Table 2 Genes with LOH or GOH mutations in multiple cancer samples^a

Chr ^c

Gene

Description

Samples with LOH sites ^e

6

AKAP12 ^d

A kinase (PRKA) anchor protein 12

Gastric1, Gastric3, Liver1

6

PARK2

Parkin RBR E3 ubiquitin protein ligase

Glioma3, Glioma5, Lung5

7

FBXL13

F-box and leucine-rich repeat protein 13

Glioma3, Liver1, Lung5

7

CUX1 ^d

Cut-like homeobox 1

Glioma5, Liver4, Lung5, Lung-Brain3

8

CSMD1 ^d

CUB and Sushi multiple domains 1

Gastric1, Glioma2 (2), Glioma3 (2), Liver1, Liver3, Liver5, Lung1, Lung5, Lung-Brain2 (1 + 1)

8

MFHAS1

Malignant fibrous histiocytoma amplified sequence 1

Gastric1, Liver4, Liver5

9

PPP2R4

Protein phosphatase 2A activator, regulatory subunit 4

Glioma1, Lung3, Lung5

9

PTPRD ^d

Protein tyrosine phosphatase, receptor type, D

Glioma1, Glioma3, Leukemia5, Liver1, Lung5 (3), Lung-Brain2

9

ROR2

Receptor tyrosine kinase-like orphan receptor 2

Gastric1 (3), Glioma3, Lung2

11

NUP98 ^d

Nucleoporin 98 kDa

Gastric3, Glioma3, Liver2, Lung-Brain1 (3)

12

CHFR

Checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase

Glioma3, Liver2, Lung-Brain4

14

EGLN3

Egl-9 family hypoxia-inducible factor 3

Lung5 (1 + 1), Lung-Brain4, Lung-Brain5

16

DNAJA3

DnaJ (Hsp40) homolog, subfamily A, member 3

Liver4, Lung1, Lung5

16

AXIN1 ^d

Axin 1

Glioma2, Liver1, Lung5

19

GLTSCR1 ^d

Glioma tumor suppressor candidate region gene 1

Glioma5, Lung5, Lung-Brain4

22

PRR5

Proline rich 5 (renal)

Glioma3, Liver3, Lung5

Chr ^c

Gene

Description

Samples with LOH sites ^e

1

SMG5

SMG5 Nonsense Mediated MRNA Decay Factor

Liver2, Lung1, Lung5 (3), Lung-Brain2, Lung-Brain4

1

KAZN

Kazrin, Periplakin Interacting Protein

Gastric3, Liver1, Lung5, Lung-Brain2

2

CTNNA2

Catenin (Cadherin-Associated Protein), Alpha 2

Lung1, Lung3, Lung5 (2 + 2)

2

DPP10

Dipeptidyl-Peptidase 10 (Non-Functional)

Gastric1, Glioma3, Glioma5

3

ERC2

ELKS/RAB6-Interacting/CAST Family Member 2

Gastric3, Glioma3, Lung2

4

ELOVL6

ELOVL Fatty Acid Elongase 6

Glioma3, Glioma4, Lung-Brain2

4

FSTL5

Follistatin-Like 5

Glioma2, Lung5, Lung-Brain2

5

AFF4

AF4/FMR2 Family, Member 4

Gastric1, Glioma3, Lung5 (2)

5

DMGDH

Dimethylglycine Dehydrogenase

Gastric1, Liver5 (2), Lung2, Lung-Brain4

7

HIP1

Huntingtin Interacting Protein 1

Gastric1, Glioma5, Liver1, Liver4, Lung2, Lung5, Lung-Brain2

7

CARD11

Caspase Recruitment Domain Family, Member 11

Glioma2, Glioma5, Lung-Brain5

8

RIMS2

regulating synaptic membrane exocytosis 2

Glioma3 (1 + 1), Lung5, Liver5

9

FNBP1

Formin Binding Protein 1

Gastric5, Glioma5, Liver2 (2)

10

SORCS1

Sortilin-Related VPS10 Domain Containing Receptor 1

Gastric1, Glioma3, Liver4

10

CTNNA3

Catenin (Cadherin-Associated Protein), Alpha 3

Gastric1 (2), Glioma2, Lung-Brain1, Lung-Brain2

10

PFKP

Phosphofructokinase, Platelet

Glioma3, Lung5, Lung-Brain4

10

TACC2

Transforming, acidic coiled-coil containing protein 2

Gastric1, Lung2, Leukemia3, Liver4

10

DLG5

Discs, Large Homolog 5 (Drosophila)

