SL5P
SNORD27\|ENSG00000251699.1
PTPRD

Genes in Wide Peak

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

Table S71. 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 4p15.2.

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

Genes
RNA5SP157
SLIT2
KCNIP4
PACRGL

Genes in Wide Peak

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

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

Genes
DLG2
TMEM126B

Genes in Wide Peak

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

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

Genes
RARA
BRCA1
ETV4
RN7SL270P
LRRC37A17P
RNU6ATAC3P
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3\|ENSG00000221496.1
RN7SL507P
U3\|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40\|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
ZNF385C
TTC25
RN7SL871P
RN7SL399P
RNA5SP442
EIF1
KRT42P
LINC00974
KRT223P
KRT222
KRT222
RNA5SP441
GJD3
ACLY
AOC2
ARL4D
ATP6V0A1
FMNL1
CDC6
CCR7
CNP
CRHR1
DHX8
DUSP3
EZH1
GAST
KAT2A
GFAP
GRN
HCRT
IFI35
IGFBP4
ITGA2B
JUP
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
NAGLU
NMT1
NSF
PPY
PYY
RAB5C
RPL27
SLC4A1
SMARCE1
STAT3
STAT5A
STAT5B
MLX
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
RND2
CNTNAP1
AOC3
BECN1
KRT38
KRT37
KRT36
HAP1
EFTUD2
GOSR2
PLEKHM1
LRRC37A
HDAC5
GJC1
PSME3
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
C1QL1
RUNDC3A
KCNH4
FAM215A
KRT23
TUBG2
NKIRAS2
COA3
PSMC3IP
SOST
ARL17A
SLC25A39
HIGD1B
KRT20
KLHL11
ATXN7L3
FKBP10
WNK4
C17orf53
TMUB2
DHX58
ACBD4
DCAKD
PLEKHH3
DBF4B
COASY
AARSD1
VPS25
TMEM101
GHDC
TNS4
G6PC3
ASB16
HSPB9
PLCD3
TMEM106A
NT5C3B
SPATA32
HEXIM2
LSM12
CCDC43
KRT40
CD300LG
KIF18B
RUNDC1
KRT25
TMEM99
NAGS
FAM134C
SPPL2C
KRT28
KRT24
ARHGAP27
STH
KANSL1
FAM171A2
C17orf104
PTRF
KLHL10
KRT27
KRT26
LINC00671
RPRML
KRT39
LRRC37A2
MIR2117
ARL17B
MIR5089
PTGES3L

Genes in Wide Peak

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

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

Genes
RN7SL525P
RN7SL693P
RNA5SP473
RN7SL526P
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
ZSCAN18
RPL23AP79
ZNF329
ZNF606
ZBTB45
ZNF837
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
MIR4754

Genes in Wide Peak

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

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

Genes
MAP2K4
GAS7
MTND1P15
UBBP4
RN7SL426P
TMEM11
KRT16P3
NOS2P3
USP32P3
UPF3AP2
RN7SL17P
U6\|ENSG00000266839.2
CCDC144CP
SNORA31\|ENSG00000252349.1
SNORA59B
MIR1180
SNORD3C
SNORD3A
GRAPL
SNORD3D
GRAP
FAM83G
RN7SL627P
ZNF286B
TBC1D28
RN7SL639P
KRT16P1
KRT17P2
SMCR8
snoU13\|ENSG00000238691.1
MIR33B
SMCR5
SMCR2
RN7SL775P
TBC1D27
KRT17P1
KRT16P2
USP32P1
RN7SL620P
ZNF287
MIR1288
RN7SL442P
RNA5SP436
ZNF286A
SNORA74\|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13\|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
SNORA74\|ENSG00000252305.1
MIR548H3
RN7SL550P
MIR744
RPL21P122
RN7SL601P
LINC00675
MAGOH2
ADPRM
RCVRN
GLP2R
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FLII
KCNJ12
LLGL1
MFAP4
MYH1
MYH2
MYH3
MYH4
MYH8
PMP22
MAPK7
MAP2K3
PRPSAP2
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
MYH13
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
DHRS7B
B9D1
TVP23B
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
ZNF286A
ZNF624
ELAC2
TEKT3
GID4
FAM106A
LRRC48
ATPAF2
SPECC1
MYOCD
ZSWIM7
SMCR7
SLC5A10
TOM1L2
SLC47A2
TRIM16L
TVP23C
CENPV
FLCN
PLD6
USP32P2
CDRT15L2
C17orf103
LINC00670
CDRT4
CCDC144B
FAM27L
LGALS9B
CCDC144NL
C17orf51
TBC1D26
CDRT1
TMEM220
SHISA6
FAM211A
PIRT
EVPLL
LGALS9C
MTRNR2L1
MIR1269B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q13.1.

