Brain Lower Grade Glioma: 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 144 tumor samples used in this analysis: 20 significant arm-level results, 6 significant focal amplifications, and 20 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 6 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
7p11.2 | 1.6527e-24 | 1.6527e-24 | chr7:54942676-55107468 | 1
12q14.1 | 7.3432e-11 | 7.3432e-11 | chr12:58125396-58163019 | 6
1q32.1 | 1.4959e-07 | 1.4959e-07 | chr1:203710591-204630921 | 17
12p13.32 | 0.00045132 | 0.00045132 | chr12:3496687-4659158 | 9
4q12 | 0.018356 | 0.018356 | chr4:48068784-56491855 | 35
19q13.2 | 0.11431 | 0.11431 | chr19:40246077-40291097 | 1

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

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

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
MARCH9
AGAP2

Genes in Wide Peak

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

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

Genes
MDM4
ATP2B4
KISS1
PIK3C2B
REN
SNRPE
SOX13
ZC3H11A
LRRN2
PLEKHA6
LAX1
ETNK2
PPP1R15B
LOC127841
GOLT1A
LINC00303
ZBED6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
CCND2
FGF6
FGF23
RAD51AP1
PRMT8
PARP11
C12orf4
C12orf5
EFCAB4B

Genes in Wide Peak

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

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

Genes
KDR
KIT
PDGFRA
CHIC2
FIP1L1
SGCB
TEC
TXK
CLOCK
NMU
DCUN1D4
OCIAD1
TMEM165
DANCR
SLAIN2
USP46
RASL11B
SRD5A3
CWH43
LNX1
OCIAD2
SPATA18
PDCL2
LOC152578
SCFD2
GSX2
SLC10A4
FRYL
ZAR1
LRRC66
RPL21P44
SNORA26
ERVMER34-1
LOC100506462
MIR4449

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
LEUTX

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 - 20 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 | 6.9653e-37 | 6.9653e-37 | chr9:21991753-22448737 | 2
2q37.3 | 1.1914e-09 | 1.1914e-09 | chr2:233736245-243199373 | 106
19q13.43 | 3.3971e-10 | 1.5129e-08 | chr19:54037464-59128983 | 244
4q35.1 | 2.4912e-06 | 2.4912e-06 | chr4:169416144-191154276 | 99
10q25.3 | 0.0010176 | 0.0010176 | chr10:111624142-135534747 | 194
14q24.3 | 0.01465 | 0.014571 | chr14:58901446-80681882 | 185
11p15.5 | 0.020932 | 0.022809 | chr11:1-71303995 | 968
19q13.41 | 7.6233e-09 | 0.058439 | chr19:42881099-59128983 | 684
6p24.1 | 0.07614 | 0.07614 | chr6:1-15538684 | 91
22q13.31 | 0.076257 | 0.07614 | chr22:39424515-51304566 | 187
1p36.23 | 0.10174 | 0.10174 | chr1:1-28845930 | 471
1q44 | 0.10804 | 0.1081 | chr1:234036808-249250621 | 132
3q13.31 | 0.10804 | 0.1081 | chr3:89150943-138203274 | 308
6q12 | 0.13046 | 0.1275 | chr6:57206295-82464215 | 59
3q29 | 0.14672 | 0.14114 | chr3:194502405-198022430 | 50
11q14.1 | 0.18231 | 0.18746 | chr11:79148041-87846595 | 28
15q21.1 | 0.18592 | 0.18746 | chr15:1-65284370 | 471
17q25.3 | 0.19934 | 0.2067 | chr17:80379333-81195210 | 12
2p25.3 | 0.23562 | 0.24564 | chr2:1-243199373 | 1516
3p14.3 | 0.2449 | 0.24564 | chr3:1-198022430 | 1276

Genes in Wide Peak

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

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

Genes
CDKN2B
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
INPP5D
NDUFA10
SEPT2
NEU2
PDCD1
PPP1R7
SAG
SPP2
DGKD
PER2
LRRFIP1
HDAC4
FARP2
ARL4C
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SH3BP4
NGEF
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
ATG16L1
USP40
HJURP
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
TRPM8
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
MSL3P1
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
FLJ43879
MIR149
DNAJB3
LOC643387
PRR21
AQP12B
SCARNA6
SCARNA5
D2HGDH
LOC728323
PP14571
LOC100286922
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

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

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

Genes
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
A1BG
FCAR
FKBP1AP1
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR1
LAIR2
NDUFA3
CNOT3
PEG3
PRKCG
PTPRH
RPL28
RPS5
RPS9
AURKC
SYT5
TNNI3
TNNT1
ZNF8
ZNF17
MZF1
ZNF132
ZNF134
ZNF135
ZNF154
UBE2M
ZNF264
NCR1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
LILRB1
LILRB5
SLC27A5
LILRB4
LILRA1
LILRB3
LILRA3
LILRA2
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
ZNF324
PRPF31
CHMP2A
ZNF544
UBE2S
CCDC106
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
NLRP2
ZNF416
ZNF446
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
ZNF71
CACNG8
CACNG7
CACNG6
ZNF667
ZSCAN18
MGC2752
TSEN34
MBOAT7
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
ZNF419
ISOC2
ZNF552
ZNF671
ZNF606
BRSK1
SUV420H2
ZBTB45
ZNF587
FIZ1
GALP
ZNF628
KIR3DX1
ZNF551
ZNF835
NLRP12
MYADM
LENG9
RDH13
ZIM3
LENG8
KIR3DL3
ZNF837
ZNF543
COX6B2
OSCAR
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
TMC4
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF497
ZNF550
ZNF579
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
LOC284379
VSTM1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
ZNF773
LOC386758
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF772
TARM1
MIR371A
MIR372
MIR373
A1BG-AS1
DPRX
DUXA
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
LOC646862
SHISA7
ZNF814
MIMT1
MIR935
LOC100128252
LOC100128398
SGK110
LOC100131691
PEG3-AS1
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
ZNF865
MIR4754
MIR4752
MIR371B

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
AGA
SLC25A4
CASP3
CLCN3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
SCRG1
PALLD
FAM149A
FBXO8
DUX2
PDLIM3
AADAT
GALNT7
CLDN22
C4orf27
NEIL3
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
SH3RF1
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
CBR4
MGC45800
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
LOC100506085
LOC100506122
LOC100506229

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.3.

