SNP6 Copy number analysis (GISTIC2)

Lung Adenocarcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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 (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1PR7V70

Overview

Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.22 (Firehose task version: 140).

Summary

There were 516 tumor samples used in this analysis: 26 significant arm-level results, 21 significant focal amplifications, and 47 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 - 21 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
14q13.3	2.5785e-58	2.5785e-58	chr14:36648432-36782887	2
1q21.3	6.2106e-25	6.5292e-25	chr1:150570986-151056062	17
5p15.33	2.0201e-23	2.0201e-23	chr5:1288616-1314315	2
8q24.21	2.7147e-22	2.7147e-22	chr8:128708285-128858688	2
20q13.33	3.8777e-13	3.8777e-13	chr20:62160482-63025520	32
12p12.1	3.247e-10	3.9557e-10	chr12:25233858-25401622	4
12q15	4.3858e-15	1.0916e-08	chr12:69212011-69244387	2
19q12	1.2289e-08	1.2289e-08	chr19:30022749-30607983	6
Xq28	1.6917e-07	1.6917e-07	chrX:153681678-153778091	9
12q14.1	1.0511e-11	1.5359e-06	chr12:58133257-58208652	9
7p11.2	3.9555e-06	3.9555e-06	chr7:54773427-55737616	5
11q13.3	1.2136e-05	1.2136e-05	chr11:68745684-69806269	10
3q26.2	1.2969e-05	1.2969e-05	chr3:168654235-171019788	21
8p11.21	3.3856e-05	3.3856e-05	chr8:41418239-42345619	14
17q23.1	7.4957e-05	0.00030723	chr17:57921224-57958614	1
7q31.2	0.00087213	0.00087213	chr7:116283302-116609814	4
17q12	0.0046241	0.018709	chr17:37804811-37917511	8
6p21.1	0.01921	0.01921	chr6:41630784-42127221	13
1p22.3	0.052589	0.055155	chr1:85979933-86006008	1
22q11.22	0.08739	0.08739	chr22:22100719-23816427	32
18q11.2	0.17983	0.17983	chr18:19442767-22804243	26

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.3.

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

Genes
RN7SKP21
MBIP

Genes in Wide Peak

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

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

Genes
ARNT
MLLT11
SNORA40\|ENSG00000253047.1
CTSK
CTSS
ENSA
ANXA9
SETDB1
CERS2
C1orf56
GOLPH3L
FAM63A
CDC42SE1
PRUNE
HORMAD1
GABPB2
BNIPL

Genes in Wide Peak

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

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

Genes
TERT
MIR4457

Genes in Wide Peak

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

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

Genes
MYC
PVT1

Genes in Wide Peak

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

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

Genes
NPBWR2
MIR647
MIR1914
C20ORF135
SLC2A4RG
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
PCMTD2
ZNF512B
C20orf195
DNAJC5
ZGPAT
HELZ2
ZBTB46
SAMD10
ABHD16B
C20orf201
LINC00176

Genes in Wide Peak

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

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

Genes
KRAS
LRMP
CASC1
LYRM5

Genes in Wide Peak

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

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

Genes
MDM2
CPM

Genes in Wide Peak

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

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

Genes
C19orf12
POP4
CCNE1
URI1
PLEKHF1
VSTM2B

Genes in Wide Peak

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

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

Genes
RN7SL742P
RN7SL697P
LAGE3
G6PD
UBL4A
SLC10A3
IKBKG
PLXNA3
FAM3A

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
TSFM
AVIL
METTL21B
MARCH9
AGAP2

Genes in Wide Peak

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

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

Genes
EGFR
SNORA73\|ENSG00000252054.1
SEC61G
LANCL2
VOPP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CCND1
FGF3
MIR3164
TPCN2
FGF4
FGF19
MYEOV
MRGPRD
MRGPRF
ORAOV1

Genes in Wide Peak

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

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

Genes
MIR569
RNY5P3
CLDN11
TERC
MECOM
PRKCI
SKIL
SLC2A2
SEC62
TNIK
GPR160
MYNN
EIF5A2
SLC7A14
LRRC31
PHC3
ACTRT3
LRRC34
RPL22L1
LRRIQ4
SAMD7

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238714.1
SNORD112\|ENSG00000238966.1
RN7SL149P
MIR486
ANK1
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
AP3M2
DKK4
AGPAT6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
TUBD1

Genes in Wide Peak

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

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

Genes
MET
RNA5SP239
CAPZA2
ST7

Genes in Wide Peak

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

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

Genes
ERBB2
MIR4728
PNMT
TCAP
GRB7
STARD3
MIEN1
PGAP3

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

Table S19. 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 22q11.22.

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

Genes
BCR
ZDHHC8P1
CES5AP1
RN7SL263P
IGLC7
IGLJ7
IGLJ6
IGLJ5
IGLJ4
IGLC3
IGLJ3
IGLC2
IGLJ2
IGLC1
IGLJ1
GGTLC2
POM121L1P
snoU13\|ENSG00000239066.1
PRAMEF24P
RNA5SP493
GNAZ
MAPK1
VPREB1
TOP3B
RAB36
PPM1F
PRAME
RTDR1
ZNF280A
ZNF280B
MIR650
IGLL5

Genes in Wide Peak

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

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

Genes
ZNF521
RN7SL247P
RNA5SP452
RN7SL745P
snoU13\|ENSG00000238537.1
snoU13\|ENSG00000238907.1
RNU6ATAC20P
RNA5SP451
GATA6
LAMA3
NPC1
RBBP8
RIOK3
CABYR
C18orf8
IMPACT
MIB1
HRH4
CTAGE1
TMEM241
CABLES1
OSBPL1A
TTC39C
ANKRD29
MIR320C2
MIR4741