Glioma5, Liver1, Lung5 (2)

10

TET1

Tet Methylcytosine Dioxygenase 1

Glioma3, Lung5 (4), Lung-Brain2 (1 + 1)

11

NUMA1

Nuclear Mitotic Apparatus Protein 1

Glioma2, Glioma4, Lung2

11

PGAP2

Post-GPI attachment to proteins 2

Lung4, Lung5, Liver2

13

FREM2

FRAS1 Related Extracellular Matrix Protein 2

Liver1, Lung2, Lung-Brain2

13

ZMYM2

Zinc Finger, MYM-Type 2

Gastric1, Liver1, Lung2

16

SLC38A8

Solute Carrier Family 38, Member 8

Glioma3, Glioma5, Lung-Brain2

16

RBFOX1

RNA Binding Protein, Fox-1 Homolog (C. Elegans) 1

Glioma3, Liver4, Lung5 (6)

17

SEPT9

Septin 9

Glioma1, Liver1, Lung5 (2)

17

CDK12

Cyclin-Dependent Kinase 12

Glioma5, Liver3, Lung5 (1 + 2)

17

DNAH9

Dynein, axonemal, heavy chain 9

Glioma3, Lung5 (2), Lung-Brain1, Lung-Brain4

17

GAS7

Growth Arrest-Specific 7

Gastric3 (2), Glioma2, Glioma3, Glioma4, Liver2, Lung-Brain4

17

RPS6KB1

Ribosomal Protein S6 Kinase, 70 kDa, Polypeptide 1

Gastric1, Liver2 (3), Liver4, Lung5

17

WIPF2

WAS/WASL Interacting Protein Family, Member 2

Liver2, Lung4, Lung-Brain2

18

MBP

Myelin Basic Protein

Gastric1, Glioma4, Lung5

18

LAMA1

Laminin, Alpha 1

Glioma3, Liver4, Lung5

18

LDLRAD4

Low Density Lipoprotein Receptor Class A Domain Containing 4

Gastric4, Glioma2, Glioma5, Lung5 (2), Lung-Brain4

18

GREB1L

Growth Regulation By Estrogen In Breast Cancer-Like

Liver4, Lung5, Lung-Brain2

19

GLTSCR1

Glioma Tumor Suppressor Candidate Region Gene 1

Glioma5, Lung-Brain4, Lung5

20

ZSWIM3

Zinc Finger, SWIM-Type Containing 3

Gastric1, Glioma3, Glioma5, Liver1

22

TRIOBP

TRIO And F-Actin Binding Protein

Glioma5, Lung5 (3), Lung-Brain2

Chr ^c

Gene

Description

Samples with GOH sites

8

CSMD1 ^f

CUB and Sushi multiple domains 1

Gastric3 (2), Gastric4, Glioma3 (2), Lung5 (2)

9

PTPRD ^f

Protein Tyrosine Phosphatase, Receptor Type, D

Glioma1, Liver1, Lung5, Lung-Brain5

9

DAPK1

Death-Associated Protein Kinase 1

Glioma4, Liver1, Lung1

9

ROR2

Receptor Tyrosine Kinase-Like Orphan Receptor

Gastric5, Glioma5, Lung5 (2)

11

ST5

Suppression of Tumorigenicity 5

Glioma3, Glioma4, Glioma5

12

CHFR

Checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase

Gastric1, Glioma5, Lung5 (3), Lung-Brain3

16

CDH1 ^f

Cadherin 1, Type 1, E-Cadherin (Epithelial)

Gastric2 (3), Lung5 (3), Lung-Brain4

22

CHEK2 ^f

Checkpoint kinase 2

Glioma3, Lung2, Lung5

Chr ^c

Gene

Description

Samples with GOH sites

1

KAZN

Kazrin, Periplakin Interacting Protein

Gastric4, Glioma4, Lung5 (4)

1

FMN2

Formin 2

Lung5, Liver1, Lung-Brain1

1

NLRP3

NLR Family, Pyrin Domain Containing 3

Glioma3 (3), Liver1 (2), Lung5

4

FSTL5

Follistatin-Like 5

Liver4, Lung2, Lung5 (2)

