Kidney Renal Clear Cell Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16 (cga svn revision 38839).

Summary

There were 489 tumor samples used in this analysis: 26 significant arm-level results, 12 significant focal amplifications, and 43 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 - 12 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
--- | --- | --- | --- | ---
5q35.3 | 6.984e-09 | 6.984e-09 | chr5:174278769-180857866 | 106
4q32.1 | 0.012821 | 0.012821 | chr4:159830759-161728055 | 5
3q26.32 | 0.017919 | 0.017919 | chr3:179275802-180624617 | 7
1q21.1 | 0.019159 | 0.019159 | chr1:144319349-144812596 | 9
1q32.1 | 0.025058 | 0.025058 | chr1:202117336-203316620 | 14
6p21.1 | 0.041949 | 0.041949 | chr6:42649635-43128398 | 15
14q13.2 | 0.06228 | 0.06228 | chr14:33505064-36474614 | 21
15q26.1 | 0.073177 | 0.073177 | chr15:88013119-88798432 | 18
11q13.4 | 0.091195 | 0.091195 | chr11:71030990-71235075 | 2
13q14.3 | 0.13764 | 0.13764 | chr13:48177243-49130490 | 9
17q12 | 0.16426 | 0.16426 | chr17:33226229-33317176 | 1
17q23.3 | 0.18076 | 0.18076 | chr17:58400997-58446484 | 1

Genes in Wide Peak

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

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

Genes
NSD1
hsa-mir-340
hsa-mir-1229
hsa-mir-1271
CANX
CLTB
DBN1
DRD1
F12
FGFR4
FLT4
GRK6
GRM6
HK3
HNRNPAB
HNRNPH1
HRH2
LTC4S
MGAT1
MAPK9
PROP1
SLC34A1
SNCB
ZNF354A
SQSTM1
PDLIM7
ADAMTS2
MAML1
GFPT2
GNB2L1
RGS14
CPLX2
BTNL3
LMAN2
MGAT4B
B4GALT7
RNF44
TBC1D9B
N4BP3
FAF2
ZNF346
TSPAN17
OR4F3
PRELID1
ZNF354C
C5orf45
DDX41
NOP16
UIMC1
RAB24
FAM193B
TMED9
PCDH24
NHP2
RNF130
KIAA1191
CLK4
CNOT6
GMCL1L
RMND5B
BTNL8
DOK3
ZFP2
RUFY1
PRR7
OR4F16
TRIM7
MXD3
THOC3
TRIM52
AGXT2L2
UNC5A
TRIM41
COL23A1
SCGB3A1
SFXN1
GPRIN1
ZNF354B
OR2Y1
BTNL9
HIGD2A
FAM153B
LOC202181
EIF4E1B
RASGEF1C
FAM153A
ARL10
OR2V2
ZNF454
C5orf60
PFN3
ZNF879
C5orf25
MIR340
SNORD95
SNORD96A
ZFP62
CBY3
FAM153C
LOC728554
AACSL
LOC729678
OR4F29
LOC100132062
LOC100132287
LOC100133331

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q32.1.

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

Genes
ETFDH
PPID
RAPGEF2
FNIP2
C4orf45

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

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

Genes
PIK3CA
KCNMB2
KCNMB3
ZNF639
MFN1
GNB4
ZMAT3

Genes in Wide Peak

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

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

Genes
PDZK1
POLR3C
CD160
RNF115
LOC200030
GPR89A
NBPF11
GPR89C
PDZK1P1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q32.1.

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

Genes
MDM4
KISS1
PIK3C2B
REN
CNTN2
SOX13
LRRN2
PLEKHA6
NFASC
ETNK2
PPP1R15B
LOC127841
GOLT1A
C1orf157

Genes in Wide Peak

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

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

Genes
MEA1
PEX6
PPP2R5D
PRPH2
TBCC
CUL7
CNPY3
UBR2
KIAA0240
GNMT
C6orf153
KLHDC3
PTCRA
RPL7L1
C6orf226

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.2.

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

Genes
NKX2-1
CFL2
NFKBIA
PAX9
PSMA6
SRP54
KIAA0391
BAZ1A
NKX2-8
MBIP
PPP2R3C
EAPP
SNX6
BRMS1L
INSM2
SLC25A21
C14orf147
RALGAPA1
SFTA3
C14orf19
FAM177A1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
IDH2
ANPEP
PLIN1
PEX11A
IQGAP1
AP3S2
SEMA4B
CIB1
GABARAPL3
NGRN
MESP1
WDR93
MESP2
ZNF774
C15orf38
ZNF710
C15orf58
TTLL13

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.4.

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

Genes
FAM86C
DEFB108B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q14.3.

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

Genes
MLNR
FNDC3A
PHF11
RCBTB1
CYSLTR2
CDADC1
CAB39L
SETDB2
ARL11

Genes in Wide Peak

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

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

Genes
LOC284100

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.3.