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 - 47 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
9p21.3	1.6366e-138	5.3358e-117	chr9:21931610-22003135	2
22q13.32	6.4554e-13	6.4554e-13	chr22:47571204-51304566	43
9p23	4.5816e-29	1.2332e-12	chr9:7887952-12687261	3
1p13.1	1.2332e-12	1.4801e-11	chr1:98382483-149881397	266
4q34.3	3.3912e-11	3.4272e-11	chr4:177091953-191154276	75
16q23.1	1.894e-10	1.894e-10	chr16:78098006-79299841	3
18q21.32	8.9504e-10	8.9504e-10	chr18:57363452-58038871	2
21q11.2	3.8991e-07	3.8991e-07	chr21:1-16335988	17
8p23.2	1.4117e-06	1.4534e-06	chr8:1897569-6268239	8
15q11.2	3.289e-13	1.6268e-06	chr15:23931399-24924361	2
13q12.11	5.1627e-16	2.7625e-06	chr13:1-20714074	16
5q12.1	1.0664e-06	9.6117e-06	chr5:58151172-59818245	3
12p13.2	8.7223e-06	1.8132e-05	chr12:7480129-18235892	140
9q21.11	5.5411e-10	3.4902e-05	chr9:38619152-71152237	57
19q13.33	3.0398e-05	4.7396e-05	chr19:48386801-48533611	2
6q26	6.5149e-06	6.5539e-05	chr6:161693099-163153207	1
13q34	2.7857e-07	8.305e-05	chr13:114202593-114304134	1
10p15.3	0.00012523	0.00012643	chr10:1-3818193	19
17p13.3	0.00014416	0.00014352	chr17:1-3301779	67
Xp22.2	0.00028487	0.00029467	chrX:9101277-11137490	7
11p15.5	0.00046092	0.00046092	chr11:1-3632258	94
14q32.12	0.00046363	0.00046092	chr14:93695207-107349540	233
15q15.1	7.4811e-11	0.001135	chr15:34148119-47478056	167
10q26.3	0.0013092	0.0012779	chr10:135190263-135534747	6
2q22.1	0.001446	0.001446	chr2:140708948-143637838	2
19p13.3	3.0369e-08	0.001446	chr19:1-437820	7
11q23.2	5.9172e-07	0.0023096	chr11:103318441-133308731	291
19p13.2	2.3171e-06	0.0036008	chr19:11040707-11207540	2
11q25	9.5488e-08	0.005887	chr11:126871640-135006516	37
12q24.33	0.0084008	0.010033	chr12:75905166-133851895	470
3q29	0.016759	0.020443	chr3:179877596-198022430	179
5q31.1	0.0019331	0.022916	chr5:66492413-180915260	816
8p11.21	0.023869	0.027976	chr8:42883855-47750537	6
6q22.31	0.00018882	0.042132	chr6:123955968-125285408	1
3p21.31	0.0014452	0.051357	chr3:45186721-53529383	218
4p16.3	0.060192	0.06183	chr4:1-14496314	152
1p36.11	0.018332	0.072442	chr1:1-35411600	573
12q12	0.01918	0.08089	chr12:33514047-39688977	7
20p13	0.10601	0.10619	chr20:1-16252980	144
13q12.13	3.8817e-09	0.12291	chr13:1-27133661	79
3q11.1	0.019886	0.13147	chr3:73667918-96336217	39
3p26.2	0.02366	0.15997	chr3:1-28286260	167
13q14.2	8.7238e-07	0.1901	chr13:40171063-88080975	228
6q11.1	0.027544	0.22616	chr6:44217668-117076132	338
19p13.2	6.5539e-05	0.24105	chr19:7536146-7569727	1
20q13.12	0.24225	0.24105	chr20:35496589-50563478	190
19q11	0.030298	0.24858	chr19:23553827-29422400	7

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

Table S23. 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
LINC00898
IL17REL
PIM3
ODF3B
SYCE3
MIR3201
MIR3667
MIR4535

Genes in Wide Peak

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

Table S24. 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 1p13.1.

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
LINC00622
snoU13\|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40\|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3\|ENSG00000221040.1
SNORA42\|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13\|ENSG00000238975.1
WNT2B
snoU13\|ENSG00000238761.1
snoU13\|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25\|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13\|ENSG00000238296.1
SCARNA16\|ENSG00000252765.1
DPH5
MIR553
LPPR5
ADORA3
AGL
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
COL11A1
CSF1
DBT
S1PR1
CELSR2
EXTL2
FCGR1A
FMO5
GJA5
GJA8
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TBX15
TSHB
VCAM1
CSDE1
HIST2H2AC
HIST2H2BE
HIST2H4A
ITGA10
CDC14A
RTCA
PEX11B
SLC16A4
CD101
CHD1L
LPPR4
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
LAMTOR5
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
ADAM30
CD160
DDX20
NTNG1
WDR47
CLCC1
SLC35A3
NBPF14
PTPN22
PHGDH
CHIA
GPSM2
SLC25A24
BOLA1
HAO2
SNX7
GPR89B
GPR88
TRMT13
RSBN1
GDAP2
FAM46C
PALMD
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
OLFML3
AMIGO1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
STRIP1
ZNF697
HENMT1
OLFM3
MAB21L3
ATXN7L2
C1orf194
LRRC39
LIX1L
DRAM2
PIFO
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
SLC30A7
NBPF12
CHIAP2
FNDC7
SASS6
PPIAL4A
UBL4B
NBPF11
SPAG17
HIPK1
AKNAD1
MAGI3
FAM19A3
NBPF16
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
MYBPHL
SLC6A17
C1orf137
NOTCH2NL
FRRS1
NBPF9
MIR197
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
NBPF6
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
NBPF20
MIR320B1
MIR137HG

Genes in Wide Peak

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

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31\|ENSG00000253013.1
TLR3
snoU13\|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13\|ENSG00000239116.1
snoU13\|ENSG00000238596.1
snoU13\|ENSG00000238319.1
U3\|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173
snoU13\|ENSG00000252388.1
RNA5SP172
RN7SKP136
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
ING2
IRF2
KLKB1
MTNR1A
VEGFC
SORBS2
FAM149A
CLDN22
NEIL3
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
WWC2
SNX25
ZFP42
SPATA4
ENPP6
ASB5
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 16q23.1.

Table S27. 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 18q21.32.