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

Genes
NPAS3

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238922.1
FLJ00325
LRRN3
IMMP2L

Genes in Wide Peak

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

Table S79. 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
snoU13\|ENSG00000239170.1
RN7SL359P
CHRND
ECEL1P2
MIR562
NPPC
MGC4771
RN7SL499P
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
PPP1R7
PTMA
SAG
SPP2
DGKD
PER2
LRRFIP1
ECEL1
EIF4E2
HDAC4
FARP2
ARL4C
RAMP1
NMUR1
STK25
CAPN10
PASK
ATG4B
SH3BP4
NGEF
SNED1
GIGYF2
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A8
UGT1A1
ATG16L1
USP40
HJURP
HES6
ACKR3
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
C2orf54
EFHD1
ILKAP
ING5
AGAP1
TWIST2
DIS3L2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LINC00471
C2orf57
TIGD1
DUSP28
MROH2A
ESPNL
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4269
MIR4786
MIR5001

Genes in Wide Peak

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

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

Genes
BHLHA9
MIR3183
TIMM22
DBIL5P
DOC2B
ABR
RPH3AL
GEMIN4
GLOD4
RNMTL1
VPS53
NXN
FAM57A
FAM101B
C17orf97

Genes in Wide Peak

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

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

Genes
RNA5SP164
RN7SKP248
GRID2
CCSER1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.2.

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

Genes
RALGDS
TSC1
BRD3
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13\|ENSG00000238657.1
CELP
GTF3C4
CEL
COL5A1
DBH
SARDH
FCN1
FCN2
LCN1
PAEP
RPL7A
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TTF1
VAV2
LHX3
GFI1B
GTF3C5
ADAMTSL2
PPP1R26
SEC16A
UBAC1
OLFM1
SDCCAG3
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
SETX
PMPCA
GPSM1
GBGT1
OBP2B
OBP2A
MRPS2
INPP5E
BARHL1
REXO4
KCNT1
DDX31
C9orf69
NACC2
C9orf116
CAMSAP1
C9orf62
C9orf163
AK8
C9orf96
QSOX2
GLT6D1
C9orf171
TMEM8C
LCN9
SOHLH1
CARD9
MIR3689A
MIR3689B
MIR3689D1
MIR3689F
MIR3689C
MIR3689D2
MIR3689E
MIR548AW

Genes in Wide Peak

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

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

Genes
BCL7A
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13\|ENSG00000238822.1
RN7SL534P
snoU13\|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9\|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9\|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70\|ENSG00000201945.1
ACADS
SCARB1
STX2
GOLGA3
GTF2H3
HPD
MMP17
P2RX4
P2RX7
POLE
PSMD9
PXMP2
CLIP1
SFSWAP
HNF1A
UBC
ZNF10
ZNF26
ZNF84
CDK2AP1
ULK1
DENR
OASL
HCAR3
HIP1R
PIWIL1
NCOR2
KNTC1
MLEC
MPHOSPH9
CAMKK2
ZNF268
TMED2
FZD10
P2RX2
SETD1B
ANKLE2
ABCB9
RIMBP2
ATP6V0A2
GALNT9
ARL6IP4
ANAPC5
RHOF
SBNO1
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
C12orf43
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
RNF34
CCDC92
PUS1
CCDC62
KDM2B
UNC119B
C12orf65
TMEM132D
SLC15A4
SPPL3
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
MORN3
DDX51
HCAR2
EP400NL
RILPL1
IL31
SETD8
ZNF605
MIR3908
MIR4419B
MIR4700
MIR5188

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q21.