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

Genes
FGFR2
DUX4
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
BNIP3
CASP7
CTBP2
CYP2E1
DMBT1
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
PRLHR
GPR26
GRK5
HABP2
HMX2
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NRAP
OAT
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PTPRE
RGS10
SLC18A2
TCF7L2
TECTB
TIAL1
UROS
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
SMC3
BUB3
BAG3
FAM53B
DCLRE1A
SMNDC1
GLRX3
DPYSL4
TACC2
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
FAM175B
ATRNL1
C10orf137
DUX2
PDCD4
VENTX
CUZD1
CALY
CHST15
ACSL5
ZRANB1
TTC40
NSMCE4A
C10orf118
WDR11
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
GPAM
KIAA1598
FAM160B1
PLEKHA1
FAM204A
LHPP
IKZF5
ZDHHC6
MCMBP
C10orf81
C10orf88
LRRC27
GPR123
NKX6-2
AFAP1L2
KNDC1
MTG1
BBIP1
FANK1
SYCE1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
PDZD8
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CASC2
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
RBM20
LOC282997
LOC283038
LOC283089
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
FAM45A
FRG2B
SPRN
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
LOC100169752
MIR2110
MIR378C
MIR4297
MIR4295
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505933
FAM24B-CUZD1
MIR4680
MIR4483
MIR4682
MIR4484
MIR4681

Genes in Wide Peak

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

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

Genes
GPHN
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
ACTN1
ACYP1
ARG2
ZFP36L1
ENTPD5
DIO2
DLST
EIF2S1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GPX2
GSTZ1
HIF1A
HSPA2
LTBP2
MAX
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SIX6
PGF
PIGH
PPM1A
PPP2R5E
PRKCH
PSEN1
ABCD4
RAD51B
RTN1
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
ZBTB25
DPF3
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
NRXN3
AKAP5
SPTLC2
RGS6
KIAA0247
KIAA0586
KIAA0317
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
SYNE2
ANGEL1
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
DCAF4
PLEK2
MLH3
KCNH5
POMT2
COQ6
FCF1
RDH11
COX16
DACT1
ATP6V1D
JKAMP
DHRS7
SIX4
ZFYVE1
EXD2
VRTN
SYNJ2BP
SLC39A9
FLVCR2
C14orf118
YLPM1
C14orf162
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
TRMT5
ZNF410
NGB
RBM25
C14orf133
SMOC1
IRF2BPL
MPP5
C14orf135
GPR135
ZC2HC1C
C14orf169
C14orf45
SGPP1
SLIRP
DNAL1
RPS6KL1
SYT16
KIAA1737
PAPLN
CHURC1
C14orf43
LIN52
NEK9
IFT43
WDR89
C14orf149
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
RDH12
ADAM21P1
PPP1R36
SLC38A6
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
FAM71D
TMEM229B
TMEM30B
SAMD15
PROX2
ZDHHC22
TMED8
C14orf178
C14orf55
C14orf39
SNORD56B
VSX2
RAB15
HEATR4
FLJ22447
PLEKHD1
LINC00238
TEX21P
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
C14orf38
LOC731223
LOC100289511
MIR1260A
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4706
HIF1A-AS2

Genes in Wide Peak

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

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

Genes
CCND1
CARS
DDB2
EXT2
FANCF
HRAS
LMO1
LMO2
MEN1
NUP98
WT1
CREB3L1
hsa-mir-548k
hsa-mir-3164
hsa-mir-3163
hsa-mir-612
hsa-mir-194-2
hsa-mir-1237
hsa-mir-1908
hsa-mir-3162
hsa-mir-130a
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ACP2
ACTN3
ADM
ADRBK1
AP2A2
APLNR
ALDH3B1
ALDH3B2
AMPD3
APBB1
RHOG
ARHGAP1
ARL2
ARNTL
ART1
ASCL2
BAD
BBS1
BDNF
SERPING1
C11orf2
MRPL49
ZNHIT2
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAPN1
CAT
CCKBR
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CFL1
CHKA
CHRM1
CHRM4
TPP1
CNGA4
CNTF
COPB1
COX8A
CPT1A
CRY2
CST6
CSTF3
CTNND1
CTSD
CTSW
DDB1
DHCR7
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
MARK2
CTTN
ESRRA
F2
FAU
MS4A2
FEN1
FGF3
FGF4
FKBP2
FOLH1
FSHB
FTH1
GAS2
GIF
GNG3
GSTP1
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
SLC29A2
HPX
DNAJC4
IGF2
IGHMBP2
ILK
INCENP
INS
IRF7
CD82
KCNA4
KCNC1
KCNJ11
KCNQ1
KRTAP5-9
LDHA
LDHC
FADS1
FADS3
LRP4
LRP5
LSP1
LTBP3
CAPRIN1
MDK
SCGB2A1
SCGB2A2
MAP3K11
MUC2
MUC6
MYBPC3
MYOD1
NAP1L4
NDUFS3
NDUFV1
NDUFS8
NELL1
NUCB2
SLC22A18
SLC22A18AS
OSBP
OVOL1
P2RX3
PAX6
PC
PDE3B
PGA5
PIK3C2A
PLCB3
POLR2G
POLR2L
PPP1CA
PPP2R5B
PRG2
PSMA1
PSMC3
PSMD13
PTH
PTPRCAP
PTPRJ
PYGM
RAB3IL1
MAP4K2
RAD9A
RAG1
RAG2
RAPSN
RARRES3
RBM4
RCN1
RELA
DPF2
RNH1
ROM1
MRPL23
RPL27A
RPLP2
RPS6KB2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SIPA1
SLC1A2
SLC3A2
SMPD1
SPI1
SPTBN2
TRIM21
SSRP1
ST5
STIM1
STX3
STX5
ABCC8
TAF10
TALDO1
TCN1
TEAD1
TH
TSPAN4
TM7SF2
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TSG101
PHLDA2
TUB
SCGB1A1
VEGFB
BEST1
WEE1
SF1
ZFPL1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
FOSL1
BBOX1
PPFIBP2
PPFIA1
SLC43A1
IFITM1
DGKZ
CHST1
API5
MADD
OR6A2
DCHS1
EIF3F
CTSF
FADD
BANF1
RPS6KA4
BRSK2
AIP
SYT7
SART1
SLC6A5
FIBP
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
SLC22A6
SLC22A8
NRXN2
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
PITPNM1
RIN1
MTL5
MICAL2
CTR9
ATG13
CKAP5
TRIM66
FGF19
CCS
RCE1
NAALADL1
NR1H3
DPP3
TSPAN32
TSSC4
USH1C
KCNK7
HIPK3
PRMT3
RASGRP2
GLYAT
CDK2AP2
TCIRG1
RTN3
MRVI1
TRIM22
PRG3
IFITM3
SPON1
RBM14
CDC42EP2
EIF3M
NXF1
DEAF1
KAT5
IPO7
SSSCA1
HTATIP2
IFITM2
DRAP1
TRIM3
TAF6L
SCGB1D2
SCGB1D1
CELF1
OR5I1
OR7E14P
OR7E12P
LYVE1
YIF1A
EHD1
C11orf58
STIP1
CLP1
KCNQ1OT1
SF3B2
CCDC85B
B3GNT1
PLA2G16
PKP3
HPS5
PTGDR2
RRAS2
ZP1
SHANK2
KDM2A
SWAP70
ATG2A
GANAB
DTX4
DENND5A
NUP160
FNBP4
RRP8
SIRT3
CLCF1
OR52A1
FAM89B
SNHG1
ARFIP2
POLA2
FLRT1
MTCH2
FJX1
C11orf41
PRDX5
ABTB2
BRMS1
C11orf20
PAMR1
ZDHHC5
ATL3
DAK
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
PPP1R14B
OR10A3
FXC1
TIMM10
MYEOV
BSCL2
ELP4
DKK3
RBMXL2
PGAP2
PRPF19
MACROD1
SLC43A3
COMMD9
C11orf21
PACSIN3
TRPM5
SAC3D1
SNX15
RHOD
EFEMP2
UBQLN3
KCNK4
RNF141
UBXN1
APIP
TMX2
GAL
SUV420H1
HSD17B12
IGF2-AS1
TMEM216
BET1L
CEND1
SLC15A3
PHF21A
MS4A4A
WT1-AS
CABP2
TRMT112
TMEM138
CYB5R2
C11orf24
TRIM34
CDHR5
TOLLIP
ZDHHC13
WDR74
TRIM44
MS4A12
MRPL16
SDHAF2
SSH3
TMEM132A
HRASLS2
USP47
VPS37C
ANO1
TRIM68
NADSYN1
NAT10
CCDC87
PPP6R3
UEVLD
LIN7C
SLC35C1
TCP11L1
LGR4
PIDD
KCNQ1DN
SOX6
CDC42BPG
OTUB1
AMBRA1
PACS1
KBTBD4
PARVA
TTC17
SLC22A11
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
GPR137
PRDM11
CABP4
CHRNA10
SLC17A6
PNPLA2
CD248
CORO1B
SCYL1
CARNS1
SYT13
PHRF1
LRRC4C
SCUBE2
POLD4
KRTAP5-8
MS4A7
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
FAM111A
ANO3
MS4A6A
MS4A5
EPS8L2
KLC2
TUT1
MRPL11
STK33
C11orf95
CHID1
LRFN4
AHNAK
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
C11orf80
E2F8
SLC25A22
ZNF408
NAA40
QSER1
AGBL2
ZBTB3
CPSF7
PRR5L
ASRGL1
ATHL1
TMEM134
MUS81
INTS5
ZFP91
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
PTDSS2
MOB2
UNC93B1
SBF2
RAB1B
KIF18A
C11orf68
MS4A8B
FERMT3
TRPT1
RBM4B
FRMD8
FAM160A2
RNASEH2C
FAR1
BTBD10
EIF1AD
NUDT22
ARFGAP2
SYVN1
ACCS
MS4A14
SPRYD5
PTPN5
MICALCL
LGALS12
TRIM5
TNKS1BP1
GAL3ST3
NAV2
SYT8
TSPAN18
DKFZp761E198
CCDC34
SLC39A13
DEPDC7
SYT12
ACY3
GLYATL1
PRKCDBP
CDCA5
RPLP0P2
SAAL1
ODF3
SLC22A9
OSBPL5
C1QTNF4
PTPMT1
LRRC56
BATF2
SLC22A12
MRGPRD
MRGPRE
MRGPRF
ART5
CATSPER1
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
CYP2R1
DBX1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
LOC120824
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
C11orf94
C11orf84
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
GPHA2
NLRP6
NS3BP
METTL15
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
MRPL21
TPCN2
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
PPP1R32
ORAOV1
TIGD3
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
PELI3
LOC254100
EHBP1L1
SNX32
TSGA10IP
CNIH2
ZDHHC24
C11orf86
NUDT8
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
TMEM151A
OR51F1
SVIP
MRGPRX1
NPAS4
C11orf31
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
KRT8P41
LOC283104
CSNK2A1P
OR51V1
LOC283116
H19
C11orf85
SLC25A45
NEAT1
OR9G4
LOC283194
LINC00301
EFCAB4A
TMEM80
CCDC88B
TTC9C
SLC22A24
RCOR2
HARBI1
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
OR5F1
OR5AP2
ANKRD13D
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
MS4A10
OR10A2
OVCH2
TBX10
PDDC1
RTN4RL2
GALNTL4
B7H6
DKFZp779M0652
FAM111B
TMEM179B
TBC1D10C
MALAT1
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
KRTAP5-10
SLC22A25
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
SLC22A10
SPDYC
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
GPR152
DOC2GP
NAV2-AS4
HNRNPKP3
FAM180B
PCNXL3
FLJ42102
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
OR4C45
SCGB1D4
MIR129-2
MIR130A
MIR192
MIR194-2
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
LOC440040
LOC440041
SLC22A20
KRTAP5-7
KRTAP5-11
LOC441601
OR5B3
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
MS4A13
OR8U8
OR9G9
MIR483
SNORA3
SNORA52
BTBD18
PGA3
PGA4
LOC644656
RASSF10
FAM86C2P
TRIM64C
LOC646813
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD67
SNORA57
SNORD97
MIR610
MIR611
MIR612
INS-IGF2
MUC5B
LOC729013
LOC729799
METTL12
C11orf83
MIR675
LOC100126784
MRVI1-AS1
LOC100130348
LOC100130987
C11orf91
FAM99B
LOC100133161
MRPL23-AS1
MIR1908
MIR1237
MIR548K
MIR670
MIR3160-2
MIR3160-1
MIR3162
MIR4298
MIR4299
MTRNR2L8
MIR3654
MIR3664
MIR3680-1
LOC100500938
MIR210HG
LOC100506305
LOC100506540
DCDC5
LOC100507205
LOC100507300
LOC100507401
RBM14-RBM4
TMX2-CTNND1
SAA2-SAA4
ARL2-SNX15
HNRNPUL2-BSCL2
MIR4486
MIR4686
MIR4485
MIR4489
MIR4690
MIR3973
MIR4688
MIR4691
MIR4694
MIR1343
MIR4687
MIR4488