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

Genes
TANC2

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 - 43 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
--- | --- | --- | --- | ---
2q37.3 | 1.2869e-17 | 1.2869e-17 | chr2:239984812-242951149 | 40
3p21.31 | 9.6943e-20 | 1.7345e-15 | chr3:46424169-46515615 | 1
9p21.3 | 2.3357e-12 | 1.0104e-09 | chr9:21855498-22438737 | 4
9p24.1 | 1.7406e-08 | 7.5799e-08 | chr9:7786330-12683402 | 2
6q26 | 1.611e-07 | 2.4125e-07 | chr6:161613089-163073197 | 1
1p36.13 | 1.0128e-06 | 1.0128e-06 | chr1:15303969-21005685 | 88
13q12.12 | 2.7154e-05 | 2.7154e-05 | chr13:23794594-24082673 | 2
3p14.2 | 1.3926e-09 | 3.7633e-05 | chr3:59009803-61522370 | 1
3p25.3 | 2.2148e-11 | 4.27e-05 | chr3:10143865-10183836 | 1
10q23.31 | 9.242e-05 | 9.7506e-05 | chr10:89564857-90024018 | 3
1p31.1 | 0.00013048 | 0.0001397 | chr1:71313038-74273894 | 1
11p15.4 | 0.00013594 | 0.0001397 | chr11:4617298-4658488 | 2
3p12.3 | 3.4316e-06 | 0.00060399 | chr3:74651634-79154756 | 6
12q15 | 0.0038029 | 0.0036829 | chr12:69031355-69197778 | 1
3p14.2 | 3.479e-07 | 0.0042254 | chr3:61209873-63067698 | 5
7q31.1 | 0.0045488 | 0.0042254 | chr7:110512908-111163100 | 1
4q35.1 | 0.0058984 | 0.0064028 | chr4:149216853-191273063 | 153
20p12.1 | 0.0061122 | 0.0064028 | chr20:14250876-15984135 | 2
17q22 | 0.0080023 | 0.0072947 | chr17:52553420-53272917 | 1
14q24.3 | 0.0065507 | 0.010234 | chr14:71466001-85169054 | 88
3p11.2 | 0.0046248 | 0.016998 | chr3:78727567-95183561 | 12
3p25.3 | 1.6721e-06 | 0.026247 | chr3:10928550-11808472 | 4
4q24 | 0.035686 | 0.03801 | chr4:102161830-114527309 | 64
6p25.3 | 0.042097 | 0.042955 | chr6:1553836-2569051 | 2
12p13.33 | 0.051705 | 0.04919 | chr12:1767041-1925787 | 2
16p13.2 | 0.04919 | 0.04919 | chr16:5085718-7704198 | 1
3p14.1 | 0.00097885 | 0.054201 | chr3:65315949-74654092 | 26
15q11.2 | 0.058772 | 0.054201 | chr15:22478867-22778701 | 3
18q22.2 | 0.069744 | 0.066971 | chr18:64614278-76117153 | 35
3p14.2 | 9.617e-06 | 0.077335 | chr3:62082390-68679319 | 19
3q21.2 | 0.064129 | 0.087928 | chr3:127270927-127544518 | 1
6q16.3 | 0.045448 | 0.087928 | chr6:90393538-117705653 | 107
11q14.3 | 0.089488 | 0.087928 | chr11:78039264-100369355 | 84
3p26.3 | 9.1553e-07 | 0.096522 | chr3:1-25620266 | 128
1q42.3 | 0.1166 | 0.11271 | chr1:205343337-247249719 | 295
3q11.2 | 0.081708 | 0.12812 | chr3:87389885-108451477 | 61
3q21.1 | 0.073695 | 0.12812 | chr3:124227750-124404912 | 1
10q23.1 | 0.15916 | 0.1482 | chr10:38502243-85905916 | 248
14q23.3 | 0.03657 | 0.17103 | chr14:46378242-72434497 | 170
3p14.2 | 8.1478e-08 | 0.17667 | chr3:46588227-61213257 | 207
5p15.33 | 0.22977 | 0.21395 | chr5:1341695-1630410 | 3
10q26.2 | 0.21597 | 0.21395 | chr10:96077857-135374737 | 318
3q22.3 | 0.24981 | 0.24981 | chr3:1-199501827 | 1158

Genes in Wide Peak

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

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

Genes
hsa-mir-149
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
RNPEPL1
GAL3ST2
C2orf54
ING5
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
C2orf85
DUSP28
AQP12A
OR6B2
MIR149
PRR21
AQP12B
D2HGDH
LOC728323
PP14571

Genes in Wide Peak

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

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

Genes
LTF

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2BAS

Genes in Wide Peak

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

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

Genes
PTPRD
C9orf123

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.13.

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

Genes
PAX7
SDHB
hsa-mir-1290
CAPZB
CASP9
CDA
CLCNKA
CLCNKB
DDOST
EPHA2
HTR6
MFAP2
NBL1
PLA2G2A
PLA2G5
RSC1A1
ZBTB17
AKR7A2
ALDH4A1
CROCC
MSTP2
MSTP9
PADI2
CTRC
AKR7A3
SPEN
KIAA0090
PLEKHM2
OTUD3
DNAJC16
UBR4
ATP13A2
PADI4
C1orf144
PLA2G2D
HSPB7
PADI1
PLA2G2E
HP1BP3
CELA2B
MRTO4
PADI3
FBXO42
RNF186
FBLIM1
PQLC2
TMEM51
ARHGEF10L
CAMK2N1
NBPF1
NECAP2
RCC2
KIF17
CELA2A
PLA2G2F
PINK1
EFHD2
C1orf89
MUL1
AGMAT
TAS1R2
ACTL8
DDI2
CROCCL1
IGSF21
CROCCL2
FHAD1
IFFO2
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
C1orf64
FAM43B
C1orf126
AKR7L
TMCO4
SLC25A34
ESPNP
FAM131C
PADI6
SPATA21
TMEM82
PLA2G2C
SH2D5
UQCRHL
C1orf151
FLJ37453

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.12.

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

Genes
PARP4
LOC374491

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
VHL

Genes in Wide Peak

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

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

Genes
PTEN
CFLP1
KILLIN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.1.

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

Genes
NEGR1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
OR51E1
OR51D1

Genes in Wide Peak

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

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

Genes
hsa-mir-1324
ROBO1
ROBO2
FAM86D
ZNF717
FRG2C

Genes in Wide Peak

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

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

Genes
KCNMB4

Genes in Wide Peak

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

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

Genes
PTPRG
CADPS
FEZF2
C3orf14
ID2B

Genes in Wide Peak

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

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

Genes
LRRN3

Genes in Wide Peak

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

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

Genes
DUX4
FBXW7
hsa-mir-1305
hsa-mir-1979
AGA
SLC25A4
ANXA2P1
CASP3
LRBA
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FGA
FGB
FGG
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
ING2
IRF2
KLKB1
NR3C2
MTNR1A
NEK1
NPY1R
NPY2R
NPY5R
PET112L
PLRG1
PPID
RPS3A
SC4MOL
SFRP2
TDO2
TLL1
TLR2
TLR3
VEGFC
GLRA3
SORBS2
SAP30
SNORD73A
LRAT
HAND2
RAPGEF2
MFAP3L
MAB21L2
MORF4
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FAM149A
FBXO8
ARFIP1
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
PDGFC
TUBB4Q
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
C4orf41
MLF1IP
NBLA00301
MAP9
WWC2
KIAA1712
SNX25
MND1
TKTL2
CBR4
FHDC1
MGC45800
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
SH3D19
C4orf38
C4orf39
C4orf45
DCLK2
TRIM60
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4A
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285501
RNF175
TRIML1
LOC340017
PRSS48
ANKRD37
TRIM61
TRIM75
HELT
FAM92A3
C4orf47
GALNTL6
FRG2
SLED1
LOC653543
LOC653544
LOC653545
LOC653548
MIR578
LOC728410
FAM160A1

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q22.