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

Genes
CDH11
CBFB
CDH1
CYLD
HERPUD1
FKSG63
PDXDC2P
MIR140
SNORA62\|ENSG00000252443.1
snoU13\|ENSG00000238683.1
COG8
CHTF8
RPS2P45
RNA5SP429
snoU109\|ENSG00000252640.1
snoU109\|ENSG00000252040.1
snoU13\|ENSG00000238343.1
SLC7A6OS
SNORA48\|ENSG00000212445.1
CTRL
NUTF2
RN7SKP118
TRADD
RN7SL543P
LINC00920
RNA5SP428
LINC00922
snoU13\|ENSG00000238507.1
RN7SKP76
RN7SL143P
SLC38A7
snoU13\|ENSG00000239121.1
SNORA50\|ENSG00000206952.2
SNORA46\|ENSG00000207493.1
RN7SL645P
TEPP
MT1DP
MT1M
MT1E
MT1L
MT2A
OGFOD1
MIR3935
IRX6
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
AGRP
AMFR
BBS2
CA7
CBLN1
CDH3
CDH5
CDH8
CDH16
CES1
CETP
CNGB1
CSNK2A2
NQO1
DYNC1LI2
E2F4
GNAO1
GOT2
HAS3
HSD11B2
HSF4
KIFC3
LCAT
MMP2
MMP15
MT1A
MT1B
MT1F
MT1G
MT1H
MT1JP
MT1X
MT3
NFATC3
PHKB
POLR2C
PSKH1
PSMB10
RBL2
RRAD
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
TERF2
TK2
CES2
NAE1
NOL3
SLC7A6
ATP6V0D1
GPR56
N4BP1
NUP93
IRX5
DNAJA2
KATNB1
ZNF267
CTCF
NFAT5
NUDT21
WWP2
CNOT1
ZNF423
RPGRIP1L
CES3
ARL2BP
ORC6
EDC4
PLA2G15
PLEKHG4
LRRC29
VPS4A
TOX3
NOB1
CCDC113
TMEM208
C16orf80
FHOD1
BRD7
ZDHHC1
PARD6A
PLLP
CKLF
NIP7
FAM96B
TPPP3
CES1P1
PRMT7
DUS2L
CHTF8
LPCAT2
HEATR3
PDPR
LRRC36
FBXL8
SMPD3
DOK4
DDX28
TSNAXIP1
COQ9
CIAPIN1
THAP11
PDP2
ZNF319
RANBP10
NOD2
PDF
DPEP2
DPEP3
PAPD5
AKTIP
GINS3
NDRG4
ACD
IRX3
FAM65A
TANGO6
USB1
ELMO3
SHCBP1
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
CYB5B
GFOD2
NETO2
ENKD1
NLRC5
CCDC135
CAPNS2
MT4
GPT2
B3GNT9
CIRH1A
ABCC11
RSPRY1
CCDC102A
ABCC12
CMTM1
NRN1L
CMTM3
C16orf78
SNX20
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
TMED6
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
CCDC79
CES4A
EXOC3L1
CLEC18C
CLEC18A
SLC6A10P
C16orf87
C16orf97
C16orf86
MIR328
KIAA0895L
TP53TG3C
TP53TG3B
MIR1538

Genes in Wide Peak

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

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

Genes
SNORA48\|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ATP5I
CTBP1
DGKQ
GAK
IDUA
MYL5
PDE6B
MAEA
PCGF3
SPON2
CPLX1
SLC26A1
FGFRL1
PIGG
UVSSA
MFSD7
TMEM175
CRIPAK
RNF212

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q23.

Table S86. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
THSD4
CT62

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.3.

Table S87. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ZFHX3

Genes in Wide Peak

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

Table S88. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BRAF
EZH2
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26\|ENSG00000212590.1
snoU13\|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13\|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112\|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3\|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6\|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13\|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40\|ENSG00000252188.1
snoU13\|ENSG00000239123.1
SNORA51\|ENSG00000201465.1
snoU13\|ENSG00000238984.1
snoU13\|ENSG00000239145.1
RN7SKP223
SNORD81\|ENSG00000202023.1
snoU13\|ENSG00000238488.1
LUZP6
C7orf73
U6\|ENSG00000272393.1
SNORD46\|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13\|ENSG00000239044.1
snoU13\|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13\|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
CPED1
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

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

Table S89. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BCL2
MALT1
snoU13\|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8\|ENSG00000199713.1
RN7SL112P
SNORD28\|ENSG00000252284.1
FECH
U3\|ENSG00000212539.1
TXNL1
SNORA73\|ENSG00000201816.1
RNA5SP459
SNORA37
DCC
snoU13\|ENSG00000238885.1
RN7SL695P
ME2
RNA5SP458
RN7SL310P
RNA5SP457
SCARNA18\|ENSG00000252139.1
SCARNA17\|ENSG00000251992.1
SCARNA17\|ENSG00000267322.1
SNORD58B
SNORD58A
SNORD58C
C18orf32
MIR4744
MIR4743
RNA5SP456
IER3IP1
RNF165
RN7SKP26
ATP5A1
CDH7
KDSR
GRP
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MC4R
MYO5B
NARS
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
RPL17
SERPINB3
SERPINB4
SLC14A1
TCF4
SERPINB7
TNFRSF11A
MBD2
PSTPIP2
PIAS2
LIPG
ONECUT2
VPS4B
CTIF
ACAA2
POLI
PHLPP1
NEDD4L
WDR7
PIGN
CDH20
CDH19
ST8SIA5
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
DYM
ZCCHC2
ZNF532
ELAC1
KIAA1468
EPG5
CCDC68
KATNAL2
MRO
HDHD2
SERPINB12
SERPINB11
SEC11C
HAUS1
ALPK2
LOXHD1
STARD6
C18orf25
CCBE1
C18orf54
TCEB3C
ZBTB7C
SKA1
CCDC11
LINC00305
DYNAP
BOD1L2
SIGLEC15
HMSD
CPLX4
MIR122
SKOR2
TCEB3CL
MIR1539
TCEB3CL2
MIR4527
MIR4529
MIR5011

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p12.

Table S90. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13\|ENSG00000238514.1
LINC00662
ZNF726
ZNF254
RPSAP58

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.2.

Table S91. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GNAQ
FANCC
OMD
SYK
XPA
NR4A3
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31\|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
snoU13\|ENSG00000238746.1
RNA5SP288
MIR27B
MIR23B
MIR2278
PCAT7
ZNF169
snoU13\|ENSG00000238792.1
MIRLET7DHG
CENPP
SNORA84
snoU13\|ENSG00000238996.1
LINC00475
LINC00484
MIR3153
SHC3
U3\|ENSG00000252299.1
U6\|ENSG00000271923.1
SPATA31C1
SNORA26\|ENSG00000212421.1
RN7SKP264
IDNK
SNORD112\|ENSG00000252256.1
snoU13\|ENSG00000238608.1
RN7SKP242
SPATA31D3
SPATA31D4
SPATA31D5P
SNORD95\|ENSG00000200969.1
RNA5SP287
TLE4
RN7SKP59
PCA3
snoU13\|ENSG00000238598.1
RNY4P1
RN7SKP47
RNA5SP286
snoU13\|ENSG00000238402.1
RNA5SP285
MIR204
RN7SL570P
CBWD3
PGM5P2
RNA5SP284
SNORA70\|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70\|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70\|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70\|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
ABCA1
ALDH1A1
ALDOB
ANXA1
APBA1
AUH
BAAT
KLF9
CKS2
COL15A1
CTSL
CYLC2
DAPK1
ECM2
S1PR3
FBP1
FOXE1
FXN
GAS1
GCNT1
HNRNPK
HSD17B3
IARS
NCBP1
NFIL3
NINJ1
NTRK2
ROR2
OGN
PCSK5
PGM5
PHF2
PPP3R2
PRKACG
PTCH1
RORB
TGFBR1
TLE1
TMOD1
CORO2A
ZNF189
ZFAND5
PIP5K1B
CDC14B
TMEFF1
FBP2
FAM189A2
TJP2
GABBR2
GDA
GNA14
TRIM14
SEMA4D
ANP32B
SPTLC1
SMC2
GADD45G
SPIN1
SEC61B
SLC35D2
ZNF510
HABP4
ERP44
SMC5
FAM120A
VPS13A
AGTPBP1
BICD2
TDRD7
CDK20
TMEM2
NIPSNAP3A
ZNF658
SPATA31A7
OSTF1
INVS
PSAT1
UBQLN1
ABHD17B
GOLM1
C9orf156
NANS
MRPL50
NUTM2F
DIRAS2
ASPN
TEX10
NMRK1
NOL8
C9orf40
RFK
NIPSNAP3B
TBC1D2
HEMGN
KIF27
BARX1
RNF20
NAA35
SLC28A3
IPPK
WNK2
SECISBP2
ZCCHC6
GALNT12
CNTNAP3
RMI1
TRPM3
GKAP1
ISCA1
ZNF484
CEP78
ANKRD20A1
C9orf64
C9orf89
HIATL2
HIATL1
C9orf3
FGD3
FAM122A
GRIN3A
TMC1
C9orf41
C9orf57
C9orf85
C9orf135
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
TRPM6
NXNL2
RASEF
FAM120AOS
TSTD2
ZNF782
PRUNE2
TMEM252
ZNF367
ANKS6
SUSD3
CBWD5
MAMDC2
FRMD3
C9orf47
SPATA31E1
OR13C9
OR13D1
FOXD4L3
MURC
FOXD4L4
PTAR1
ERCC6L2
SPATA31A6
SPATA31D1
C9orf153
CTSL3P
OR13C2
FAM74A4
C9orf170
MIRLET7A1
MIRLET7D
MIRLET7F1
ANKRD20A3
ANKRD20A2
NUTM2G
FOXB2
C9orf129
FAM27A
SPATA31A2
SPATA31A4
CBWD6
SPATA31A1
FOXD4L6
FOXD4L5
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR3074
MIR4291
MIR4290
MIR4289
CCDC180
MIR4477A
MIR4670