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.41.

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

Genes
BCL3
ERCC2
KLK2
PPP2R1A
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
A1BG
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
BAX
BCAT2
CEACAM1
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
CEACAM8
CKM
AP2S1
CLPTM1
CRX
DBP
DMPK
DMWD
EMP3
ERCC1
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
LIPE
BCAM
MYBPC2
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PEG3
PLAUR
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
RPS5
RPS9
RPS11
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SYT5
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
UBE2M
CYTH2
ZNF235
ZNF264
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
TOMM40
ZNF211
TRAPPC2P1
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
CLASRP
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
ZNF616
ZNF766
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
IRGQ
ZNF428
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
CADM4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
ZNF233
LILRA5
IGFL1
ZNF773
LOC386758
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
LOC390940
ZNF805
ZNF321P
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC646508
SBK2
LOC646862
PSG10P
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
SGK110
BSPH1
LOC100131691
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
SNAR-A14
ERVV-2
LOC100287177
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR642B
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
APOC4-APOC2
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.1.

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

Genes
IRF4
BMP6
BPHL
DSP
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
SSR1
TFAP2A
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
LY86
EEF1E1
RANBP9
ECI2
FARS2
RPP40
SIRT5
FAM50B
SLC35B3
TBC1D7
NRN1
NOL7
TMEM14C
GFOD1
ELOVL2
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
MUTED
CCDC90A
TXNDC5
TMEM14B
RIOK1
ADTRP
FOXQ1
HUS1B
SNRNP48
C6orf195
PIP5K1P1
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM217A
LOC285768
LY86-AS1
CAGE1
MYLK4
TUBB2B
C6orf52
PSMG4
DKFZP686I15217
C6orf201
ERVFRD-1
PPP1R3G
HULC
TMEM170B
SCARNA27
LOC100130275
LOC100130357
MIR3691
LOC100506207
LOC100506409
LOC100507194
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
MIR4645