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

Genes
MSI2

Genes in Wide Peak

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

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

Genes
TSHR
hsa-mir-1260
ACYP1
BCYRN1
ENTPD5
DIO2
DLST
ESRRB
FOS
GSTZ1
GTF2A1
LTBP2
ALDH6A1
PGF
PSEN1
ABCD4
SEL1L
TGFB3
DPF3
NUMB
ALKBH1
EIF2B2
PNMA1
NRXN3
SPTLC2
RGS6
KIAA0317
BATF
NPC2
AHSA1
ACOT2
TMED10
C14orf1
VASH1
SNW1
TTLL5
ANGEL1
FLRT2
DCAF4
MLH3
POMT2
COQ6
FCF1
ZFYVE1
C14orf115
FLVCR2
C14orf118
YLPM1
ADCK1
TMEM63C
ZNF410
NGB
RBM25
C14orf133
C14orf4
FAM164C
C14orf169
C14orf45
C14orf156
DNAL1
RPS6KL1
STON2
KIAA1737
PAPLN
C14orf43
LIN52
NEK9
C14orf179
C14orf148
JDP2
ISCA2
ACOT4
PTGR2
FAM161B
C14orf166B
ISM2
C14orf145
C14orf174
PROX2
ZDHHC22
TMED8
C14orf178
VSX2
HEATR4
ACOT1
ACOT6
TMEM90A
SNORA79

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.2.

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

Genes
EPHA3
GBE1
HTR1F
POU1F1
PROS1
ROBO1
CGGBP1
CHMP2B
ZNF654
CADM2
C3orf38
VGLL3

Genes in Wide Peak

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

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

Genes
HRH1
SLC6A1
VGLL4
ATG7

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q24.

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

Genes
TET2
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
ANK2
CASP6
CENPE
EGF
ENPEP
HADH
CFI
MANBA
NFKB1
PITX2
PPP3CA
RPL34
TACR3
UBE2D3
PAPSS1
AIMP1
SEC24B
RRH
PPA2
DKK2
LEF1
LARP7
GAR1
FLJ20184
CCDC109B
BANK1
C4orf21
AP1AR
BDH2
INTS12
OSTC
NEUROG2
SLC39A8
AGXT2L1
ELOVL6
GSTCD
ALPK1
CXXC4
PLA2G12A
COL25A1
TIFA
TBCK
CYP2U1
C4orf32
NHEDC2
NHEDC1
SGMS2
NPNT
LOC285456
LRIT3
MIR302A
EEF1AL7
MIR302B
MIR302C
MIR302D
MIR367
CISD2
LOC641518

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

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

Genes
FOXC1
GMDS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.33.

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

Genes
CACNA2D4
LRTM2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.2.

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

Genes
A2BP1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.1.

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

Genes
MITF
FOXP1
hsa-mir-1284
GPR27
CNTN3
TMF1
SUCLG2
UBA3
MAGI1
ARL6IP5
PDZRN3
FRMD4B
RYBP
LRIG1
FLJ10213
SHQ1
LMOD3
PROK2
KBTBD8
SLC25A26
FAM19A4
PPP4R2
C3orf64
EIF4E3
FAM19A1
GLT8D4

Genes in Wide Peak

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

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

Genes
SNRPN
SNURF
SNORD107

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.2.

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

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
SOCS6
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
SALL3
C18orf55
ZNF407
CNDP2
CCDC102B
C18orf22
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
DOK6
ZADH2
C18orf62
LOC284276
ATP9B
LOC400657
HSBP1L1
LOC100130522

Genes in Wide Peak

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

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

Genes
ATXN7
CADPS
SUCLG2
MAGI1
PSMD6
LRIG1
FEZF2
ADAMTS9
C3orf14
THOC7
ID2B
KBTBD8
SLC25A26
C3orf49
SNTN
SYNPR
PRICKLE2
LOC285401
FAM19A1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q21.2.

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

Genes
ALDH1L1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.3.

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
AIM1
AMD1
CCNC
COL10A1
EPHA7
FOXO3
FRK
FYN
GPR6
GRIK2
HDAC2
KPNA5
LAMA4
MARCKS
POU3F2
PREP
REV3L
SIM1
SMPD2
MAP3K7
NR2E1
TSPYL1
DDO
SNX3
CD164
WISP3
WASF1
FHL5
ATG5
ZBTB24
FIG4
CASP8AP2
FUT9
TRAF3IP2
ASCC3
BVES
SEC63
CDC2L6
MDN1
TSPYL4
KIAA0776
SFRS18
FBXL4
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
COQ3
SOBP
QRSL1
PDSS2
LYRM2
HACE1
BEND3
PRDM13
BACH2
POPDC3
MICAL1
MANEA
GPR63
ARMC2
RPF2
MCHR2
C6orf168
GJA10
RTN4IP1
USP45
SLC22A16
KIAA1919
GTF3C6
KLHL32
SLC16A10
C6orf185
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
VGLL2
LACE1
C6orf167
FAM26E
SCML4
C6orf182
PPIL6
FLJ34503
RSPH4A
LIN28B
FAM26F
LOC442245
RFPL4B
LOC553137
C6orf225
TSG1
LOC728402
C6orf186
BET3L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.3.

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

Genes
PICALM
MAML2
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-708
CTSC
DLG2
FUT4
GRM5
MRE11A
MTNR1B
PRCP
TYR
FZD4
JRKL
EED
MTMR2
MED17
CEP57
NAALAD2
ME3
GPR83
SFRS2B
PRSS23
ENDOD1
RAB38
PANX1
ODZ4
CHORDC1
RAB30
C11orf54
NOX4
C11orf73
CWC15
PCF11
CNTN5
SYTL2
ANKRD49
KDM4D
TMEM126B
C11orf75
TRIM49
CREBZF
CCDC90B
CCDC81
TMEM135
TAF1D
CCDC82
TMEM126A
KIAA1731
SLC36A4
FAT3
TRIM64
FAM76B
SESN3
PIWIL4
FLJ32810
AMOTL1
CCDC67
FOLH1B
C11orf82
CCDC83
FAM181B
CCDC89
ANKRD42
HEPHL1
C11orf90
TRIM77
FOLR4
KDM4DL
SCARNA9
TRIM64B
TRIM53
UBTFL1
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
LOC729384

Genes in Wide Peak

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

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

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-563
hsa-mir-885
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RARB
RPL15
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
THRB
TIMP4
NR2C2
UBE2E1
UBE2E2
WNT7A
BRPF1
COLQ
CAMK1
BHLHE40
KAT2B
SH3BP5
VGLL4
EDEM1
TBC1D5
TATDN2
IQSEC1
NR1D2
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LSM3
NKIRAS1
LOH3CR2A
LMCD1
C3orf32
TRNT1
CRBN
C3orf19
GHRL
ARL8B
SETD5
TMEM40
TMEM111
C3orf10
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
ZNF385D
HDAC11
TSEN2
GRIP2
C3orf20
JAGN1
C3orf42
IL17RC
EAF1
OXNAD1
C3orf24
GALNTL2
KCNH8
CHCHD4
METTL6
C3orf31
IL17RE
SGOL1
C3orf48
EFHB
CPNE9
LOC152024
FGD5
CIDECP
CNTN4
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
DVWA
TPRXL
LHFPL4
VENTXP7
LOC401052
LOC440944
SNORA7A
MIR563
MIR885
EGOT
GHRLOS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.3.

