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Table 2 Genes with LOH or GOH mutations in multiple cancer samplesa

From: Massive interstitial copy-neutral loss-of-heterozygosity as evidence for cancer being a disease of the DNA-damage response

A. Genes in TSGene database with LOH occurrence in three or more cancer samplesb
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
B. Additional genes present in NCG4.0 database with LOH occurrence in three or more cancer samples b
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
C. Genes present in TSGene database with GOH occurrence in three or more cancer samples b
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
D. Additional genes present in NCG4.0 database with GOH occurrence in three or more cancer samples b
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
E. Additional genes present in Ensemble database with extensive LOH occurrences g
  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
F. Additional genes present in Ensemble database with extensive GOH occurrences g
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
  1. aSee Additional file 9: Table S7A-F for complete lists of genes with LOH or GOH occurrence
  2. bTSGene: Tumor Suppressor Gene Database, containing 860 genes; NCG4.0: Network of Cancer Genes, containing 2000 genes
  3. c Chromosome on which the indicated gene is located
  4. dLOH-containing genes present in both TSGene and NCG4.0 databases are only listed in Table 2A but not Table 2B
  5. eThe bold-fonted LOH occurrences represent Mm-to-mm conversions, and the non-bold-fonted LOH occurrences represent Mm-to-MM conversions. Where a sample contained more than one LOH, the number of LOHs is indicated inside parenthesis, either in bold font for LOHs yielding mm genotypes, or in non-bold font for LOHs yielding MM genotypes
  6. fGOH-containing genes present in both TSGene and NCG4.0 databases are only listed in Table 2C but not Table 2D
  7. gThe list includes LOH- or GOH-bearing genes in Ensemble database (GRCh37.p13), which contains 57,736 genes, that are not in TSGene or NCG4.0
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