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

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

Genes
EP300
PDGFB
MKL1
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
hsa-mir-33a
hsa-mir-1281
ACR
ACO2
ADSL
ARSA
ATF4
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
MCHR1
MGAT3
NAGA
NDUFA6
NHP2L1
PMM1
PPARA
MAPK11
RANGAP1
RPL3
MAPK12
SBF1
SREBF2
ST13
TCF20
TEF
UPK3A
WNT7B
CACNA1I
SYNGR1
GRAP2
CELSR1
PPP6R2
ZBED4
RBX1
SCO2
PKDREJ
TAB1
SLC25A17
NUP50
TOB2
RABL2B
PACSIN2
TNRC6B
GRAMD4
TTLL12
MLC1
ZC3H7B
KIAA0930
CBX7
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SNORD43
SMC1B
CSDC2
RRP7A
MCAT
PPPDE2
SGSM3
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
SMCR7L
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
SEPT3
PANX2
APOBEC3G
XPNPEP3
PARVG
CERK
EFCAB6
CENPM
ALG12
CRELD2
C22orf46
CCDC134
ADM2
SCUBE1
TRABD
PNPLA3
SELO
L3MBTL2
HDAC10
LDOC1L
POLDIP3
PHF5A
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
RPS19BP1
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
FAM83F
TNFRSF13C
RNU86
SNORD83A
SNORD83B
ENTHD1
DNAJB7
CHADL
MEI1
FAM109B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
APOBEC3H
WBP2NL
POLR3H
APOBEC3F
SERHL2
RNU12
ATP5L2
LOC284933
RPL23AP82
BK250D10.8
LOC339685
C22orf34
CHKB-CPT1B
LOC388906
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
MIR33A
LINC00229
FAM116B
PIM3
SHISA8
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100130899
LOC100132273
LOC100144603
LOC100271722
MIR1249
MIR1281
MIR3201
MIR3619
LOC100506472
LOC100506714
MIR4763
MIR4762
MIR4766
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
C1orf38
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
AHDC1
SMPDL3B
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
FH
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
ACTN2
ADSS
CHML
LYST
CHRM3
GNG4
HNRNPU
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
ZNF124
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZNF238
SDCCAG8
RBM34
OPN3
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
PPPDE1
SCCPDH
ARID4B
KIF26B
HEATR1
ZNF692
ERO1LB
FMN2
ZNF695
ZP4
TFB2M
GREM2
SMYD3
ZNF669
ZNF672
SH3BP5L
OR2G3
OR2G2
OR2C3
EFCAB2
ZNF496
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
EDARADD
SLC35F3
B3GALNT2
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
LOC339535
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR2W5
OR13G1
RPS7P5
LOC646627
SNORA14B
LOC731275
LOC100130331
LGALS8-AS1
MIR1537
LINC00184
MIR3123
MIR3124
MIR3916
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4677
MIR4671

Genes in Wide Peak

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

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

Genes
CBLB
GATA2
RPN1
TFG
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
ACPP
ADCY5
ADPRH
ALCAM
ATP6V1A
CASR
CD80
CD86
CD47
COL8A1
CPOX
CSTA
DRD3
EPHA3
EPHB1
GAP43
GOLGB1
GP9
GPR15
GSK3B
GTF2E1
HCLS1
HGD
ITGB5
KPNA1
LSAMP
MCM2
CD200
MYLK
NCK1
NDUFB4
PCCB
PLXNA1
PPP2R3A
PROS1
RHO
RPL24
RYK
SLC15A2
SLCO2A1
TF
TRH
UPK1B
UMPS
CNBP
ZNF80
ZNF148
RAB7A
SOX14
BFSP2
RUVBL1
B4GALT4
SNX4
NR1I2
MBD4
H1FX
KALRN
STXBP5L
GUCA1C
IQCB1
DZIP3
TOMM70A
COX17
CD96
STAG1
ST3GAL6
POLQ
ALDH1L1
PDIA5
TOPBP1
HHLA2
FSTL1
MRPL3
FILIP1L
MGLL
MRAS
COPG
MYH15
TMCC1
PLXND1
DNAJC13
C3orf27
ANAPC13
ARMC8
C3orf17
ABI3BP
PVRL3
ZBTB20
OR5K1
OR5H1
FAM162A
SEC22A
NPHP3
ATP2C1
ZBTB11
MORC1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
SEC61A1
PIK3R4
PODXL2
TRAT1
IMPG2
A4GNT
DBR1
CLDN18
TIMMDC1
PLA1A
AMOTL2
CCRL1
RAB6B
FBXO40
IL20RB
SEMA5B
WDR5B
PARP14
GRAMD1C
ROPN1
SIDT1
RG9MTD1
SLC41A3
SLC35A5
TMEM45A
IFT57
MSL2
DPPA4
TMEM39A
ABHD10
CDV3
IFT122
TBC1D23
WDR52
EAF2
CLDND1
MUC13
C3orf37
NIT2
POGLUT1
BBX
PCNP
SENP7
ISY1
HEG1
KIAA1257
ARHGAP31
KIAA1407
KIAA1524
SRPRB
EEFSEC
NSUN3
POPDC2
NFKBIZ
ATG3
CCDC14
TMEM108
OR5H6
OR5H2
ZXDC
ZBED2
CEP97
HSPBAP1
C3orf52
QTRTD1
CCDC48
NEK11
UBA5
C3orf36
NAA50
CEP63
ABTB1
TMEM22
OR5AC2
PARP9
ESYT3
ARL6
ACAD11
CHCHD6
C3orf26
SLC12A8
RETNLB
CCDC54
MINA
GPR128
DIRC2
C3orf15
PHLDB2
LOC90246
C3orf25
BOC
FAM55C
TXNRD3
OSBPL11
LRRC58
CPNE4
CCDC58
ZPLD1
CD200R1
DCBLD2
TPRA1
UROC1
NUDT16
COL6A6
FAM172BP
RPL32P3
H1FOO
DTX3L
LOC151658
DPPA2
CCDC80
BTLA
ROPN1B
C3orf22
SPICE1
NUDT16P1
LOC152225
IGSF11
C3orf30
PARP15
DNAJB8
GPR156
CHST13
KBTBD12
DZIP1L
ALG1L
ARL13B
DHFRL1
GABRR3
PTPLB
TIGIT
KIAA2018
ZDHHC23
LOC255025
NUP210P1
COL6A5
PLCXD2
GCET2
LSAMP-AS3
LOC285205
EPHA6
DNAJB8-AS1
RABL3
SLC9A10
LOC285359
ILDR1
RAB43
KY
LOC339874
H1FX-AS1
LOC344595
TMPRSS7
CD200R1L
NME9
LNP1
CCDC37
NPHP3-AS1
FLJ22763
FLJ25363
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIR198
STX19
ARGFX
TMEM30C
ALG1L2
TXNRD3NB
COL6A4P2
LOC653712
LINC00488
SNORA7B
SNORA58
MIR548A3
MIR567
MIR568
FAM86HP
LOC100009676
LOC100125556
LOC100129550
ZBTB20-AS1
MIR1280
MIR548I1
LOC100302640
MIR548G
MIR3921
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
LOC100507032
NPHP3-ACAD11
ISY1-RAB43
MIR4796
MIR4788
MIR4446

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q12.