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

Genes
FH
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-205
hsa-mir-29b-2
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
C4BPA
CAPN2
CD34
CENPF
CHML
LYST
CHRM3
CR1
CR1L
CR2
CD55
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
HNRNPU
HSD11B1
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
NEK2
NID1
NVL
PLXNA2
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
LPGAT1
AKT3
BPNT1
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
RPS6KC1
C1orf107
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
G0S2
RRP15
PPPDE1
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MOSC2
SUSD4
KIF26B
GPATCH2
HEATR1
TMEM206
BATF3
SLC30A10
ZNF692
IARS2
HHAT
ENAH
NUP133
RCOR3
SERTAD4
ERO1LB
FMN2
SMYD2
CABC1
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MOSC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
C1orf124
OBSCN
C1orf57
EFCAB2
KIAA1804
C1orf97
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
ZNF670
NLRP3
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
C1orf58
SLC35F3
LOC148696
B3GALNT2
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
CNST
C1orf65
PLD5
C1orf100
C1orf69
OR2T6
SYT14
C1orf101
PGBD2
OR2L13
OR14A16
NCRNA00201
LIN9
VN1R5
ZNF678
PRSS38
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
LOC400804
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR194-1
MIR205
MIR215
MIR29B2
MIR29C
TRIM67
MAP1LC3C
LOC440926
OR2W5
OR13G1
DUSP5P
C1orf133
LOC642587
LQK1
LOC646627
SNORA14B
SNORA36B
SNORA16B
LOC731275
LOC100130093
LOC100130331
TSNAX-DISC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.2.

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

Genes
CBLB
TFG
ALCAM
COL8A1
CPOX
EPHA3
GPR15
HTR1F
POU1F1
PROS1
RPL24
CGGBP1
TOMM70A
ST3GAL6
FILIP1L
ABI3BP
OR5K1
OR5H1
ZBTB11
IMPG2
RG9MTD1
TMEM45A
ZNF654
TBC1D23
CLDND1
NIT2
PCNP
SENP7
NSUN3
NFKBIZ
OR5H6
OR5H2
CEP97
OR5AC2
ARL6
C3orf26
MINA
GPR128
FAM55C
ZPLD1
CRYBG3
DCBLD2
LOC152225
ARL13B
DHFRL1
GABRR3
LOC255025
EPHA6
C3orf38
LOC285359
LOC344595
LNP1
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
STX19
TMEM30C
LOC100009676
LOC100302640

Genes in Wide Peak

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

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

Genes
PDIA5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.1.

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

Genes
PRF1
RET
NCOA4
MYST4
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
ADK
ALOX5
ANXA8L2
ANK3
ANXA2P3
ANXA7
ANXA11
CAMK2G
CDC2
CHAT
COL13A1
DNA2
EGR2
EIF4EBP2
ERCC6
GDF2
GDF10
HK1
HNRNPF
HNRNPH3
KCNMA1
MAT1A
MBL2
MSMB
NODAL
P4HA1
PCBD1
PLAU
PPA1
PPP3CB
PPYR1
SRGN
PRKG1
MAPK8
PSAP
RBP3
RPS24
CXCL12
SFTPD
SLC18A3
SUPV3L1
TACR2
TFAM
UBE2D1
VCL
VDAC2
ZNF22
ZNF32
ZNF33B
CCDC6
SLC25A16
ZNF239
PARG
NDST2
MBL1P1
SGPL1
DDX21
DLG5
CHST3
VPS26A
SEC24C
GPRIN2
BMS1
SPOCK2
RHOBTB1
PPIF
HNRNPA3P1
CBARA1
TIMM23
NRG3
C10orf10
POLR3A
ZWINT
ECD
ZNF365
DKK1
KIAA0913
DNAJC9
CSTF2T
SIRT1
TSPAN15
NUDT13
HERC4
PTPN20B
KIAA1279
AP3M1
GHITM
KIAA1274
CTNNA3
A1CF
NRBF2
NEUROG3
ASCC1
MRPS16
DUSP13
FXYD4
DDIT4
DNAJB12
LRRC20
SLC29A3
CSGALNACT2
H2AFY2
RUFY2
FAM21B
CCAR1
OGDHL
CISD1
DNAJC12
ASAH2
SAR1A
ZMIZ1
WDFY4
ARHGAP22
MYOZ1
CDH23
PBLD
NPFFR1
C10orf54
PCDH15
DDX50
OR13A1
SYNPO2L
BICC1
C10orf57
HKDC1
TET1
TSPAN14
SYT15
RASSF4
C10orf11
ARID5B
C10orf58
DYDC2
PHYHIPL
PLA2G12B
MYPN
LOC84856
ZNF503
AIFM2
ADO
LOC84989
CCDC109A
ANUBL1
C10orf71
CHCHD1
ZMYND17
TTC18
ZNF488
COMTD1
AGAP4
C10orf104
ADAMTS14
SAMD8
FRMPD2
DYDC1
EIF5AL1
HSD17B7P2
USP54
FAM170B
C10orf128
FUT11
OIT3
ANTXRL
C10orf72
LOC219347
PLAC9
C10orf107
TMEM26
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
C10orf27
ATOH7
SLC16A9
FAM13C
MARCH8
C10orf25
ZNF485
RASGEF1A
REEP3
JMJD1C
IPMK
FAM21C
SGMS1
PGBD3
C10orf53
C10orf40
LOC283050
CDC10L
FAM149B1
DUPD1
LRRTM3
FAM21A
SH2D4B
LOC399744
LOC399753
BMS1P5
C10orf105
AGAP6
C10orf55
FAM35B
FAM35B2
LOC441666
LRRC18
LOC642361
ZNF487
LOC642826
TMEM72
FAM25C
DRGX
LOC650623
PTPN20A
ANXA8
AGAP7
ASAH2B
SFTPA1
SNORD98
MIR605
BMS1P1
ANXA8L1
AGAP8
LOC728407
FRMPD2L2
LOC728640
LOC728643
FRMPD2L1
AGAP5
BMS1P4
SFTPA2
LOC100128292
LOC100129055
ZNF37B
C10orf41
FAM25B
FAM25G
LOC100133308