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

Genes
RN7SL342P
PMAIP1

Genes in Wide Peak

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

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

Genes
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70\|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
HSPA13
TPTE
RBM11
SAMSN1
LIPI
ABCC13
POTED
MIR3687

Genes in Wide Peak

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

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

Genes
RN7SKP159
RN7SL318P
SNORA70\|ENSG00000206661.1
RN7SL872P
RNA5SP251
MYOM2
KBTBD11
CSMD1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

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

Genes
PWRN1
PWRN2

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
ZMYM2
ZMYM5
MPHOSPH8
TPTE2

Genes in Wide Peak

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

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

Genes
FKSG52
MIR582
PDE4D

Genes in Wide Peak

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

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

Genes
ETV6
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75\|ENSG00000212432.1
SNORA75\|ENSG00000212440.1
LINC00987
A2MP1
LINC00612
SCARNA11\|ENSG00000252727.1
FAM86FP
FAM66C
NANOGP1
A2M
APOBEC1
ARHGDIB
C3AR1
CD69
CDKN1B
CREBL2
PHC1
EMP1
EPS8
GPR19
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PTPRO
PZP
SLC2A3
MFAP5
KLRC4
YBX3
CD163
GDF3
KLRG1
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
NECAP1
CLEC4E
TAS2R9
TAS2R7
TAS2R13
TAS2R10
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
MANSC1
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
LMO3
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
NANOG
APOLD1
GSG1
RERG
CLEC6A
LOH12CR1
TMEM52B
HIST4H4
SLC2A14
A2ML1
CLEC12A
CLECL1
CLEC4C
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CD163L1
CLEC9A
C12orf36
CLEC4D
TAS2R42
DPPA3
NANOGNB
CLEC2A
CLEC12B
LINC00937
ZNF705A
SMCO3
PRB2
MIR614
SLC15A5

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
ELSPBP1
BSPH1

Genes in Wide Peak

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

Table S37. 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 13q34.

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

Genes
TFDP1

Genes in Wide Peak

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

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

Genes
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
IDI1
PFKP
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
IDI2
LINC00200
PRR26

Genes in Wide Peak

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

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

Genes
OR1E1
OR1D4
RN7SL605P
MIR1253
RN7SL608P
snoU13\|ENSG00000239024.1
RN7SL33P
SNORD91A
SNORD91B
RN7SL624P
TLCD2
snoU13\|ENSG00000238946.1
RN7SL105P
BHLHA9
MIR3183
TIMM22
DBIL5P
DOC2B
ABR
CRK
DPH1
HIC1
MNT
MYO1C
OR1D2
OR3A1
OR3A2
PAFAH1B1
SERPINF1
PITPNA
SERPINF2
RPA1
YWHAE
OR1A1
OR1D5
OR1G1
SCARF1
RPH3AL
SGSM2
PRPF8
RAP1GAP2
CLUH
SMG6
OR1A2
GEMIN4
GLOD4
INPP5K
RNMTL1
VPS53
TSR1
SRR
NXN
METTL16
FAM57A
RILP
SMYD4
OVCA2
SLC43A2
WDR81
RTN4RL1
TUSC5
FAM101B
OR3A4P
C17orf97
MIR132
MIR212
MIR22HG

Genes in Wide Peak

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

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

Genes
RNA5SP499
SHROOM2
CLCN4
MID1
GPR143
TBL1X
WWC3

Genes in Wide Peak

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

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

Genes
CARS
HRAS
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1\|ENSG00000130592.9
MUC2
MUC6
NAP1L4
SLC22A18
POLR2L
PSMD13
RNH1
MRPL23
TALDO1
TH
TSPAN4
TNNI2
TNNT3
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
TRPM5
BET1L
CEND1
CDHR5
TOLLIP
PIDD
KCNQ1DN
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
SYT8
OSBPL5
LRRC56
MRGPRE
SCGB1C1
NLRP6
C11orf35
EFCAB4A
ANO9
B4GALNT4
PDDC1
MRGPRG
IFITM5
FAM99A
IFITM10
MIR210
MUC5B
MIR4298
MIR4686

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.12.

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

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

Genes in Wide Peak

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

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

Genes
BUB1B
FKSG62
RN7SKP101
SNORD11\|ENSG00000238819.1
SNORA41\|ENSG00000207516.1
HMGN2P46
snoU13\|ENSG00000238583.1
SLC30A4
SNORA11\|ENSG00000261709.2
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13\|ENSG00000238494.1
snoU13\|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13\|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13\|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13\|ENSG00000238564.1
THBS1
FAM98B
U3\|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18\|ENSG00000252425.1
SLC12A6
ACTC1
CAPN3
CHRM5
CKMT1B
EPB42
GANC
GATM
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
SPINT1
SRP14
TP53BP1
TYRO3
EIF3J
SNAP23
SLC28A2
TGM5
PPIP5K1
AQR
LCMT2
RASGRP1
GPR176
CHP1
OIP5
BAHD1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
SERF2
TMEM87A
RPAP1
BLOC1S6
RPUSD2
TUBGCP4
EHD4
DUOX2
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
PPP1R14D
ZNF770
HAUS2
RMDN3
DNAJC17
NOP10
EMC7
PAK6
CASC5
AVEN
STARD9
VPS18
SQRDL
ZNF106
SPATA5L1
CHAC1
KATNBL1
WDR76
TMEM62
SPG11
ELL3
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
NUTM1
PLA2G4D
C15orf52
C15orf53
C15orf54
DUOXA2
GOLGA8B
EIF2AK4
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4510

Genes in Wide Peak

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

Table S45. 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 2q22.1.

Table S46. 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 19p13.3.

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

Genes
OR4F17
FAM138F
WASH5P
PPAP2C
THEG
MIER2
C2CD4C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
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
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11\|ENSG00000252992.1
RNY4P6
ZNF259
snoU13\|ENSG00000238625.1
LINC00900
snoU13\|ENSG00000239153.1
ACA59\|ENSG00000252870.1
snoU13\|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39\|ENSG00000264997.1
RNA5SP349
RNA5SP348
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NCAM1
NFRKB
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
BARX2
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
EXPH5
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
DCPS
ZBTB44
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR4301
CASP12
MIR4493
MIR4491
MIR4492
MIR4693

Genes in Wide Peak

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

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

Genes
SMARCA4
RN7SL192P

Genes in Wide Peak

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

Table S50. 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
APLP2
ETS1
KCNJ1
NFRKB
OPCML
ST14
BARX2
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
PRDM10
TP53AIP1
JAM3
GLB1L2
VPS26B
GLB1L3
TMEM45B
ADAMTS15
C11orf45
SPATA19
C11orf44
SNX19
MIR4697