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

Genes
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
BAI3
BCKDHB
COL9A1
COL12A1
COL19A1
COX7A2
EEF1A1
HTR1B
IMPG1
MYO6
RNY4
ELOVL4
TTK
PTP4A1
HMGN3
RIMS1
PHF3
MTO1
SENP6
SLC17A5
FILIP1
LGSN
PHIP
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
FAM135A
SMAP1
OGFRL1
LINC00472
KHDC1
SH3BGRL2
C6orf7
MB21D1
IRAK1BP1
B3GAT2
C6orf57
CD109
C6orf221
LCA5
KHDRBS2
DPPA5
EYS
GUSBP4
C6orf147
MIR30A
MIR30C2
OOEP
MCART3P
KHDC1L
LOC100288198
MIR4282
LOC100506804

Genes in Wide Peak

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

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

Genes
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
APOD
BDH1
DLG1
MFI2
MUC4
PAK2
PCYT1A
PPP1R2
RPL35A
KIAA0226
TNK2
NCBP2
ACAP2
UBXN7
PIGX
PIGZ
IQCG
FYTTD1
LRCH3
CEP19
LMLN
TM4SF19
ZDHHC19
XXYLT1
LOC152217
RNF168
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
TCTEX1D2
C3orf43
SDHAP1
WDR53
ANKRD18DP
LRRC33
LOC401109
MIR570
SDHAP2
FAM157A
MIR922
MFI2-AS1
LOC100507086
TM4SF19-TCTEX1D2
MIR4797

Genes in Wide Peak

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

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

Genes
PICALM
hsa-mir-4300
DLG2
PRCP
FZD4
OR7E2P
EED
ME3
PRSS23
RAB30
C11orf73
PCF11
SYTL2
TMEM126B
CREBZF
CCDC90B
CCDC81
TMEM135
TMEM126A
C11orf82
CCDC83
FAM181B
CCDC89
ANKRD42
SNORA70E
MIR4300
LOC100506233
LOC100506368

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

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

Genes
BUB1B
TCF12
FLJ27352
C15orf55
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
NBEAP1
BNIP2
CA12
CAPN3
CHRM5
CHRNA7
CKMT1B
CYP19A1
DUT
EPB42
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ONECUT1
IPW
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OAZ2
OCA2
PLCB2
PPIB
MAPK6
RAB27A
RAD51
RORA
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TPM1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
ALDH1A2
HERC2
HERC1
SNURF
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TRIP4
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
USP3
SLC12A6
BCL2L10
RASGRP1
SERF2
GNB5
ARPP19
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
CCNDBP1
DAPK2
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PYGO1
PLDN
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
SPG21
SPTBN5
CTDSPL2
KLF13
RAB8B
DUOX1
CSNK1G1
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
PPP1R14D
MTMR10
ZNF770
FLJ10038
HAUS2
FAM82A2
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
RFX7
SPATA5L1
CHAC1
NARG2
C15orf29
SLTM
SNX22
ATP8B4
WDR76
TMEM62
SEMA6D
PIF1
SPG11
ELL3
PLEKHO2
POLR2M
NIPA2
APH1B
TLN2
FAM96A
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LDHAL6B
CHST14
CASC4
LACTB
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
MGC15885
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
HMGN2P46
SLC24A5
PRTG
LOC283663
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
GLDN
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
LOC348120
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
GOLGA8E
OR4M2
OR4N3P
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR190A
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
HSP90AB4P
MIR626
MIR627
MIR628
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
LOC100128714
LOC100129387
LOC100130855
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1272
MIR1266
MIR1282
LOC100306975
MIR2116
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4509-3
MIR4712
MIR4715
TMCO5B
MYZAP