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
KTN1
RAD51L1
GPHN
NIN
hsa-mir-625
hsa-mir-548h-1
ACTN1
ARF6
ARG2
BMP4
ZFP36L1
CDKN3
EIF2S1
ERH
ESR2
FNTB
FUT8
GCH1
GMFB
GPX2
HIF1A
HSPA2
LGALS3
MAX
MGAT2
MAP3K9
MNAT1
MTHFD1
SIX6
OTX2
PIGH
POLE2
PPM1A
PPP2R5E
PRKCH
PSMA3
PSMC6
PTGDR
PTGER2
PYGL
ARID4A
RPL36AL
RPS29
RTN1
SFRS5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
STYX
ZBTB25
DPF3
ADAM21
ADAM20
CDKL1
DCAF5
SDCCAG1
AKAP5
RGS6
KIAA0247
KIAA0586
DLGAP5
MED6
CNIH
VTI1B
EXOC5
CGRRF1
FERMT2
WDHD1
MAP4K5
NID2
KIAA0831
ZBTB1
PCNX
DAAM1
SAMD4A
SYNE2
ZFYVE26
TTC9
KLHDC2
PLEKHG3
SIPA1L1
PLEK2
TIMM9
ATP5S
KCNH5
ERO1L
ATL1
RDH11
COX16
DACT1
ATP6V1D
JKAMP
DHRS7
C14orf166
SIX4
GNG2
C14orf101
FBXO34
C14orf104
C14orf105
EXD2
SYNJ2BP
SLC39A9
MUDENG
ACTR10
C14orf162
PELI2
RHOJ
GALNTL1
PLEKHH1
TXNDC16
TRMT5
SAV1
SMOC1
MPP5
C14orf135
GPR135
GNPNAT1
C14orf138
L2HGDH
DDHD1
SGPP1
TMX1
SYT16
CHURC1
MAPK1IP1L
WDR89
C14orf149
TRIM9
PPIL5
KLHDC1
FRMD6
SOCS4
NAT12
GPHB5
RDH12
ADAM21P
C14orf50
SLC38A6
C14orf37
ABHD12B
LOC145474
FAM71D
TMEM229B
TMEM30B
MDGA2
C14orf183
C14orf182
GPR137C
C14orf39
SNORD56B
SLC35F4
RAB15
FLJ31306
TBPL2
TOMM20L
C14orf181
FLJ44817
C14orf53
LOC645431
RPL13AP3
C14orf34
FLJ43390
C14orf38
C14orf33
LOC100289511
OTX2OS1

Genes in Wide Peak

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

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

Genes
FHIT
BAP1
SETD2
PBRM1
hsa-mir-135a-1
hsa-let-7g
hsa-mir-566
hsa-mir-191
hsa-mir-1226
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CDC25A
CISH
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
MAP4
MST1
MST1R
MYL3
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
PTH1R
QARS
RPL29
SEMA3F
SMARCC1
NEK4
TCTA
TDGF1
TKT
TNNC1
UBA7
USP4
UQCRC1
WNT5A
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
HYAL2
HESX1
BSN
RRP9
CACNA2D2
VPRBP
IP6K1
PARP3
RBM6
RBM5
NME6
TRAIP
ARIH2
TUSC4
CSPG5
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
DHX30
SCAP
LAMB2L
RAD54L2
STAB1
NBEAL2
C3orf63
KLHL18
NAT6
ABHD14A
WDR51A
NDUFAF3
PTPN23
DNAH1
ERC2
APPL1
GNL3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
P4HTM
IL17RD
C3orf75
QRICH1
PXK
DALRD3
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
SEMA3G
PCBP4
ABHD6
LRTM1
SELK
RNF123
KIF9
CCDC71
NT5DC2
SLC26A6
CAMKV
CCDC51
WDR82
ATRIP
NICN1
MON1A
ABHD14B
UCN2
RFT1
ACTR8
GPR62
FAM3D
IQCF1
GLYCTK
PPM1M
C3orf45
ASB14
CCDC12
C3orf67
KCTD6
KLHDC8B
DNAH12
PDE12
FAM116A
ALS2CL
TMIE
FBXW12
CCDC66
CCDC36
PRSS42
SPATA12
C3orf62
TMEM110
PRSS45
AMIGO3
CDH29
C3orf54
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR191
TMEM89
IQCF6
LOC440957
MIR425
SPINK8
C3orf71
LOC646498
SNORD19
SNORD69
HESRG
SNORD19B
C3orf74
LOC100129354

Genes in Wide Peak

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

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

Genes
SLC6A3
LPCAT1
CLPTM1L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.2.

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-2110
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-608
hsa-mir-1287
hsa-mir-607
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HELLS
HMX2
HPS1
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
ALDH18A1
RGS10
SCD
SFRP5
FBXW4
SLC18A2
SLIT1
TAF5
TCF7L2
TECTB
TIAL1
TLL2
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
PDLIM1
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
ZNF518A
DCLRE1A
FRAT1
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
RP11-529I10.4
SEC31B
ATRNL1
C10orf137
TCTN3
C10orf12
ANKRD2
CNNM1
PDCD4
VENTX
C10orf28
POLL
BLNK
KCNIP2
CUZD1
CALY
EXOSC1
CALHM2
CUTC
CHST15
ACSL5
CCNJ
ZRANB1
NSMCE4A
CNNM2
C10orf26
C10orf118
CRTAC1
CWF19L1
PI4K2A
HIF1AN
BRWD2
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
TM9SF3
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
HPSE2
C10orf84
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
C10orf119
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
C10orf79
LRRC27
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
PCGF6
LOXL4
ZDHHC16
GPR123
LZTS2
LCOR
NKX6-2
MRPL43
AFAP1L2
PYROXD2
USMG5
ARHGAP19
KNDC1
ITPRIP
C10orf75
MTG1
NCRNA00081
FANK1
OPALIN
SYCE1
DHDPSL
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
SFXN2
PDZD8
C10orf32
GSTO2
C10orf78
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
NKX2-3
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
C10orf93
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
CC2D2B
ARMS2
C10orf122
GUCY2G
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FOXI2
GOLGA7B
FAM45A
C10orf62
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
LOC653543
LOC653544
LOC653545
LOC653548
SNORA12
MIR608
MIR609
LOC728410
LOC729020
TLX1NB
C10orf131
LOC100169752
NCRNA00093
LOC100270710