5

PCDHGC5

Protocadherin Gamma Subfamily C, 5

Liver2, Lung2, Lung5 (2)

7

KMT2C

Lysine (K)-Specific Methyltransferase 2C

Gastric2, Gastric5 (2), Leukemia4, Liver2, Liver4

9

FNBP1

Formin Binding Protein 1

Glioma5, Lung5, Lung-Brain1

9

TRPM6

Transient Receptor Potential Cation Channel, Subfamily M, Member 6

Glioma3, Liver4, Lung5

10

CTNNA3

Catenin (Cadherin-Associated Protein), Alpha 3

Glioma3, Liver1, Lung2, Lung5

10

PFKP

Phosphofructokinase, Platelet

Gastric1, Glioma1, Lung5

12

SP1

Sp1 Transcription Factor

Glioma3, Glioma4, Lung4 (2)

12

KDM2B

Lysine (K)-specific demethylase 2B

Glioma5, Lung5, Lung-Brain4

12

ERC1

ELKS/RAB6-Interacting/CAST Family Member 1

Gastric1, Lung2, Lung5, Liver5

13

ATP11A

ATPase, class VI, type 11A

Glioma3, Liver1, Liver2

16

CNOT1

CCR4-NOT Transcription Complex, Subunit 1

Glioma2, Glioma3, Lung5

16

SNX29

Sorting nexin 29

Gastric5, Lung5 (3), Liver1, Lung-Brain2

16

RBFOX1

RNA Binding Protein, Fox-1 Homolog (C. Elegans) 1

Gastric2, Glioma3 (4), Liver1 (2), Liver2, Lung4, Lung5 (3)

17

SEPT9

Septin 9

Liver1, Lung3, Lung5

17

RPS6KB1

Ribosomal Protein S6 Kinase, 70 kDa, Polypeptide 1

Gastric3, Glioma4, Lung-Brain3

17

TRIM37

Tripartite Motif Containing 37

Glioma1 (2), Glioma3, Glioma4

17

ITGAE

Integrin, Alpha E (Antigen CD103, Human Mucosal Lymphocyte Antigen 1; Alpha Polypeptide)

Glioma3, Glioma4 (2), Glioma5, Lung5 (2)

18

GREB1L

Growth Regulation By Estrogen In Breast Cancer-Like

Lung2, Lung4, Lung-Brain2 (2)

19

PTPRS

Protein tyrosine phosphatase, receptor type, S

Gastric1, Glioma5, Lung4

22

TUBA8

Tubulin, alpha 8

Gastric5, Glioma3, Lung5

Gene

Description

Samples with LOH sites ^e

2

MTA3

Metastasis associated 1 family, member 3 [Source:HGNC Symbol;Acc:23784]

Gastric1, Lung-Brain2, Lung3 (2), Liver2, Lung-Brain3

3

EIF2B5

Eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82 kDa [Source:HGNC Symbol;Acc:3261]

Glioma3, Lung5 (8), Liver5, Leukemia1

4

SMIM14

Small integral membrane protein 14 [Source:HGNC Symbol;Acc:27,321]

Liver2, Lung-Brain5, Glioma3, Leukemia5, Lung1 (2)

6

ATXN1

Ataxin 1 [Source:HGNC Symbol;Acc:10548]

Glioma5, Lung4, Lung5, Liver1, Lung-Brain5

6

RP11-146I2.1

Not Applicable

Glioma3, Lung3, Lung5, Liver2, Lung-Brain4

7

COL26A1

Collagen, type XXVI, alpha 1 [Source:HGNC Symbol;Acc:18038]

Gastric1, Lung1, Lung2, Liver1, Lung-Brain1

7

TYW1B

tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:33908]

Gastric1, Glioma3, Glioma5, Lung1, Lung5

8

LOXL2

Lysyl oxidase-like 2 [Source:HGNC Symbol;Acc:6666]

Liver2 (2), Glioma3, Glioma4, Liver1, Liver3

8

RP11-124B13.1

Not Applicable

Gastric1, Glioma1, Glioma3, Lung2, Liver2

9

DMRT1

Doublesex and mab-3 related transcription factor 1 [Source:HGNC Symbol;Acc:2934]