Genes in Wide Peak

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

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

Genes
FOXK2
TBCD
RAB40B
NARF
WDR45L
FN3K
C17orf62
FN3KRP
ZNF750
B3GNTL1
METRNL
FLJ43681

Genes in Wide Peak

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

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

Genes
ALK
ATIC
CHN1
CREB1
DNMT3A
ERCC3
ACSL3
MSH6
HOXD11
HOXD13
IDH1
MSH2
MYCN
NFE2L2
PAX3
PMS1
REL
PAX8
NCOA1
EML4
BCL11A
FEV
TTL
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-128-1
hsa-mir-663b
hsa-mir-1302-3
hsa-mir-4267
hsa-mir-4266
hsa-mir-4265
hsa-mir-3127
hsa-mir-4264
hsa-mir-1285-2
hsa-mir-3126
hsa-mir-216b
hsa-mir-559
hsa-mir-558
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
AAMP
ACADL
ACP1
ACTG2
ACVR1
ACVR2A
ACYP2
ADCY3
ADD2
ADRA2B
AGXT
ALPI
ALPP
ALPPL2
BIN1
ANXA4
AOX1
APOB
RHOB
RND3
ATP5G3
ATP6V1B1
KIF1A
AUP1
BARD1
BCS1L
BMPR2
BOK
ZFP36L2
BUB1
CACNB4
CAD
CALM2
CAPG
CASP8
CASP10
CCNT2
CD8A
CD8B
CD28
CENPA
CHRNA1
CHRND
CHRNG
CLK1
CNGA3
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
COX5B
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CTNNA2
CYP1B1
CYP27A1
DARS
DBI
DCTN1
DDX1
DES
DGUOK
LOC1720
DLX1
DLX2
DNAH6
DYNC1I2
DOK1
DPP4
DTNB
DTYMK
DUSP2
E2F6
EEF1B2
EGR4
EMX1
EN1
EPAS1
EPHA4
ERBB4
FABP1
FAP
EFEMP1
FHL2
FKBP1B
FN1
FOSL2
FRZB
FSHR
FTH1P3
GAD1
GALNT3
GBX2
GCG
GCKR
MSTN
GFPT1
GGCX
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GTF3C2
GYPC
HADHA
HADHB
HDLBP
HK2
HNMT
TLX2
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
HPCAL1
AGFG1
DNAJB2
HSPD1
HSPE1
FOXN2
HTR2B
ID2
SP110
IGFBP2
IGFBP5
IHH
IL1A
IL1B
IL1R1
IL1RN
CXCR1
CXCR2
CXCR2P1
INHA
INHBB
INPP1
INPP4A
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNF1
KCNJ3
KCNJ13
KCNK3
KCNS3
KHK
KIF3C
KIF5C
AFF3
LCT
LHCGR
LIMS1
LRP2
LTBP1
LY75
EPCAM
MXD1
MAL
MAP2
MAT2A
MATN3
MCM6
MDH1
MEIS1
MGAT5
MPV17
MYO1B
MTIF2
MYL1
MYO7B
NAB1
NCL
NEB
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPAS2
NPHP1
NPPC
NR4A2
ODC1
ORC2
ORC4
OTX1
REG3A
PCBP1
PDCD1
PDE1A
PDE6D
PDK1
PEX13
VIT
SERPINE2
PIGF
PLCL1
PLEK
PLGLB2
PLGLB1
POLR2D
POMC
POU3F3
PPM1B
PPM1G
PPP1CB
PPP1R7
PPP3R1
PRKCE
EIF2AK2
PROC
PSMD1
PTH2R
PTMA
PTPN4
PTPRN
RAB1A
RALB
RANBP2
RBMS1
REG1A
REG1B
REG1P
SNORD20
RPE
RPL31
RPL37A
RPS7
RPS27A
RRM2
RTKN
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SCTR
CCL20
SDC1
SRSF7
SFTPB
SIX3
SLC4A3
SLC1A4
SLC3A1
SLC8A1
SLC9A2
SLC11A1
SLC20A1
SNRPG
SOS1
SOX11
SP3
SP100
SPAST
SPP2
SPR
SPTBN1
SRD5A2
SSB
SSFA2
STAT1
STAT4
STRN
SULT1C2
ADAM17
TACR1
GCFC2
TFPI
TGFA
TIA1
TNFAIP6
TNP1
TNS1
TPO
TSN
TSSC1
TTN
TUBA4A
SUMO1
UCN
UGP2
VIL1
VRK2
VSNL1
WIPF1
WNT6
XDH
XPO1
XRCC5
ZAP70
ZNF2
ZNF142
SLC30A3
PXDN
ALMS1
MOGS
RNF103
IL1R2
MALL
CXCR4
FZD5
SCG2
DYSF
FZD7
SDPR
NCK2
DUSP11
CUL3
KLF11
MAP4K3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
VAMP8
MARCO
B3GALT1
ADAM23
SUCLG1
IL18RAP
IL1RL2
IL18R1
NRP2
CFLAR
ASAP2
PER2
ST3GAL5
SLC5A6
DDX18
EIF2B4
CDK5R2
KYNU
TAF1B
NAT8
NMI
RQCD1
COX7A2L
TMSB10
IL1RL1
LRRFIP1
STK17B
ITGB1BP1
GPR55
TRIP12
GTF3C3
PPIG
NRXN1
OTOF
CIAO1
TGFBRAP1
HS6ST1
CRIPT
ECEL1
MAP4K4
EIF2AK3
EIF4E2
ROCK2
CHST10
TP53I3
CIR1
MRPL33
BRE
PREPL
CYTIP
FEZ2
GCC2
TTLL4
SOCS5
EIF5B
GREB1
BZW1
USP34
LAPTM4A
HDAC4
RNF144A
SNX17
SERTAD2
MRPL19
ZEB2
FARP2
TLK1
SUPT7L
CD302
ARHGAP25
TANK
BCL2L11
FARSB
ABCB6
ACTR3
ACTR2
ARPC2
PREB
ACTR1B
ARL4C
LRPPRC
PDIA6
ABI2
CEBPZ
DHRS9
TXNDC9
MPHOSPH10
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
SMYD5
KBTBD10
MYCNOS
C1D
MERTK
UBE2E3
STK25
SEMA4F
CCT7
CCT4
GNLY
CDC42EP3
STAMBP
TGOLN2
MTX2
CGREF1
B3GNT2
USP39
TBR1
SIX2
MAP3K2
NCKAP1
VAMP5
MTHFD2
ARID5A
PROKR1
RAB10
EDAR
COPS8
GPR75
YWHAQ
IMMT
SNRNP27
GTF2A1L
STON1
RAPGEF4
EMILIN1
CAPN10
TBC1D8
RABL2A
GALNT5
NXPH2
GPR45
SP140
MGAT4A
GPN1
IKZF2
COBLL1
AAK1
FASTKD2
MAPRE3
PLA2R1
RAB3GAP1
RPIA
SLC4A1AP
EFR3B
SNRNP200
MYT1L
WDR43
LPIN1
CEP68
PASK
UBXN4
ATG4B
PSME4
EXOC6B
EHBP1
SATB2
CLASP1
OBSL1
PUM2
NCAPH
RHOQ
SF3B1
HAAO
TMEM131
R3HDM1
DNPEP
PSD4
WBP1
NTSR2
TMEFF2
SH3BP4
PRKD3
KCNE4
RASGRP3
NGEF
QPCT
GCA
VAX2
SNORD82
MOB4
POLR1A
CNRIP1
FAM98A
PNKD
UNC50
SNED1
GORASP2
SPATS2L
RAB11FIP5
GIGYF2
EPC2
TRAF3IP1
ABCA12
IFT172
ARL5A
HIBCH
PTPN18
CNNM4
CNNM3
IL36RN
SH3YL1
SNORD53
SNORD51
CNPPD1
STK36
IL36B
IL37
IL36A
SULT1C4
NFU1
ERLEC1
MMADHC
BMP10
ZNF638
STK39
HTRA2
TRIB2
CPS1-IT1
METTL5
LGALSL
OLA1
C2orf27A
GRHL1
TFCP2L1
ICOS
GMPPA
NRBP1
BAZ2B
SLC40A1
KCNIP3
EHD3
SMARCAL1
CD207
ITSN2
ANO7
ARHGEF4
PDE11A
TPRKB
FAHD2A
PRLH
WDPCP
MEMO1
THAP4
TRAPPC12
ASB3
INSIG2
CRIM1
ANKRD39
FAM178B
RNF181
MRPL30
DNAJC27
ANKMY1
KRCC1
MRPL35
C2orf28
PCYOX1
GULP1
REV1
NAT8B
SCLY
VPS54
NBAS
LIPT1
NOP58
DYNC2LI1
SF3B14
YPEL5
CHMP3
FKBP7
ASB1
CPSF3
CAB39
ZAK
LRP1B
PRKAG3
PPIL3
SNTG2
DNAJC10
ATAD2B
ETAA1
HEATR5B
CCDC93
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
AFTPH
MFSD6
TMEM214
RETSAT
INO80D
SEMA4C
C2orf18
C2orf42
TRMT61B
PID1
PTCD3
PLEKHB2
ATG16L1
FANCL
SRBD1
FIGN
ANKZF1
RIF1
USP40
MOB1A
STEAP3
ASXL2
ADI1
THNSL2
ACOXL
WDR33
HJURP
STRADB
C2orf56
HES6
ACCN4
C2orf29
NAGK
DOCK10
TTC27
SMPD4
TMEM127
PRPF40A
SLC30A6
IWS1
LIMS2
KANSL3
MREG
CCDC88A
WDR12
MBD5
KDM3A
ALLC
PECR
ARHGAP15
ZC3H15
CFC1
DNAH7
GKN1
IL36G
RPRM
CYP26B1
POLE4
KCNK12
UGGT1
KCMF1
DPYSL5
PNO1
STARD7
C2orf83
MFF
RPL23AP32
CXCR7
RNPEPL1
RTN4
TRIM54
PELI1
SLC39A10
TTC7A
SMEK2
SLC4A10
CYP20A1
SPC25
BIRC6
ERMN
KIDINS220
MTA3
HECW2
WDR35
MARCH4
WDFY1
NYAP2
DPP10
RDH14
EPB41L5
ALS2
ZDBF2
USP37
CWC22
ANKRD36B
G6PC2
SLC4A5
CTDSP1
NLRC4
MPP4
SLC5A7
NIF3L1
AGBL5
C2orf43
THADA
PCGEM1
RBKS
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
ATL2
ABCG5
ABCG8
RAB17
RNF25
HS1BP3
GMCL1
TTC31
ANAPC1
COPS7B
RMND5A
FNDC4
MARCH7
OBFC2A
PAPOLG
MRPS9
MRPS5
REEP1
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
SOWAHC
PLEKHA3
TRAK2
BOLL
COLEC11
PDCL3
TRPM8
ATG9A
C2orf49
MLPH
TMEM185B
FAM134A
CENPO
OR7E91P
GLB1L
C2orf47
SPAG16
CHPF
SAP130
GALNT14
SCRN3
CCDC121
FASTKD1
SMC6
GTDC1
CLIP4
IQCA1
ALS2CR8
TTC21B
CAMKMT
METTL8
GEMIN6
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
NOL10
ANKRD53
CSRNP3
PGAP1
LRRTM4
DCAF17
TUBA4B
MZT2B
YSK4
UXS1
FBXO11
ARMC9
COQ10B
SLC35F5
EFHD1
C2orf44
SPHKAP
WNT10A
SLC19A3
TSGA10
THSD7B
THUMPD2
TMEM177
KIAA1715
ILKAP
FAM49A
LMAN2L
LBH
TMEM163
ITM2C
TCF7L1
INO80B
AMMECR1L
CDCA7
WDR54
ZRANB3
RAB6C
WDR75
FAM161A
FAM176A
ANTXR1
POLR1B
ELMOD3
RGPD5
C2orf16
RHBDD1
CHCHD5
YIPF4
PRADC1
C2orf88
ING5
CCDC115
MKI67IP
C2orf40
ZNF512
ZC3H8
KIAA1841
ST6GAL2
IL1F10
DPY30
MCEE
LOXL3
ABHD1
PCGF1
DDX11L2
MFSD9
PLCD4
SFT2D3
CCDC142
ZNF514
FAM136A
TMEM87B
ATOH8
LOC84931
MGC16025
TANC1
EPT1
LBX2
PNPT1
KCNH7
FER1L5
MCFD2
ATP6V1E2
LOC90499
CCDC74A
LOC90784
DHX57
LOC91149
SESTD1
CCDC74B
PKDCC
ANKRD44
RSAD2
ZNF804A
TTC30A
DAPL1
CAPN13
TMEM169
DNER
CCDC164
IMP4
HNRPLL
MARS2
B3GNT7
NT5C1B
NEURL3
SP140L
SFXN5
ORMDL1
LIMS3
LINC00152
TUBA3E
CCDC104
TEX261
TUBA3D
STK11IP
FMNL2
CCDC85A
GALNT13
KLHL29
OSBPL6
NOSTRIN
DIRC1
WDR92
MOGAT1
LYPD1
MRPL53
AGAP1
TWIST2
PARD3B
RPL23AP7
PPP1R21
C2orf89
TMEM150A
NUP35
XIRP2
TYW5
NMS
LYG1
MITD1
DIS3L2
CMPK2
MBOAT2
CNTNAP5
TMEM18
FBLN7
NEU4
RBM45
C2orf73
TRIM43
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
CIB4
REG3G
RFTN2
C2orf63
PLEKHH2
AP1S3
C2orf76
SGPP2
ACVR1C
OSR1
TTC32
UBR3
KCTD18
ALS2CR12
ZNF513
SPATA3
LYPD6
LYPD6B
GALM
TMEM198
ZFAND2B
TMEM178
CPO
MDH1B
C2orf50
PQLC3
TMEM182
AHSA2
FBXO36
MTERFD2
CCDC148
C2orf65
MYO3B
TMEM37
UBE2F
DUSP19
CKAP2L
CBWD2
TEKT4
LOC150527
FLJ32063
LOC150568
SMYD1
C2orf15
LOC150622
OTOS
MYEOV2
OR6B3
COMMD1
PROM2
ANKAR
FBXO41
TTC30B
GPAT2
ITPRIPL1
LOC150776
WTH3DI
FAM117B
TCF23
LOC150935
FAM59B
PUS10
PKI55
LINC00309
LOC151009
SEPT10
C2orf67
PLB1
ZSWIM2
ZNF385B
LOC151171
LOC151174
ARL6IP6
METTL21A
CCNYL1
KLHL23
SULT1C2P1
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
LOC151300
GPBAR1
FAHD2B
MYADML
FAM84A
FAM82A1
GDF7
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
ASPRV1
WDSUB1
UPP2
LOC151534
GPR155
WDR69
LONRF2
CCDC138
GPR113
C2orf57
OXER1
FAM179A
FAM171B
C1QL2
UBXN2A
CLEC4F
DQX1
KCNG3
CYS1
FOXD4L1
PCDP1
VWA3B
CREG2
ALMS1P
TET3
GKN2
C2orf51
ANKRD23
APLF
PIKFYVE
KRTCAP3
LOC200726
TMEM17
SPRED2
TIGD1
LOC200772
FAM123C
LINC00116
C2orf69
HNRNPA3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
CCDC75
CERS6
METAP1D
LOC254128
LYG2
CCDC108
C2orf72
SH2D6
LOC284950
CCDC150
RNF149
LOC284998
LOC285000
FAM150B
CCDC141
LOC285033
LINC00486
C2orf61
LOC285074
LOC285084
CXXC11
LOC285103
DNAJC5G
IAH1
FLJ33534
CYP1B1-AS1
FAM126B
UNC80
RUFY4
PLGLA
RGPD4
DUSP28
STON1-GTF2A1L
SPOPL
MLK7-AS1
CYP27C1
ESPNL
C2orf70
C2orf53
LOC339788
LINC00299
LOC339803
C2orf74
LOC339807
LOC339822
MSGN1
C2orf55
FIGLA
NOTO
NCKAP5
FOXI3
EVX2
CDKL4
PRORSD1P
AOX2P
SH3RF3
GPR148
ECEL1P2
LRRTM1
GEN1
C2orf48
FONG
LOC348761
PFN4
LOC375190
LOC375196
ANKRD36
WASH2P
RBM43
LOC375295
CERKL
C2orf62
RBM44
AQP12A
ZC3H6
KLHL30
LOC386597
MFSD2B
C2orf71
LOC388942
LOC388946
LOC388948
TSPYL6
C2orf78
BOLA3
C2orf81
FUNDC2P2
C2orf68
SLC9A4
LOC389023
LOC389033
LOC389043
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
PTRHD1
SULT6B1
DYTN
LOC400940
LINC00487
FLJ12334
LOC400950
UNQ6975
EML6
FLJ30838
FLJ16341
LOC400958
PCBP1-AS1
PAIP2B
RGPD1
FLJ42351
LOC401010
DKFZp686O1327
LOC401022
FSIP2
C2orf66
ASB18
FLJ43879
VWC2L
MIR10B
MIR128-1
MIR149
MIR153-1
MIR216A
MIR217
MIR26B
C2orf27B
DNAJB3
ASTL
CAPN14
ACTR3BP2
LOC440894
LOC440895
LOC440900
LOC440905
LOC440910
POTEKP
LOC440925
LOC442028
SULT1C3
POTEE
COA5
PHOSPHO2
CHAC2
MIR375
DFNB59
LOC541471
LOC554201
ANKRD30BL
FBXO48
SNORA41
FAM110C
LOC643387
PRR21
LOC644838
GGT8P
ANKRD36BP2
LOC645949
LOC646324
LOC646736
LOC646743
PRSS56
LOC647012
C2orf84
TRIM43B
CFC1B
AQP12B
RGPD3
MZT2A
SNORA75
LOC654342
FAM138B
LOC654433
SCARNA6
SCARNA5
SNORD11
SNORD70
SNORD89
SNORD92
SNORD94
MIR558
MIR559
MIR561
RGPD8
LOC727982
D2HGDH
LOC728323
POTEF
LOC728537
LOC728730
PABPC1P2
LOC728819
LOC729121
ANKRD20A8P
LOC729234
RAD51AP2
RGPD6
DIRC3
DNAJC27-AS1
RGPD2
MORN2
LOC730811
RFX8
SNORD11B
SNORA36C
SNORA70B
MIR216B
MIR933
LOC100128590
OST4
LOC100129175
LOC100129726
LOC100129961
PP14571
LOC100130451
LOC100130452
LOC100130691
TMEM194B
LOC100131320
SP9
LOC100132215
CYP4F30P
LOC100133985
LOC100134259
LOC100144595
RNU4ATAC
DBIL5P2
SNAR-H
LOC100189589
LOC100216479
ARHGEF33
LOC100271832
LIMS3-LOC440895
LOC100286922
LOC100286979
LOC100287010
LOC100287216
LOC100288570
LIMS3L
LOC100288911
MIR1471
MIR1246
MIR548N
MIR1258
MIR1245A
MIR1301
MIR1244-1
LOC100302650
GPR75-ASB3
SNORA80B
ZEB2-AS1
MIR548F2
MIR663B
LOC100329109
SNORA70F
BOK-AS1
MIR3128
MIR4265
MIR1244-3
MIR1244-2
MIR4264
MIR3129
MIR3127
MIR4261
MIR3131
MIR4268
MIR4263
MIR3125
MIR3130-1
MIR4267
MIR4262
MIR3130-2
MIR4266
MIR3126
MIR2355
MIR3132
MIR4269
LOC100499194
MIR3606
MIR3682
MIR3679
LOC100505624
LOC100505695
LOC100505716
LOC100505876
LOC100505964
LOC100506054
LOC100506123
LOC100506124
LOC100506134
LOC100506274
LOC100506421
LOC100506474
LOC100506783
LOC100506866
LOC100507140
BOLA3-AS1
LOC100507334
LOC100507443
LOC100507600
LY75-CD302
RNF103-CHMP3
NT5C1B-RDH14
PHOSPHO2-KLHL23
HSPE1-MOB4
INO80B-WBP1
UBE2F-SCLY
MIR4436B1
MIR4772
MIR4779
MIR4783
MIR4439
MIR4782
MIR4437
MIR4765
MIR4776-1
MIR4757
MIR4777
MIR1245B
MIR4435-2
MIR4426
MIR4774
MIR2467
MIR4775
MIR4785
MIR4784
MIR4773-1
MIR4444-1
MIR4440
MIR4436A
MIR4786
MIR4773-2
MIR4434
MIR4780
MIR4778
MIR4429
MIR4776-2
MIR4432
MIR548AD
MIR4441
MIR4435-1
LOC100630918
LOC100861402