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
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
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
DGKG
DLG1
DVL3
EHHADH
EIF4G1
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
MFI2
MUC4
OPA1
PAK2
PCYT1A
POLR2H
PPP1R2
MASP1
PSMD2
RFC4
RPL35A
ST6GAL1
SST
THPO
FXR1
TP63
CHRD
EIF2B5
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
IGF2BP2
CLDN16
NCBP2
MCF2L2
ATP11B
VPS8
ACAP2
FETUB
LAMP3
DNAJB11
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
YEATS2
MCCC1
HRASLS
MAGEF1
ATP13A3
MAP6D1
PIGZ
B3GNT5
IQCG
ATP13A4
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
MB21D2
XXYLT1
CCDC50
PYDC2
RNF168
HTR3C
LIPH
HTR3D
SLC51A
FBXO45
MUC20
SENP5
TCTEX1D2
SMCO1
UTS2B
HTR3E
C3orf70
TPRG1
CCDC39
RTP2
OSTN
ATP13A5
WDR53
ANKRD18DP
NRROS
LINC00885
C3orf65
GMNC
MIR570
MIR922
MIR4448

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q31.1.

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

Genes
APC
CD74
EBF1
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
TRIM52
SNORD95\|ENSG00000264549.1
SNORD96A
LINC00847
MIR340
RN7SKP150
MIR1229
HMGB3P22
RN7SL71P
ZNF879
ZNF354B
AACSP1
RN7SKP70
RN7SL646P
RN7SL562P
EIF4E1B
MIR4281
RN7SL684P
MIR1271
ARL10
RN7SKP148
snoU13\|ENSG00000239026.1
NSG2
RNA5SP200
SNORA74B
ATP6V0E1
MIR5003
SNORA57\|ENSG00000212529.1
C5orf50
SNORA70\|ENSG00000206909.1
RN7SL339P
snoU13\|ENSG00000252387.1
RN7SL623P
MIR4454
KCNMB1
LCP2
C5orf58
MIR378E
MIR585
MIR103A1
PANK3
FBLL1
SNORA40\|ENSG00000253065.1
RN7SKP60
NUDCD2
MIR3142
RN7SL295P
ADRA1B
RNU4ATAC2P
SNORA68\|ENSG00000252458.1
LSM11
THG1L
RNA5SP199
RN7SL439P
RN7SL655P
MIR1294
RN7SL177P
RNA5SP198
RN7SKP232
RNA5SP197
ZNF300P1
snoU13\|ENSG00000239191.1
snoU13\|ENSG00000238369.1
MIR378A
RN7SL868P
U3\|ENSG00000221043.1
MIR143HG
RN7SKP145
MIR584
SH3TC2
SPINK13
RN7SL791P
RNA5SP196
GPR151
RN7SKP246
KCTD16
RN7SL87P
RN7SL68P
PCDHGB8P
PCDHB18
PCDHB17
PCDHA14
WDR55
MIR3655
SNORA27\|ENSG00000200235.1
SNORD45\|ENSG00000200051.1
CYSTM1
PURA
TMEM173
ECSCR
RN7SKP64
RNA5SP195
SNORA74A
SNORA74\|ENSG00000252213.1
RNA5SP194
RN7SL867P
snoU13\|ENSG00000238745.1
SNORD63\|ENSG00000206989.1
SNORD63\|ENSG00000222937.1
RN7SL682P
snoU13\|ENSG00000238605.1
NPY6R
MIR874
RNA5SP193
FBXL21
TIFAB
MIR4461
MIR4461
PCBD2
RN7SL541P
PPP2CA
SKP1
snoU13\|ENSG00000238796.1
HSPA4
LEAP2
UQCRQ
RNA5SP192
snoZ6\|ENSG00000253067.1
HINT1
RNA5SP191
RNU6ATAC10P
KIAA1024L
MIR4633
C5orf63
RN7SKP117
RN7SL711P
RN7SL689P
snoU13\|ENSG00000239103.1
snoU13\|ENSG00000252295.1
snoU13\|ENSG00000239067.1
snoU13\|ENSG00000239084.1
RNA5SP190
RN7SL174P
TNFAIP8
MIR5706
snoU13\|ENSG00000239011.1
DTWD2
ARL14EPL
AP3S1
RN7SKP89
RNU4ATAC13P
ZRSR1
SRP19
FLJ11235
SNORA13
RN7SKP57
CAMK4
SNORA51\|ENSG00000207177.1
MIR548F3
TMEM232
RN7SKP230
FER
RN7SKP122
RN7SL782P
SNORA31\|ENSG00000252337.1
RNA5SP189
RN7SL255P
LINC00491
LINC00492
RN7SKP68
RNA5SP188
RN7SL802P
MIR548P
RN7SKP62
GPR150
LUCAT1
SNORA70\|ENSG00000206958.1
RNA5SP187
RN7SL629P
RN7SKP34
MIR3607
COX7C
NBPF22P
RN7SKP295
SCARNA18\|ENSG00000238835.1
RN7SL378P
SSBP2
SNORA31\|ENSG00000251828.1
snoU13\|ENSG00000239159.1
MTX3
HOMER1
SNORA18\|ENSG00000206592.1
RNY3P1
BHMT2
OTP
WDR41
SNORA47
ZBED3
RNU6ATAC36P
S100Z
RN7SL208P
snoU13\|ENSG00000238688.1
RNA5SP186
POLK
SNORA40\|ENSG00000212363.1
RN7SL814P
MIR4804
RN7SL153P
MIR4803
snoU13\|ENSG00000238451.1
GTF2H2B
RN7SL9P
snoU13\|ENSG00000238740.1
GUSBP3
RN7SL616P
RN7SL476P
snoU13\|ENSG00000238334.1
SNORA50\|ENSG00000220986.1
RN7SL103P
7SK\|ENSG00000249352.3
U8\|ENSG00000212249.2
ADRB2
ANXA6
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
CLTB
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
HARS
HEXB
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNN2
TNPO1
LECT2
LMNB1
LNPEP
LOX
LTC4S
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MFAP3
MGAT1
MSH3
MSX2
NAIP
NDUFA2
NEUROG1
PAM
PCDH1
PCDHGC3
PCSK1
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2R2B
MAPK9
PROP1
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATG12
PTTG1
PDLIM7
NREP
CNOT8
HAND1
MED7
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
APBB3
TNIP1
GNB2L1
NSA2
SLU7
POLR3G
RGS14
IQGAP2
SEC24A
CPLX2
FAXDC2
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
KLHL3
TSPAN17
OR4F3
OR2V1
HAVCR1
CYFIP2
PKD2L2
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FAM193B
TMED9
ZCCHC10
CDHR2
GIN1
SPDL1
AGGF1
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
BDP1
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
TENM2
CNOT6
ZNF608
SEMA6A
ARRDC3
PCDHB16
ANKRA2
HMHB1
C5orf54
MCCC2
EPB41L4A
ERAP2
ARHGEF28
SIL1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
PCYOX1L
CCNJL
SAP30L
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
PSD2
ANKRD32
THOC3
GFM2
MEGF10
SPINK7
SPZ1
HAVCR2
PHYKPL
SMIM3
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
MARCH3
FCHO2
LYSMD3
SCGB3A2
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
POC5
STARD4
WDR36
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
CREBRF
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
PAPD4
DCP2
LIX1
ZNF366
FAM151B
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
CCDC125
C5orf27
CMYA5
STK32A
AQPEP
SLC36A1
RASGEF1C
ANKRD31
SERINC5
EFCAB9
SH3PXD2B
FAM153A
KIAA0825
RELL2
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
RGMB
RFESD
CHSY3
FAM170A
ARSI
ANKRD34B
PFN3
IRGM
FAM174A
CATSPER3
NIPAL4
SLCO4C1
DND1
SIMC1
C5orf48
PROB1
C5orf46
ARHGEF37
SPINK6
ANKHD1
MIR143
MIR145
MIR146A
LINC00461
SPINK14
FNDC9
C5orf56
IGIP
CTXN3
GRXCR2
SPINK9
ZFP62
CCNI2
CBY3
FAM153C
MIR583
GTF2H2C
SERF1B
ANKDD1B
FAM196B
C5orf52
MIR1303
TICAM2
MIR2277
MIR4280
MIR3141
MTRNR2L2
MIR3660
MIR3912
MIR3936
MIR3661
OCLN
MIR4634
MIR378H
MIR4460
MIR4638
MIR5197
MIR5692C1