Glioma5, Gastric3, Lung5, Glioma1, Gastric1, Lung-Brain2

9

ODF2

Outer dense fiber of sperm tails 2 [Source:HGNC Symbol;Acc:8114]

Lung-Brain2, Lung5 (2), Glioma5, Lung4, Lung-Brain4, Liver4

10

CAMK1D

Calcium/calmodulin-dependent protein kinase ID [Source:HGNC Symbol;Acc:19341]

Lung5 (4), Liver5, Glioma5 (2), Leukemia4, Lung-Brain4, Liver1 (1 + 1), Glioma3

10

FRMD4A

FERM domain containing 4A [Source:HGNC Symbol;Acc:25491]

Lung5 (2 + 8), Glioma5, Glioma3, Gastric1, Liver5

11

TMEM135

Transmembrane protein 135 [Source:HGNC Symbol;Acc:26167]

Gastric1, Glioma3, Glioma4, Glioma5, Lung3

14

KLC1

Kinesin light chain 1 [Source:HGNC Symbol;Acc:6387]

Liver5, Lung-Brain2, Gastric1, Glioma3, Liver2, Lung5

16

ABCC1

ATP-binding cassette, sub-family C (CFTR/MRP), member 1 [Source:HGNC Symbol;Acc:51]

Lung5 (2 + 2), Lung1, Liver2, Lung-Brain2, Lung-Brain1

16

C16orf45

Chromosome 16 open reading frame 45 [Source:HGNC Symbol;Acc:19213]

Gastric1, Glioma3, Lung2, Lung5, Lung-Brain5

17

NMT1

N-myristoyltransferase 1 [Source:HGNC Symbol;Acc:7857]

Glioma5, Liver4, Lung5 (2), Gastric1 (2), Glioma3,

17

PITPNC1

Phosphatidylinositol transfer protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:21045]

Gastric1, Gastric4, Glioma3, Glioma5, Lung2

17

RAP1GAP2

RAP1 GTPase activating protein 2 [Source:HGNC Symbol;Acc:29176]

Liver2 (2), Glioma5 (2), Lung-Brain2 (2 + 1), Gastric5, Gastric1, Lung4, Lung5

17

RBFOX3

RNA binding protein, fox-1 homolog (C. elegans) 3 [Source:HGNC Symbol;Acc:27097]

Glioma3, Glioma5, Liver3, Lung-Brain4 (1 + 3), Lung-Brain5

18

DLGAP1

Discs, large (Drosophila) homolog-associated protein 1 [Source:HGNC Symbol;Acc:2905]

Lung-Brain2, Lung5 (2 + 1), Gastric4, Gastric1, Lung-Brain2, Glioma3

19

INSR

Insulin receptor [Source:HGNC Symbol;Acc:6091]

Liver3, Liver4, Lung2, Lung5 (1 + 1), Gastric1 (2)

19

SIPA1L3

Signal-induced proliferation-associated 1 like 3 [Source:HGNC Symbol;Acc:23801]

Glioma3, Lung-Brain2, Liver2, Lung5, Glioma3, Lung5

19

TDRD12

Tudor domain containing 12 [Source:HGNC Symbol;Acc:25044]

Lung-Brain1, Glioma5, Lung1, Glioma5, Glioma2, Liver2

19

GNG7

Guanine nucleotide binding protein (G protein), gamma 7 [Source:HGNC Symbol;Acc:4410]

Lung5 (1 + 7), Lung-Brain4 (3)

22

SYN3

Synapsin III [Source:HGNC Symbol;Acc:11496]

Lung3, Lung5, Lung-Brain4, Glioma3 (1 + 2), Glioma5

Chr ^c

Gene

Description

Samples with GOH sites ^e

1

RPRD2

Regulation of nuclear pre-mRNA domain containing 2 [Source:HGNC Symbol;Acc:29039]

Gastric2, Glioma3, Glioma4, Glioma5 (2), Liver1, Lung4, Lung5

1

CLSTN1

Calsyntenin 1 [Source:HGNC Symbol;Acc:17447]

Gastric5, Lung2, Lung5, Lung-Brain2, Lung-Brain4

1

KIF26B

Kinesin family member 26B [Source:HGNC Symbol;Acc:25484]

Liver3, Glioma3, Glioma5 (2), Lung5 (3), Gastric1

1

GON4L

Gon-4-like (C. elegans) [Source:HGNC Symbol;Acc:25973]