Genes in Wide Peak

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

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

Genes
BCL6
FOXL2
CBLB
CTNNB1
EIF4A2
ETV5
FANCD2
FHIT
GATA2
LPP
MITF
MLF1
MLH1
MYD88
PIK3CA
PPARG
RAF1
RPN1
SOX2
TFRC
VHL
XPC
BAP1
GMPS
SRGAP3
TFG
FOXP1
SETD2
PBRM1
hsa-mir-922
hsa-mir-570
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-198
hsa-mir-568
hsa-mir-567
hsa-mir-1324
hsa-mir-1284
hsa-mir-135a-1
hsa-let-7g
hsa-mir-566
hsa-mir-191
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-563
hsa-mir-885
AADAC
ACAA1
ACPP
ACTL6A
ACVR2B
ACY1
ADCY5
ADPRH
AGTR1
AHSG
ALAS1
ALCAM
AMT
APEH
APOD
ARF4
RHOA
ATP1B3
ATP2B2
ATP6V1A
ATR
BCHE
BDH1
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CASR
CAV3
CCK
CD80
CD86
ENTPD3
CD47
CDC25A
CISH
AP2M1
CLCN2
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CP
CPA3
CPB1
CPN2
CPOX
CRYGS
CSTA
CX3CR1
CYP8B1
DAG1
DGKG
DAZL
DLG1
DNASE1L3
DOCK3
DRD3
DUSP7
DVL3
ECT2
CELSR3
EHHADH
EIF4G1
EPHA3
EPHB1
EPHB3
MECOM
FBLN2
FGF12
FLNB
GAP43
GBE1
GHSR
GLB1
GNAI2
GNAT1
GOLGA4
GOLGB1
GP5
GP9
XCR1
GPR15
GPR27
GPX1
GRM2
GRM7
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRH1
HRG
HES1
HTR1F
HYAL1
IL1RAP
IL5RA
IL12A
IMPDH2
IRAK2
ITGA9
ITGB5
ITIH1
ITIH3
ITIH4
ITPR1
KNG1
KPNA1
KPNA4
LAMB2
RPSA
LSAMP
LTF
TM4SF1
MAP4
MBNL1
MCM2
MFI2
MME
MOBP
CD200
MST1
MST1R
MUC4
MYL3
MYLK
NCK1
NDUFB4
NDUFB5
NKTR
OGG1
OPA1
CLDN11
OXTR
P2RY1
PAK2
CNTN3
PCCB
PCYT1A
PDHB
PFKFB4
PFN2
SERPINI1
SERPINI2
PIK3CB
PLCD1
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
PLXNB1
POLR2H
POU1F1
PPP1R2
PPP2R3A
PRKAR2A
PRKCD
PRKCI
PROS1
MASP1
PSMD2
PTH1R
PTPRG
PTX3
QARS
RAB5A
RAP2B
RARB
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
SNORA62
ROBO1
ROBO2
RPL15
RPL24
RPL29
RPL32
RPL35A
RYK
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
SETMAR
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC6A1
SLC6A6
SLC6A11
SLC15A2
SLCO2A1
HLTF
SMARCC1
SSR3
SST
STAC
NEK4
SYN2
TCTA
TDGF1
TERC
TF
TFDP2
TGM4
TGFBR2
THPO
THRB
TIMP4
TKT
SEC62
TM4SF4
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
TRH
TRPC1
UBA7
UBE2E1
UBE2E2
UBP1
UPK1B
UMPS
USP4
UQCRC1
CLRN1
VIPR1
WNT5A
WNT7A
ZIC1
CNBP
ZNF35
ZNF80
ZNF148
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
RAB7A
KCNAB1
FXR1
COLQ
ACOX2
EOMES
HYAL3
SOX14
BFSP2
CAMK1
CGGBP1
BHLHE40
RUVBL1
CADPS
TP63
CHRD
HYAL2
B4GALT4
B3GALNT1
SNX4
TNFSF10
SUCLG2
HESX1
KAT2B
NR1I2
EIF2B5
BSN
MBD4
H1FX
USP13
LIMD1
KALRN
CCRL2
UBA3
RPL14
CLDN1
SEC22C
RRP9
MAP3K13
SLC33A1
LRRFIP2
MAGI1
CACNA2D2
COPB2
ADIPOQ
SLC22A14
SLC22A13
CHST2
SH3BP5
SLC4A7
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
VGLL4
EDEM1
KIAA0226
ECE2
VPRBP
TBC1D5
TATDN2
IP6K1
TSC22D2
EPM2AIP1
PSMD6
TOMM70A
TRANK1
IQSEC1
P2RY14
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
SMC4
ABCC5
COX17
ARPC4
ZNF197
RBM6
RBM5
TNK2
ALG3
NME6
CTDSPL
CD96
KCNMB2
STAG1
EIF1B
TRAIP
ST3GAL6
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
TUSC4
IGF2BP2
CXCR6
CSPG5
CLDN16
POLQ
CHL1
ARPP-21
CCR9
ALDH1L1
USP19
PDIA5
SLC38A3
CYB561D2
TMEM115
TOPBP1
RPP14
HHLA2
FSTL1
FAM107A
WDR6
RASSF1
NISCH
MRPL3
PDCD10
FILIP1L
TREX1
SCN11A
TUSC2
RNF13
MGLL
TWF2
MRAS
COPG
SLITRK3
NLGN1
TRAK1
DHX30
SACM1L
NCBP2
SCAP
LAMB2L
MYH15
PLCH1
EXOSC7
TMCC1
PDZRN3
TNIK
CAND2
MCF2L2
CLASP2
PLXND1
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
ATP11B
NBEAL2
NUP210
PLCL2
ANKRD28
C3orf63
KLHL18
DNAJC13
SR140
VPS8
LARS2
RYBP
C3orf27
CAPN7
ACAP2
MKRN2
NAT6
FBXL2
ANAPC13
ARMC8
ABHD14A
C3orf17
WDR51A
ABI3BP
CNOT10
TMEM158
NDUFAF3
THUMPD3
MYRIP
PTPN23
WWTR1
PVRL3
TIPARP
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
UBXN7
ERC2
APPL1
HACL1
SGEF
ZBTB20
TTLL3
OR5K1
OR5H1
GNL3
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
ZBTB11
MORC1
SERP1
CNTN6
LSM3
RBMS3
GOLIM4
NKIRAS1
SPCS1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
PRSS50
RBM15B
GPR171
GMPPB
SEC61A1
LOH3CR2A
SCHIP1
LMCD1
PIK3R4
PODXL2
ARHGEF3
TRAT1
VILL
IMPG2
C3orf32
NMD3
TRNT1
ABHD5
COMMD2
DYNC1LI1
A4GNT
C3orf18
DBR1
CRBN
SS18L2
ZNF639
CLDN18
C3orf19
SHISA5
C3orf1
ZDHHC3
RSRC1
ZMYND10
PLA1A
TEX264
CCDC72
ZNF589
HEMK1
AMOTL2
IP6K2
SFMBT1
NCKIPSD
PHF7
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