Genes in Wide Peak

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

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

Genes
RN7SKP41
U3\|ENSG00000201329.1
POTEA
FNTA
SGK196
HGSNAT

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q22.31.

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

Genes
NKAIN2

Genes in Wide Peak

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

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

Genes
BAP1
SETD2
PBRM1
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
ALAS1
AMT
APEH
RHOA
SLC25A20
CAMP
CDC25A
CISH
CCR1
CCR3
CCR5
COL7A1
DAG1
DOCK3
DUSP7
CELSR3
GNAI2
XCR1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
LTF
MAP4
MST1
MST1R
MYL3
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TKT
TNNC1
UBA7
USP4
UQCRC1
IFRD2
MAPKAPK3
MANF
HYAL3
HYAL2
BSN
ACKR5
RRP9
CACNA2D2
IP6K1
PARP3
RBM6
RBM5
NME6
TRAIP
ARIH2
NPRL2
CXCR6
CCR9
USP19
CYB561D2
TMEM115
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SACM1L
SCAP
RAD54L2
STAB1
NBEAL2
KLHL18
LARS2
NAT6
ABHD14A
POC1A
TMEM158
PTPN23
DNAH1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
C3orf18
SHISA5
ZMYND10
TEX264
TMA7
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
ELP6
QRICH1
DALRD3
DCP1A
GLT8D1
SEMA3G
PCBP4
RNF123
KIF9
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
WDR82
ATRIP
NICN1
MON1A
ABHD14B
UCN2
RFT1
GPR62
IQCF1
GLYCTK
PPM1M
LSMEM2
CCDC12
KLHDC8B
ALS2CL
TMIE
FBXW12
CCDC36
PRSS42
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 4p16.3.

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

Genes
FGFR3
WHSC1
HSP90AB2P
RNA5SP156
HS3ST1
CLNK
RNA5SP155
MIR3138
RNA5SP154
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48\|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
SH3BP2
WFS1
NELFA
SLBP
ACOX3
CPZ
NOP14
FAM193A
RAB28
KIAA0232
WDR1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
NSG1
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
BLOC1S4
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
UVSSA
ZFYVE28
AFAP1
TNIP2
HAUS3
MFSD7
TMEM175
ABLIM2
TMEM128
ZNF518B
TMEM129
MRFAP1
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
JAKMIP1
FAM53A
TRMT44
ZBTB49
CCDC96
BOD1L1
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
DEFB131
MIR572
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
USP17L30
PSAPL1
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR548I2
MIR378D1
MIR4800
MIR5091

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
LCK
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
SNORD112\|ENSG00000252728.1
SMIM12
RNA5SP42
RN7SKP16
MIR3605
FKSG48
ZBTB8OS
ZBTB8B
RN7SL122P
MTMR9LP
MIR5585
MIR4254
FABP3
SNORD85
SNORD103B
SNORD103A
SDC3
RN7SKP91
MIR4420
SCARNA24\|ENSG00000252777.1
RNU11
RAB42
SNORD99
SNHG12
snoU13\|ENSG00000238821.1
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18\|ENSG00000252691.1
SCARNA17\|ENSG00000252190.1
MAN1C1
snoU13\|ENSG00000238889.1
SYF2
snoU13\|ENSG00000238986.1
RN7SL857P
snoU13\|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13\|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13\|ENSG00000239020.1
PADI6
MIR3972
U1\|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1\|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13\|ENSG00000238818.1
DDI2
AGMAT
SCARNA21\|ENSG00000251866.1
C1orf195
SCARNA11\|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13\|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70\|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13\|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16\|ENSG00000252404.1
RN7SL451P
SNORA77\|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13\|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
AK2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
PHC2
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GJA4
GJB3
GJB5
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGCL
HPCA
HSPG2
HTR1D
HTR6
ID3
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RBBP4
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZSCAN20
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
KCNAB2
FCN3
YARS
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
THEMIS2
H6PD
ISG15
PLCH2
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
AHDC1
SMPDL3B
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
TRIM62
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
KIAA1522
HES4
GRHL3
DLGAP3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
S100PBP
CEP85
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
AUNIP
CCDC28B
EFHD2
MMEL1
RSG1
NKAIN1
MUL1
NOL9
LIN28A
LINC00115
MORN1
FAM110D
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
SYNC
ACTL8
TSSK3
CCNL2
SESN2
ESPN
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
FAM167B
C1orf170
SYTL1
IGSF21
C1orf94
KIAA2013
THAP3
STPG1
SPOCD1
UBXN11
FBXO44
ATPIF1
ADC
TMEM54
CSMD2
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
GJB4
HMGB4
RNF19B
A3GALT2
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
DCDC2B
ZNF362
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
ATAD3C
AKR7L
FNDC5
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
ZBTB8A
PRAMEF22
PRAMEF15
PRAMEF16
MIR552
CDK11A
SLC35E2B
C1orf234
OR4F29
FAM229A
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

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

Table S59. 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 20p13.

