Table 1. Prominent methods for cancer gene discovery by somatic exome analysis.
| Method | Data type (method)* | Analysis principle | No. tissue cohorts (no. patients) | Total genes identified | Genes non-unique/unique to method | CGC non-unique/unique to method† | Ref. |
|---|---|---|---|---|---|---|---|
| MAIN-METHODS | |||||||
| MutSig Suite | SNV (WES) | Combined (frequency, function, clustering) | 21 (4,742) | 260 | 191/69 | 98/7 | 9,18 |
| OncodriverFM | SNV (WES) | Function | 28 (6,792) | 426 | 281/145 | 127/31 | 29 |
| OncodriverCL | SNV (WES) | Clustering | 28 (6,792) | 79 | 72/7 | 52/2 | 30 |
| ActiveDriver | SNV (WES) | Clustering (+phos-associated mutations) | 12 (3,205) | 106 | 74/32 | 30/5 | 15,17 |
| MuSIC | SNV (WES) | Combined (frequency, function, clustering, correlation with clinical phenotype) | 12 (3,205) | 182 | 141/41 | 81/3 | 13,15 |
| ALT-METHODS | |||||||
| Gistic2.0—amplifications | CNV (SNP6) | Frequency | 34 (10,752) | 1,569 | 432/1137 | 53/21 | 14 |
| Gistic2.0—deletions | CNV (SNP6) | Frequency | 34 (10,752) | 6,897 | 671/6226 | 98/65 | 14 |
| IntOGen—CNV | CNV (SNP6) | Frequency+RNA expression | 16 (4,068) | 29 | 28/1 | 25/0 | 16 |
| Dendrix | SNV (WES) | Mutual exclusivity | 12 (3,281) | 17 | 28/2 | 23/1 | 32 |
| HotNet2 | SNV+CNV (WES+SNP6) | Network | 12 (3,281) | 147 | 96/51 | 43/0 | 31 |
| Fusion/translocations | FUS (RNA-seq) | Recurrent fusions | 13 (4,366) | 492 | 236/256 | 41/18 | 33 |
| TOTALS: | 42 | 8,871 | 906/7,967 | 175/153 | |||
*Data types: CNV, copy number variant; FUS, gene fusion; SNV, single nucleotide variant. Methods: RNA-seq, RNA sequencing; SNP6, affymetrix SNP array; WES, whole-exome sequencing.
†Number of genes identified within the CGC-positive reference set.