GHRL
P2RY13
IL20RB
GPR87
TLR9
DCUN1D1
SEMA5B
XRN1
WDR5B
LZTFL1
PARP14
P4HTM
SLC6A20
IL17RD
GRAMD1C
ROPN1
KLHL24
SIDT1
C3orf75
SNRK
QRICH1
PXK
CMTM6
RG9MTD1
SLC41A3
PIGX
SLC25A38
ULK4
OXSM
SLC35A5
TMEM45A
FEZF2
IFT57
FLJ10213
ANO10
DALRD3
SHQ1
MSL2
TBCCD1
FAIM
SLC25A36
ARL8B
SETD5
DPPA4
LEPREL1
TMEM39A
ZNF654
TMEM40
ABCF3
LSG1
ABHD10
CHDH
PARL
IL17RB
CDV3
MFN1
YEATS2
IFT122
NGLY1
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
TMEM111
EAF2
C3orf10
ZNF167
MYNN
LMOD3
EIF5A2
CLDND1
MUC13
SUCNR1
RAD18
SEMA3G
MCCC1
LXN
C3orf37
MRPS22
NIT2
KTELC1
BBX
KIF15
ADAMTS9
CCNL1
PLSCR2
PCBP4
PLSCR4
PCNP
HRASLS
MRPL47
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
ISY1
HHATL
HEG1
KIAA1257
CDGAP
NCEH1
IFT80
KIAA1407
WDR48
LRRN1
KIAA1524
SLC7A14
SRPRB
SELK
SENP2
GNB4
BPESC1
PROK2
EEFSEC
RNF123
NSUN3
CIDEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZFYVE20
KIF9
NFKBIZ
AZI2
ZMAT3
MTMR14
ATG3
MRPS25
CSRNP1
GORASP1
MFSD1
CCDC14
FNDC3B
P2RY12
CDCP1
CCDC71
NT5DC2
SLC26A6
TMEM108
CRELD1
CAMKV
TMEM43
OR5H6
OR5H2
ZXDC
ZBED2
LRRC2
FYCO1
ATP13A3
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC51
TBL1XR1
ZBBX
ZNF385D
LRRC31
CCDC48
NEK11
UBA5
HDAC11
MAP6D1
PHC3
C3orf36
ARL14
THOC7
NAT13
PIGZ
CEP63
CEP70
ABTB1
WDR82
TMEM22
TSEN2
GRIP2
OR5AC2
RTP3
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
C3orf20
ID2B
ARL6
ZIC4
ATRIP
ACAD11
IQCG
ATP13A4
FYTTD1
NICN1
CHCHD6
MON1A
C3orf26
HPS3
ARPM1
JAGN1
KBTBD8
SLC12A8
C3orf42
RETNLB
CCDC54
MGC2889
IL17RC
ABHD14B
LRCH3
MINA
GPR128
C3orf39
DIRC2
C3orf34
EAF1
DCLK3
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
UCN2
LOC90246
C3orf25
TMEM41A
ZNF502
BOC
FAM55C
RFT1
OXNAD1
SPSB4
ACPL2
ZBTB47
TMEM44
C3orf50
ACTR8
CAMK2N2
CMTM7
OSBPL10
OSBPL11
SLC25A26
ZNF501
C3orf24
LRRC58
LRRC3B
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1OS
GALNTL2
GPR62
CPNE4
CCDC58
KCNH8
DNAJC19
OTOL1
FAM3D
ZPLD1
LYZL4
KBTBD5
TRIM71
FAM131A
CD200R1
CHCHD4
ZDHHC19
CRYBG3
DCBLD2
LRRC15
FAM43A
TPRA1
TMEM42
UROC1
FAM194A
NUDT16
COL6A6
GRK7
TMEM207
METTL6
C3orf31
IL17RE
RTP1
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
RPL32P3
H1FOO
PISRT1
ASB14
TTC14
DTX3L
FAM19A4
SGOL1
C3orf48
EFHB
LOC151658
PPM1L
WDR49
LRRC34
CPNE9
DPPA2
CCDC80
BTLA
CCDC12
C3orf59
PPP4R2
C3orf21
ROPN1B
LOC152024
C3orf22
C3orf55
ZCWPW2
CMC1
NEK10
C3orf79
CCDC50
PYDC2
CCDC52
CMTM8
NUDT16P
CCDC13
LOC152217
LOC152225
FGD5
CIDECP
CNTN4
IGSF11
C3orf30
PARP15
C3orf57
DNAJB8
GPR156
XIRP1
RNF168
CHST13
PRICKLE2
KBTBD12
DHX36
HTR3C
DZIP1L
TTC21A
ALG1L
C3orf67
KCTD6
LIPH
ARL13B
DHFRL1
HTR3D
RPL22L1
OSTalpha
FBXO45
KLHDC8B
MUC20
GABRR3
PTPLB
STT3B
DNAH12
PDE12
FAM116A
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
CADM2
ZNF620
NAALADL2
ZDHHC23
LOC255025
TCTEX1D2
C3orf43
SDHALP1
COL29A1
GK5
PLCXD2
GCET2
UTS2D
ALS2CL
TMIE
LOC285194
SLC9A9
C3orf64
LOC285205
EPHA6
FBXW12
C3orf38
HTR3E
ZNF619
ZNF621
RABL3
IGSF10
C3orf33
CCDC66
SLC9A10
C3orf23
ZNF660
LOC285359
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
C3orf70
TPRG1
LOC285401
ILDR1
TRIM59
TRIM42
EIF4E3
RAB43
CCDC39
CCDC36
KY
C3orf35
GADL1
PRSS42
C3orf47
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
ZNF860
TMPRSS7
CD200R1L
PAQR9
DVWA
RTP2
OSTN
ATP13A5
SOX2OT
TXNDC6
WDR53
LNP1
CCDC37
NCRNA00119
TPRXL
LOC348840
NMNAT3
ZNF445
SPATA12
LHFPL4
C3orf77
C3orf62
TMEM110
LRRC33
PRSS45
AMIGO3
ZNF662
CDH29
C3orf54
IQCF2
IQCF5
MUSTN1
VGLL3
PRR23B
PRR23C
PLSCR5
C3orf16
LEKR1
TMEM212
VENTXP7
LOC401052
IQCF3
FLJ25363
C3orf72
LOC401093
FLJ42393
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR15B
MIR16-2
MIR191
MIR198
MIR26A1
FAM19A1
STX19
LOC440944
TMEM89
IQCF6
LOC440957
MIR425
ARGFX
SNORA6
SNORA7A
SNORD2
SNORA4
TMPPE
TMEM30C
ALG1L2
TXNRD3IT1
TMEM14E
COL6A4P2
SPINK8
C3orf71
LOC646498
C3orf65
PA2G4P4
LOC647309
IQCJ
SCARNA7
C3orf66
SNORA7B
SNORA58
SNORA81
SNORD19
FAM86D
SNORD66
SNORD69
MIR551B
MIR563
MIR564
MIR567
MIR568
MIR569
MIR570
GLT8D4
SDHALP2
FAM157A
FAM198A
CCR2
LOC729375
PRR23A
HESRG
LOC100009676
SNORD19B
LOC100125556
MIR922
MIR885
MIR944
EGOT
GHRLOS
LOC100128023
LOC100128164
C3orf74
LOC100128640
LOC100129354
LOC100129550
LOC100131551
ZNF717
SNAR-I
MIR1224
LOC100287227
FRG2C
LOC100302640

