Table 2.
Genes with LOH or GOH mutations in multiple cancer samplesa
| 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 |
aSee Additional file 9: Table S7A-F for complete lists of genes with LOH or GOH occurrence
bTSGene: Tumor Suppressor Gene Database, containing 860 genes; NCG4.0: Network of Cancer Genes, containing 2000 genes
c Chromosome on which the indicated gene is located
dLOH-containing genes present in both TSGene and NCG4.0 databases are only listed in Table 2A but not Table 2B
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
fGOH-containing genes present in both TSGene and NCG4.0 databases are only listed in Table 2C but not Table 2D
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