Lung2 (2), Lung5 (2), Glioma4 (2), Lung-Brain1, Gastric4

1

NMNAT2

Calsyntenin 1 [Source:HGNC Symbol;Acc:17447]

Glioma5, Lung1, Lung5, Liver1, Lung-Brain1

2

FAM178B

Family with sequence similarity 178, member B [Source:HGNC Symbol;Acc:28036]

Gastric5, Glioma3, Liver3, Liver5, Lung3

2

MTA3

Metastasis associated 1 family, member 3 [Source:HGNC Symbol;Acc:23784]

Glioma1, Glioma2, Glioma4, Liver1, Lung-Brain3

3

EIF2B5

Eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82 kDa [Source:HGNC Symbol;Acc:3261]

Gastric3, Glioma5 (3), Lung5, Lung-Brain2, Lung-Brain4

4

AFAP1

Actin filament associated protein 1 [Source:HGNC Symbol;Acc:24017]

Glioma3 (2), Liver1, Lung5 (6), Leukemia4, Liver4, Glioma5

5

PDZD2

PDZ domain containing 2 [Source:HGNC Symbol;Acc:18486]

Lung2, Lung5 (4), Glioma1, Gastric2, Glioma3 (2)

5

PCDHGA1

Protocadherin gamma subfamily A, 1 [Source:HGNC Symbol;Acc:8696]

Glioma3, Glioma5, Liver2, Lung2, Lung5 (2)

7

CALN1

Calneuron 1 [Source:HGNC Symbol;Acc:13248]

Glioma3, Glioma3, Lung2 (5), Lung4, Lung5 (2)

7

KMT2C

Protocadherin gamma subfamily A, 1 [Source:HGNC Symbol;Acc:8696]

Gastric2, Gastric5 (2), Liver2, Liver4, Leukemia4

7

TYW1

tRNA-yW synthesizing protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25598]

Glioma3, Glioma5 (3), Liver1, Lung-Brain1 (5)

8

PSD3

Pleckstrin and Sec7 domain containing 3 [Source:HGNC Symbol;Acc:19093]

Lung3, Lung5 (9)

10

CAMK1D

Calcium/calmodulin-dependent protein kinase ID [Source:HGNC Symbol;Acc:19341]

Glioma3, Liver1, Lung3, Lung4 (5), Lung5 (5), Glioma4

11

SHANK2

SH3 and multiple ankyrin repeat domains 2 [Source:HGNC Symbol;Acc:14295]

Glioma3, Lung3, Lung5, Liver1, Liver5

12

MPHOSPH9

M-phase phosphoprotein 9 [Source:HGNC Symbol;Acc:7215]

Leukemia3, Lung-Brain5, Lung2, Lung4 (2), Lung5, Glioma4

17

STX8

Syntaxin 8 [Source:HGNC Symbol;Acc:11443]

Glioma3, Glioma4 (2), Lung2, Lung4 (2), Leukemia2

17

USP43

SH3 and multiple ankyrin repeat domains 2 [Source:HGNC Symbol;Acc:14295]

Liver1, Lung2, Lung5, Glioma5, Lung-Brain4

19

INSR

Insulin receptor [Source:HGNC Symbol;Acc:6091]

Liver4, Glioma3 (2), Glioma4 (2), Lung-Brain3, Lung5 (3)

19

CTC-490E21.12

Not Applicable

Gastric2, Gastric3, Glioma4, Glioma5, Lung1

19

CTC-525D6.1

Not Applicable

Gastric2 (4), Lung5 (8)

19

SAE1

SUMO1 activating enzyme subunit 1 [Source:HGNC Symbol;Acc:30660]

Glioma3, Lung2, Lung4, Lung5, Liver1

20

ATP9A

ATPase, class II, type 9A [Source:HGNC Symbol;Acc:13540]

Liver1 (3), Glioma4, Gastric3, Lung4, Lung5 (2)

22

LARGE

Like-glycosyltransferase [Source:HGNC Symbol;Acc:6511]

Liver1 (2), Lung1, Lung2, Leukemia5 (2), Glioma5 (3), Gastric5 (2)

22

SGSM1

Lysine (K)-specific methyltransferase 2C [Source:HGNC Symbol;Acc:13726]

Gastric2, Glioma3, Leukemia5, Lung-Brain2 (2), Lung-Brain3