Arm-level results

Table 3. Get Full Table Arm-level significance table - 26 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1731 | 0.03 | -2.32 | 1 | 0.08 | 3.1 | 0.00339
1q | 1572 | 0.07 | 1.78 | 0.113 | 0.05 | -0.746 | 1
2p | 753 | 0.09 | 1.89 | 0.0963 | 0.02 | -3.84 | 1
2q | 1235 | 0.10 | 3.76 | 0.000367 | 0.03 | -2.98 | 1
3p | 853 | 0.04 | -1.42 | 1 | 0.74 | 57.9 | 0
3q | 917 | 0.08 | 0.987 | 0.451 | 0.20 | 11.5 | 0
4p | 366 | 0.02 | -4.9 | 1 | 0.08 | -0.27 | 1
4q | 865 | 0.02 | -4.16 | 1 | 0.07 | 0.301 | 1
5p | 207 | 0.31 | 17.9 | 0 | 0.01 | -5.17 | 1
5q | 1246 | 0.43 | 33.6 | 0 | 0.01 | -3.54 | 1
6p | 937 | 0.01 | -4.81 | 1 | 0.13 | 5.07 | 8.59e-07
6q | 692 | 0.01 | -4.98 | 1 | 0.20 | 10.7 | 0
7p | 508 | 0.26 | 14.8 | 0 | 0.00 | -5.32 | 1
7q | 1071 | 0.26 | 17.7 | 0 | 0.00 | -4.79 | 1
8p | 495 | 0.03 | -3.2 | 1 | 0.22 | 11.7 | 0
8q | 697 | 0.06 | -0.744 | 1 | 0.14 | 5.58 | 5.74e-08
9p | 343 | 0.02 | -4.29 | 1 | 0.18 | 8.25 | 6.19e-16
9q | 916 | 0.02 | -3.85 | 1 | 0.18 | 9.78 | 0
10p | 312 | 0.01 | -5.32 | 1 | 0.07 | -0.888 | 1
10q | 1050 | 0.01 | -4.94 | 1 | 0.11 | 4.08 | 8.97e-05
11p | 731 | 0.03 | -3.18 | 1 | 0.01 | -5.53 | 1
11q | 1279 | 0.03 | -2.5 | 1 | 0.02 | -3.97 | 1
12p | 484 | 0.15 | 5.97 | 7.72e-09 | 0.01 | -5.37 | 1
12q | 1162 | 0.15 | 8.29 | 8.66e-16 | 0.01 | -4.67 | 1
13q | 554 | 0.04 | -3.29 | 1 | 0.07 | -0.18 | 1
14q | 1144 | 0.02 | -3.39 | 1 | 0.33 | 23.6 | 0
15q | 1132 | 0.03 | -3.25 | 1 | 0.03 | -3.25 | 1
16p | 719 | 0.14 | 5.33 | 2.69e-07 | 0.00 | -5.57 | 1
16q | 562 | 0.12 | 3.47 | 0.000936 | 0.01 | -5.05 | 1
17p | 575 | 0.04 | -3.2 | 1 | 0.05 | -2.22 | 1
17q | 1321 | 0.04 | -1.8 | 1 | 0.03 | -2.72 | 1
18p | 117 | 0.04 | -3.32 | 1 | 0.11 | 1.92 | 0.0829
18q | 340 | 0.04 | -3.03 | 1 | 0.11 | 2.52 | 0.0189
19p | 870 | 0.05 | -1.53 | 1 | 0.01 | -4.96 | 1
19q | 1452 | 0.06 | 0.482 | 0.819 | 0.01 | -4.65 | 1
20p | 295 | 0.13 | 3.55 | 0.000754 | 0.01 | -5.29 | 1
20q | 627 | 0.13 | 4.46 | 1.98e-05 | 0.01 | -5.13 | 1
21q | 422 | 0.07 | -0.729 | 1 | 0.07 | -0.889 | 1
22q | 764 | 0.05 | -1.83 | 1 | 0.02 | -4.19 | 1

Methods & Data
Input

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/KIRC/1216689/2.GDAC_MergeDataFiles.Finished/KIRC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt

- Reference Genome = /xchip/cga/reference/gistic/hg18_with_miR_20091116.mat

- CNV Files = /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt

- Amplification Threshold = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 489 Input Tumor Samples.

Tumor Sample Names
TCGA-A3-3306-01A-01D-0858-01
TCGA-A3-3307-01A-01D-0858-01
TCGA-A3-3308-01A-02D-1322-01
TCGA-A3-3311-01A-02D-1322-01
TCGA-A3-3313-01A-02D-1322-01
TCGA-A3-3316-01A-01D-0858-01
TCGA-A3-3317-01A-02D-1322-01
TCGA-A3-3319-01A-02D-1322-01
TCGA-A3-3320-01A-02D-1322-01
TCGA-A3-3322-01A-02D-1322-01

Figure 3. Segmented copy number profiles in the input data

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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

- Maintainer = Dan DiCara

Copyright © 2011 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle