Table 1 Prominent methods for cancer gene discovery by somatic exome analysis.
From: Challenges in identifying cancer genes by analysis of exome sequencing data
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 | |
OncodriverFM | SNV (WES) | Function | 28 (6,792) | 426 | 281/145 | 127/31 | |
OncodriverCL | SNV (WES) | Clustering | 28 (6,792) | 79 | 72/7 | 52/2 | |
ActiveDriver | SNV (WES) | Clustering (+phos-associated mutations) | 12 (3,205) | 106 | 74/32 | 30/5 | |
MuSIC | SNV (WES) | Combined (frequency, function, clustering, correlation with clinical phenotype) | 12 (3,205) | 182 | 141/41 | 81/3 | |
ALT-METHODS | |||||||
Gistic2.0—amplifications | CNV (SNP6) | Frequency | 34 (10,752) | 1,569 | 432/1137 | 53/21 | |
Gistic2.0—deletions | CNV (SNP6) | Frequency | 34 (10,752) | 6,897 | 671/6226 | 98/65 | |
IntOGen—CNV | CNV (SNP6) | Frequency+RNA expression | 16 (4,068) | 29 | 28/1 | 25/0 | |
Dendrix | SNV (WES) | Mutual exclusivity | 12 (3,281) | 17 | 28/2 | 23/1 | |
HotNet2 | SNV+CNV (WES+SNP6) | Network | 12 (3,281) | 147 | 96/51 | 43/0 | |
Fusion/translocations | FUS (RNA-seq) | Recurrent fusions | 13 (4,366) | 492 | 236/256 | 41/18 | |
TOTALS: | 42 | 8,871 | 906/7,967 | 175/153 | |||