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

Genes
RNA5SP475
RN7SL864P
RN7SKP111
LINC00687
C20orf187
JAG1
RNU105B
TMX4
RN7SL547P
snoR26
RN7SL498P
LINC00654
LINC00658
SNORA26\|ENSG00000212517.1
RNA5SP474
RN7SL514P
snoU13\|ENSG00000252058.1
SNORA31\|ENSG00000252096.1
MIR103A2
MAVS
U3\|ENSG00000201346.1
RN7SL839P
RN7SL555P
TMEM239
SNORD57
SNORD56\|ENSG00000229686.1
SNORD86
SNORA51\|ENSG00000271798.1
SNORD110
MIR1292
SNORD119
RN7SL561P
TCF15
CSNK2A1
DEFB128
DEFB127
DEFB126
DEFB125
ADRA1D
JAG1
AVP
BMP2
CDC25B
CENPB
CHGB
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PCNA
PDYN
PLCB4
PRNP
PTPRA
SIGLEC1
SNAP25
SNRPB
SOX12
TGM3
MKKS
ATRN
CDS2
PSMF1
SNPH
LZTS3
RASSF2
SLC23A2
SIRPB1
NOP56
RBCK1
RNF24
UBOX5
BTBD3
PLCB1
PRND
FLRT3
LAMP5
SPEF1
C20orf194
SDCBP2
TMEM230
ANGPT4
ESF1
TRMT6
HAO1
SMOX
CRLS1
C20orf27
SPTLC3
AP5S1
TMEM74B
SIRPG
FERMT1
TASP1
NSFL1C
GPCPD1
CPXM1
PAK7
EBF4
TRIB3
FASTKD5
ANKEF1
GFRA4
VPS16
PCED1A
MRPS26
DDRGK1
NDUFAF5
ZNF343
NRSN2
PANK2
ADAM33
SEL1L2
FAM110A
SLC4A11
MCM8
ZCCHC3
SCRT2
SLC52A3
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
PROKR2
SLX4IP
C20orf96
MACROD2
SRXN1
ISM1
DEFB129
SIRPA
STK35
PRNT
C20orf196
LRRN4
SIRPB2
RSPO4
TGM6
DEFB132
C20orf202
RAD21L1
TMEM239

Genes in Wide Peak

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

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

Genes
LINC00415
RNY1P3
RN7SL741P
RN7SL289P
PABPC3
LSP1\|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
MIR2276
ANKRD20A19P
LINC00352
LINC00327
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
PARP4
ATP12A
CDK8
FGF9
GJA3
GJB2
MIPEP
RNF6
SGCG
ZMYM2
IFT88
MTMR6
ZMYM5
NUPL1
SAP18
GJB6
SACS
LATS2
CRYL1
ATP8A2
IL17D
MPHOSPH8
TNFRSF19
CENPJ
RNF17
XPO4
MRP63
TPTE2
AMER2
N6AMT2
SKA3
MICU2
SPATA13
C1QTNF9
C1QTNF9B
SHISA2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.1.

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

Genes
MTHFD2P1
LINC00879
NSUN3
U3\|ENSG00000212598.1
HTR1F
RNU6ATAC6P
RN7SKP284
snoZ40
MIR5688
LINC00971
RN7SL751P
RN7SKP61
RN7SL647P
RN7SL92P
ZNF717
LINC00960
FAM86DP
RN7SL294P
EPHA3
GBE1
CNTN3
POU1F1
PROS1
ROBO1
ROBO2
CGGBP1
CHMP2B
ZNF654
ARL13B
DHFRL1
CADM2
C3orf38
VGLL3
STX19
FRG2C
MIR1324
MIR4273
MIR3923
MIR4795

Genes in Wide Peak

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

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

Genes
VHL
FANCD2
PPARG
RAF1
XPC
SRGAP3
RN7SL859P
SNORD5\|ENSG00000272166.1
RNA5SP126
RNA5SP125
RN7SL216P
LINC00691
UBE2E2
HMGB1P5
RNY4P22
MIR3135A
U7\|ENSG00000271841.1
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13\|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13\|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13\|ENSG00000238345.1
snoU13\|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43\|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13\|ENSG00000239126.1
EGOT
SNORA43\|ENSG00000253049.1
RN7SKP144
RN7SL120P
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RARB
RPL15
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
THRB
TIMP4
TOP2B
UBE2E1
BRPF1
COLQ
EOMES
CAMK1
BHLHE40
KAT2B
SH3BP5
SLC4A7
VGLL4
EDEM1
TBC1D5
TATDN2
IQSEC1
NR1D2
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
NKIRAS1
LMCD1
SSUH2
TRNT1
CRBN
CCDC174
GHRL
OXSM
ARL8B
SETD5
TMEM40
NGLY1
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
ZNF385D
HDAC11
TSEN2
C3orf20
JAGN1
IL17RC
EAF1
OXNAD1
FANCD2OS
LRRC3B
GALNT15
KCNH8
CHCHD4
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
NEK10
FGD5
CNTN4
LINC00692
SUMF1
RPUSD3
PRRT3
TPRXL
MIR563
MIR378B
MIR3714
MIR4791
MIR4790
MIR4792
MIR4442