Genes in Wide Peak

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

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

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

Arm-level results

Table 3. Get Full Table Arm-level significance table - 20 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.05 | -0.431 | 0.996 | 0.29 | 11.9 | 0
1q | 1955 | 0.05 | -0.399 | 0.996 | 0.17 | 5.45 | 1.36e-07
2p | 924 | 0.01 | -2.52 | 0.996 | 0.01 | -2.16 | 0.998
2q | 1556 | 0.01 | -2.58 | 0.996 | 0.01 | -2.58 | 0.998
3p | 1062 | 0.01 | -2.51 | 0.996 | 0.03 | -1.45 | 0.998
3q | 1139 | 0.01 | -2.49 | 0.996 | 0.04 | -0.727 | 0.998
4p | 489 | 0.02 | -1.94 | 0.996 | 0.11 | 2.71 | 0.0102
4q | 1049 | 0.01 | -2.31 | 0.996 | 0.14 | 4.39 | 2.47e-05
5p | 270 | 0.01 | -2.35 | 0.996 | 0.08 | 1.61 | 0.132
5q | 1427 | 0.01 | -2.49 | 0.996 | 0.06 | -0.0382 | 0.998
6p | 1173 | 0.01 | -2.16 | 0.996 | 0.02 | -1.81 | 0.998
6q | 839 | 0.01 | -2.32 | 0.996 | 0.13 | 3.71 | 0.000374
7p | 641 | 0.20 | 7.8 | 6.06e-14 | 0.01 | -2.17 | 0.998
7q | 1277 | 0.30 | 12.7 | 0 | 0.01 | -2.02 | 0.998
8p | 580 | 0.09 | 1.97 | 0.188 | 0.02 | -1.59 | 0.998
8q | 859 | 0.15 | 5.17 | 1.55e-06 | 0.01 | -2.27 | 0.998
9p | 422 | 0.03 | -1.22 | 0.996 | 0.25 | 10.2 | 0
9q | 1113 | 0.01 | -2.12 | 0.996 | 0.04 | -0.706 | 0.998
10p | 409 | 0.14 | 4.21 | 0.000125 | 0.18 | 6.34 | 7.66e-10
10q | 1268 | 0.02 | -1.84 | 0.996 | 0.19 | 6.92 | 1.72e-11
11p | 862 | 0.04 | -0.818 | 0.996 | 0.11 | 2.72 | 0.0102
11q | 1515 | 0.07 | 0.695 | 0.996 | 0.01 | -2.1 | 0.998
12p | 575 | 0.06 | 0.14 | 0.996 | 0.03 | -1.29 | 0.998
12q | 1447 | 0.01 | -2.13 | 0.996 | 0.05 | -0.383 | 0.998
13q | 654 | 0.00 | -2.69 | 0.996 | 0.13 | 4.08 | 8.77e-05
14q | 1341 | 0.01 | -2.3 | 0.996 | 0.16 | 5.41 | 1.55e-07
15q | 1355 | 0.02 | -1.71 | 0.996 | 0.07 | 0.742 | 0.496
16p | 872 | 0.01 | -2.5 | 0.996 | 0.02 | -1.79 | 0.998
16q | 702 | 0.01 | -2.47 | 0.996 | 0.03 | -1.04 | 0.998
17p | 683 | 0.02 | -1.77 | 0.996 | 0.01 | -2.49 | 0.998
17q | 1592 | 0.03 | -1.16 | 0.996 | 0.00 | -2.9 | 0.998
18p | 143 | 0.03 | -1.18 | 0.996 | 0.09 | 1.71 | 0.114
18q | 446 | 0.02 | -1.95 | 0.996 | 0.10 | 2.34 | 0.0267
19p | 995 | 0.09 | 1.47 | 0.46 | 0.22 | 8.13 | 2.16e-15
19q | 1709 | 0.07 | 0.349 | 0.996 | 0.38 | 16.5 | 0
20p | 355 | 0.07 | 0.874 | 0.996 | 0.01 | -2 | 0.998
20q | 753 | 0.07 | 0.765 | 0.996 | 0.00 | -2.79 | 0.998
21q | 509 | 0.02 | -1.7 | 0.996 | 0.04 | -0.986 | 0.998
22q | 921 | 0.01 | -2.42 | 0.996 | 0.07 | 0.762 | 0.496

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.

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

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

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

Values

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

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LGG/1444823/2.GDAC_MergeDataFiles.Finished/LGG.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.30

- 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 144 Input Tumor Samples.

Tumor Sample Names
TCGA-CS-4938-01B-11D-1892-01
TCGA-CS-4941-01A-01D-1466-01
TCGA-CS-4942-01A-01D-1466-01
TCGA-CS-4943-01A-01D-1466-01
TCGA-CS-4944-01A-01D-1466-01
TCGA-CS-5390-01A-02D-1466-01
TCGA-CS-5393-01A-01D-1466-01
TCGA-CS-5394-01A-01D-1466-01
TCGA-CS-5395-01A-01D-1466-01
TCGA-CS-5396-01A-02D-1466-01

Figure 3. Segmented copy number profiles in the input data

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

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

Region Data

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

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

2. Descriptor: The genomic descriptor of that region.

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

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

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

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

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

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

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

Sample Data

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

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

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

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

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

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

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

Gistic Scores File (scores.gistic)

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

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

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

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

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

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

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

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

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

Broad Significance Results (broad_significance_results.txt)

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

Broad Values By Arm (broad_values_by_arm.txt)

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

All Data By Genes (all_data_by_genes.txt)

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

Broad Data By Genes (broad_data_by_genes.txt)

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

Focal Data By Genes (focal_data_by_genes.txt)

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

All Thresholded By Genes (all_thresholded.by_genes.txt)

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

Sample Cutoffs (sample_cutoffs.txt)

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

Focal Input To Gistic (focal_input.seg.txt)

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

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

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

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

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

GISTIC

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

CNV Description

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

Download Results

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

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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