Genes in Wide Peak

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

Table S92. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DNMT3A
MYCN
NCOA1
KCNK3
RN7SL856P
EFR3B
SNORD14
PTRHD1
RNA5SP88
SCARNA21\|ENSG00000251805.1
PFN4
RN7SL610P
UBXN2A
RN7SKP27
RNA5SP87
RN7SL117P
TDRD15
GDF7
RNA5SP86
RN7SL140P
LINC00954
SNORA40\|ENSG00000212455.1
RN7SKP168
SNORA40\|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13\|ENSG00000238371.1
LINC00276
MIR3125
SNORD18\|ENSG00000238503.1
MIR548S
RN7SL674P
RNA5SP85
RNA5SP84
LINC00570
RN7SL832P
SNORA80B
SNORA51\|ENSG00000206898.1
RN7SL66P
SNORA2\|ENSG00000206647.1
SNORA26\|ENSG00000212558.1
snoU13\|ENSG00000238462.1
IAH1
snoU13\|ENSG00000238888.1
MBOAT2
RNU6ATAC37P
RN7SKP112
FLJ30594
SNORA31\|ENSG00000252238.1
RN7SL531P
DCDC2C
SNORA73\|ENSG00000252531.1
snoU13\|ENSG00000238722.1
TMEM18
FAM110C
ACP1
ADCY3
APOB
RHOB
CENPA
DDX1
DTNB
E2F6
FKBP1B
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNS3
KIF3C
MATN3
ODC1
POMC
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
GREB1
LAPTM4A
RNF144A
PDIA6
RAB10
YWHAQ
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
ITSN2
TRAPPC12
DNAJC27
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
SLC35F6
ASXL2
ADI1
ALLC
DPYSL5
KIDINS220
WDR35
RDH14
C2orf43
HS1BP3
COLEC11
CENPO
SMC6
NOL10
C2orf44
FAM49A
EPT1
RSAD2
DRC1
NT5C1B
KLHL29
CMPK2
CIB4
OSR1
TTC32
C2orf50
PQLC3
GAREML
FAM84A
GPR113
CYS1
ATP6V1C2
RNASEH1
FAM150B
C2orf70
LINC00299
MSGN1
GEN1
C2orf48
FAM228B
MFSD2B
LINC00487
FAM228A
RAD51AP2
MIR1301
MIR4261
MIR4262
MIR3681
MIR4757
MIR4429

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q11.