Genes in Wide Peak

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

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

Genes
LCP1
RB1
LINC00351
LINC00333
PTMAP5
LINC00564
RNA5SP33
LINC00331
RNY3P3
LINC00446
RN7SL810P
RNY3P7
CLN5
RN7SL571P
LINC00561
C13orf45
LINC00347
LINC00381
RNY1P5
LINC00402
LINC00392
LINC00393
RNY1P8
SNORA9\|ENSG00000199282.1
SNORA68\|ENSG00000251715.1
SNORD37\|ENSG00000212377.1
RNA5SP32
LINC00348
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13\|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13\|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31\|ENSG00000199477.1
SNORA31\|ENSG00000253051.1
7SK\|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13\|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13\|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116\|ENSG00000212553.1
RNY4P14
ATP7B
KLF5
RCBTB2
CPB2
DACH1
EDNRB
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
LMO7
NEK3
PCDH8
PCDH9
POU4F1
TPT1
UCHL3
TNFSF11
SCEL
SUCLA2
ITM2B
MTRF1
UTP14C
TBC1D4
LPAR6
TRIM13
MRPS31
SPRY2
DLEU1
PIBF1
OLFM4
LECT1
WBP4
AKAP11
KLF12
FNDC3A
DIS3
MYCBP2
VWA8
ZC3H13
LRCH1
FBXL3
INTS6
CKAP2
NUFIP1
PCDH17
RGCC
MED4
DNAJC15
VPS36
PHF11
NDFIP2
ENOX1
RCBTB1
NUDT15
KIAA1704
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
PCDH20
SMIM2
RNF219
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
SLITRK6
EBPL
KBTBD6
EPSTI1
SLITRK1
KCTD12
ARL11
WDFY2
SLAIN1
PRR20A
FAM216B
LACC1
HNRNPA1L2
DGKH
CCDC122
COMMD6
FAM194B
SPERT
FAM124A
LRRC63
SLC25A30
SIAH3
KCNRG
NEK5
KCTD4
SERP2
DLEU2
ALG11
MZT1
SERPINE3
MIR621
PRR20B
PRR20C
PRR20D
PRR20E
IRG1
MIR759
MIR320D1
MIR3168
MIR4305
MIR3169
MIR3665
MIR3613
MIR4704
MIR548X2
MIR4703
MIR5007
MIR5693

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q11.1.

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

Genes
PRDM1
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13\|ENSG00000238563.1
U3\|ENSG00000253091.1
snoU13\|ENSG00000239095.1
snoU13\|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13\|ENSG00000238775.1
SNORA40\|ENSG00000212587.1
RN7SL617P
snoU13\|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13\|ENSG00000238974.1
SNORA73\|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33\|ENSG00000202283.1
snoU13\|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
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
FKBP1C
LINC00680
PRIM2
RAB23
BAG2
FAM83B
RN7SKP256
U3\|ENSG00000251930.1
RN7SL244P
RN7SK
GSTA1
RN7SL580P
SNORD66\|ENSG00000212532.1
DEFB133
GLYATL3
OPN5
RN7SKP116
ANKRD66
MIR586
MIR4642
TCTE1
TMEM151B
CRISP1
AIM1
AMD1
BAI3
BCKDHB
BMP5
DST
RUNX2
CCNC
CDC5L
CGA
CNR1
COL9A1
COL10A1
COL12A1
COX7A2
EEF1A1
EPHA7
FOXO3
FYN
GABRR1
GABRR2
GCLC
GPR6
GRIK2
GSTA2
GSTA3
GSTA4
HCRTR2
HDAC2
HTR1E
IL17A
IMPG1
KPNA5
LAMA4
MARCKS
MCM3
ME1
MEP1A
MUT
MYO6
NFKBIE
NT5E
PGK2
PGM3
PKHD1
POU3F2
PREP
REV3L
RHAG
SIM1
SMPD2
ELOVL4
MAP3K7
TFAP2B
NR2E1
TPBG
CRISP2
TTK
PTP4A1
PLA2G7
SUPT3H
GCM1
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
SLC25A27
TRAM2
ZBTB24
SNAP91
FIG4
RCAN2
CRISP3
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ICK
ENPP4
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
PHF3
ORC3
CD2AP
MTO1
PNISR
IBTK
ZNF451
SENP6
FBXL4
FBXO9
SLC17A5
FILIP1
TNFRSF21
SESN1
TINAG
OSTM1
TMEM14A
NDUFAF4
DSE
TUBE1
C6orf203
CYP39A1
CDC40
RWDD1
UBE2J1
LGSN
COQ3
CLIC5
HMGCLL1
PHIP
SOBP
AKIRIN2
CENPQ
LRRC1
QRSL1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
SMIM8
LYRM2
SNX14
AARS2
HACE1
FAM135A
BEND3
KIAA1586
RRAGD
ENPP5
BACH2
ELOVL5
SMAP1
C6orf164
MICAL1
MANEA
LINC00472
KHDC1
GPR63
COL21A1
SPACA1
SH3BGRL2
TFAP2D
ARMC2
MCHR2
FAXC
GJA10
USP45
PAQR8
SLC22A16
UBE3D
MLIP
GTF3C6
MRAP2
IL17F
EFHC1
KLHL32
SLC16A10
RIPPLY2
IRAK1BP1
CD109
PM20D2
SRSF12
C6orf141
KHDC3L
C6orf165
PRSS35
LCA5
KHDRBS2
C6orf163
AK9
FAM26D
ZUFSP
BEND6
GSTA5
GPR115
GPR116
TDRD6
SPATS1
HS3ST5
GPR111
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
MMS22L
GPR110
CEP57L1
PPIL6
DPPA5
RSPH4A
EYS
SLC35B2
GJB7
GFRAL
LIN28B
KLHL31
MIR206
MIR30A
MIR30C2
TMEM151B
FAM26F
PTCHD4
RFPL4B
MIR133B
FAM229B
MIR587
METTL24
TRAPPC3L
KHDC1L
MIR2113
MIR548U
MIR4282
MTRNR2L9
MIR4464
MIR4647
MIR4643
MIR548AI
MIR4463
MIR5685

Genes in Wide Peak

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

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

Genes
PEX11G

Genes in Wide Peak

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

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

Genes
TOP1
MAFB
RN7SL603P
MIR3194
RN7SL672P
RN7SL636P
LINC00651
snoU13\|ENSG00000239157.1
RN7SL197P
KCNB1
SNORD12
SNORD12B
SNORD12C
ZFAS1
LINC00494
SNORD36\|ENSG00000252227.1
RNA5SP486
RN7SL243P
MIR3616
RN7SKP33
SNX21
RNU6ATAC38P
SPINT4
WFDC10A
RNA5SP485
RBPJL
RN7SL31P
KCNK15
MIR3646
R3HDML
FITM2
RN7SL443P
SCARNA15\|ENSG00000252193.1
RN7SL666P
RN7SKP100
SNORA26\|ENSG00000212224.1
RN7SL615P
RNA5SP484
SNORD112\|ENSG00000252434.1
RN7SL194P
RN7SL680P
RN7SL116P
RN7SKP173
ARHGAP40
MIR548O2
SNORA60
SNORA71\|ENSG00000201811.1
SNORA71D
SNORA71C
SNORA71A
SNORA71B
SNHG17
RN7SL237P
RN7SKP185
LINC00489
RBL1
RN7SL156P
ADA
BPI
CD40
CEBPB
CSE1L
EYA2
GHRH
HNF4A
KCNG1
KCNS1
LBP
MMP9
MYBL2
NFATC2
NNAT
PI3
PLCG1
PLTP
CTSA
PTGIS
PTPN1
RBL1
RPN2
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SNAI1
SRC
STAU1
STK4
TGM2
TNNC2
UBE2V1
YWHAB
NCOA3
MATN4
DPM1
WISP2
B4GALT5
TTI1
SPATA2
ACOT8
ATP9A
SGK2
WFDC2
ARFGEF2
SPINT3
BLCAP
TOMM34
SERINC3
UBE2C
PTPRT
PKIG
ZHX3
SLC9A8
ADNP
ZMYND8
SAMHD1
L3MBTL1
PPP1R16B
TP53TG5
MOCS3
SLC35C2
IFT52
OSER1
PIGT
BCAS4
DDX27
ZNF334
DBNDD2
RNF114
SULF2
CTNNBL1
EPPIN
RALGAPB
JPH2
SALL4
ZNFX1
SLC12A5
PREX1
NCOA5
RPRD1B
DHX35
MANBAL
ELMO2
ZNF335
PCIF1
CDH22
SLC13A3
LPIN3
GDAP1L1
TTPAL
ACTR5
PABPC1L
SLC2A10
FAM83D
CHD6
PARD6B
TOX2
KIAA1755
EMILIN3
SYS1
WFDC8
ZSWIM1
TP53RK
DNTTIP1
VSTM2L
SNHG11
WFDC12
SPATA25
OCSTAMP
SLC32A1
WFDC3
MROH8
TLDC2
RIMS4
NEURL2
ZSWIM3
C20orf62
WFDC6
FAM65C
ADIG
GTSF1L
WFDC5
WFDC13
WFDC11
WFDC9
WFDC10B
TMEM189
MIR645
MIR3617

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q11.

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

Genes
snoU13\|ENSG00000238514.1
LINC00662
ZNF726
ZNF254
ZNF681
ZNF675
RPSAP58

Arm-level results

Table 3. Get Full Table Arm-level significance table - 26 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	0.33	3.61	0.000795	0.25	-0.322	0.988
1q	1195	0.62	17	0	0.28	0.592	0.541
2p	624	0.31	-0.189	1	0.09	-9.29	1
2q	967	0.28	0.042	1	0.09	-8.46	1
3p	644	0.11	-7.39	1	0.46	6.91	1.02e-11
3q	733	0.20	-4.03	1	0.37	2.96	0.00422
4p	289	0.18	-6.56	1	0.29	-2.07	1
4q	670	0.11	-8.26	1	0.30	-0.226	0.966
5p	183	0.53	7.94	1.02e-14	0.34	-0.203	0.966
5q	905	0.30	0.572	0.895	0.42	6.09	1.93e-09
6p	710	0.32	0.575	0.895	0.32	0.726	0.505
6q	556	0.15	-5.93	1	0.50	8.37	0
7p	389	0.53	9.08	0	0.19	-4.86	1
7q	783	0.44	6.7	8.53e-11	0.18	-4.62	1
8p	338	0.34	0.073	1	0.56	9.91	0
8q	551	0.51	8.6	0	0.28	-1.35	1
9p	301	0.16	-5.88	1	0.58	11.1	0
9q	700	0.12	-6.44	1	0.52	10.5	0
10p	253	0.26	-3.64	1	0.30	-1.84	1
10q	738	0.20	-4.37	1	0.32	0.595	0.541
11p	509	0.23	-4.1	1	0.28	-1.69	1
11q	975	0.25	-1.51	1	0.25	-1.59	1
12p	339	0.34	0.0646	1	0.30	-1.3	1
12q	904	0.30	0.628	0.895	0.28	-0.471	1
13q	560	0.17	-5.16	1	0.55	10.8	0
14q	938	0.32	1.38	0.34	0.30	0.758	0.505
15q	810	0.14	-5.84	1	0.51	10	0
16p	559	0.32	-0.083	1	0.32	0.139	0.793
16q	455	0.25	-3.15	1	0.36	1.56	0.144
17p	415	0.22	-3.87	1	0.53	8.88	0
17q	972	0.39	4.85	4.29e-06	0.23	-2.26	1
18p	104	0.25	-4.04	1	0.43	3.26	0.00161
18q	275	0.21	-4.7	1	0.48	6.38	3.39e-10
19p	681	0.09	-7.67	1	0.52	10.1	0
19q	935	0.19	-3.99	1	0.38	4.4	1.67e-05
20p	234	0.41	2.85	0.00999	0.35	0.214	0.774
20q	448	0.41	3.74	0.000535	0.25	-3.18	1
21q	258	0.27	-2.75	1	0.40	2.43	0.0193
22q	564	0.20	-4.26	1	0.48	7.5	1.49e-13
Xp	418	0.10	-9.93	1	0.25	-3.83	1
Xq	668	0.16	-6.93	1	0.17	-6.14	1

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/LUAD-TP/19078135/GDAC_MergeDataFiles_12185497/LUAD-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 516 Input Tumor Samples.

Tumor Sample Names
TCGA-05-4244-01A-01D-1877-01
TCGA-05-4249-01A-01D-1877-01
TCGA-05-4250-01A-01D-1877-01
TCGA-05-4382-01A-01D-1204-01
TCGA-05-4384-01A-01D-1752-01
TCGA-05-4389-01A-01D-1204-01
TCGA-05-4390-01A-02D-1752-01
TCGA-05-4395-01A-01D-1204-01
TCGA-05-4396-01A-21D-1854-01
TCGA-05-4397-01A-01D-1204-01

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

Made with Nozzle