Table S93. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LINC00362
RNY3P4
LINC00621
SNORD36\|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13\|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27\|ENSG00000252128.1
snoU13\|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13\|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
FGF9
GJA3
GJB2
SGCG
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
XPO4
MRP63
TPTE2
N6AMT2
SKA3
MICU2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.22.

Table S94. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL371P
AUTS2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 29 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	0.10	0.376	0.795	0.05	-3.16	1
1q	1195	0.35	19.7	0	0.06	-2.56	1
2p	624	0.18	4.44	2.26e-05	0.03	-5.69	1
2q	967	0.15	3.58	0.000765	0.04	-4.69	1
3p	644	0.10	-1.1	1	0.11	-0.59	1
3q	733	0.16	3.15	0.00327	0.08	-1.98	1
4p	289	0.03	-6.16	1	0.20	5.31	2.02e-07
4q	670	0.02	-6.24	1	0.20	6.12	3.16e-09
5p	183	0.10	-2.2	1	0.12	-0.534	1
5q	905	0.04	-4.82	1	0.15	3.11	0.00288
6p	710	0.15	2.75	0.0108	0.04	-4.68	1
6q	556	0.12	0.386	0.795	0.05	-4.25	1
7p	389	0.13	0.365	0.795	0.10	-1.47	1
7q	783	0.13	1.52	0.215	0.09	-1.33	1
8p	338	0.23	6.73	5.57e-11	0.22	6.02	4.98e-09
8q	551	0.31	13.2	0	0.07	-2.7	1
9p	301	0.04	-5.54	1	0.21	5.69	2.77e-08
9q	700	0.02	-6.17	1	0.23	8.8	0
10p	253	0.23	6.8	4.19e-11	0.11	-1.06	1
10q	738	0.21	7.26	1.97e-12	0.10	-0.79	1
11p	509	0.05	-4.88	1	0.15	2.09	0.0455
11q	975	0.04	-4.45	1	0.14	2.63	0.0121
12p	339	0.14	0.898	0.527	0.10	-1.77	1
12q	904	0.10	-0.139	1	0.08	-1.99	1
13q	560	0.07	-3.28	1	0.18	4.6	7.19e-06
14q	938	0.08	-1.94	1	0.12	1.24	0.246
15q	810	0.02	-5.69	1	0.21	7.32	1.25e-12
16p	559	0.06	-3.94	1	0.19	5.31	2.02e-07
16q	455	0.02	-5.89	1	0.26	9.9	0
17p	415	0.02	-6.01	1	0.25	8.96	0
17q	972	0.07	-2.65	1	0.18	6	4.98e-09
18p	104	0.13	-0.393	1	0.13	0.0768	0.894
18q	275	0.08	-2.95	1	0.14	1.14	0.266
19p	681	0.11	-0.558	1	0.13	1.09	0.274
19q	935	0.11	0.561	0.767	0.12	1.22	0.246
20p	234	0.21	5.41	1.79e-07	0.06	-4.51	1
20q	448	0.25	8.83	0	0.03	-5.83	1
21q	258	0.08	-3.1	1	0.11	-1.29	1
22q	564	0.07	-2.9	1	0.21	6.84	3.25e-11
Xq	668	0.13	1.45	0.225	0.15	2.59	0.0128

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/UCEC-TP/11449785/GDAC_MergeDataFiles_10784950/UCEC-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 539 Input Tumor Samples.

Tumor Sample Names
TCGA-2E-A9G8-01A-11D-A402-01
TCGA-4E-A92E-01A-11D-A37M-01
TCGA-5B-A90C-01A-11D-A37M-01
TCGA-5S-A9Q8-01A-11D-A402-01
TCGA-A5-A0G1-01A-11D-A120-01
TCGA-A5-A0G2-01A-11D-A042-01
TCGA-A5-A0G5-01A-11D-A042-01
TCGA-A5-A0G9-01A-11D-A042-01
TCGA-A5-A0GA-01A-11D-A042-01
TCGA-A5-A0GB-01A-11D-A042-01

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:

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

References

[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)

[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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