Table 1. Cancer genome sequencing studies.
| Tumour type | Genes sequenced | Mutations | Mutated genes | Non-syn. mutations per tumour | Known cancer genes (%)* | New cancer-associated genes (%)* | Predominant mutation type | Refs |
|---|---|---|---|---|---|---|---|---|
| Exon sequencing | ||||||||
| Breast (n = 11) | 18,191 | 1,243 | 1,137 | 101 | TP53 (33%), PIK3CA (17%) | CHD5 (3%) | CG→TA (35%), CG→GC (29%) | 101,102 |
| Colorectal (n = 11) | 18,191 | 942 | 848 | 77 | APC (67%), TP53 (50%), KRAS (46%) | TGM3 (8.3%) | CG→TA (59%) | 101,102 |
| Colorectal (MSI n = 1, MSS n = 1) | Exome capture | MSI = 1,304, MSS = 198 | NA | MSI = 359, MSS = 45 | BRAF (∼10%), TP53 (∼50%) | NA | CG→TA (∼35%) | 103 |
| Pancreatic (n = 24) | 20,661 | 1,163 | 1,007 | 48 | KRAS (99%), TP53 (86%), SMAD4 (26%), CDKN2A (24%) | NA | CG→TA (54%) | 104 |
| Pancreatic neuroendocrine (n = 10) | ∼18,000 | 157 | 149 | 16 | MEN1 (45%) | DAXX (24%), ATRX (19%) | CG→TA (42%), CG→GC (18%) | 105 |
| Glioblastoma (n = 21) | 20,661 | 748 | 685 | 47 | CDKN2A (50%), TP53 (40%), EGFR (37%) | IDH1 (12%) | CG→TA (64%) | 106 |
| Lung (n = 188) | 623 | 1,013 | 348‡ | NA | TP53 (35%), KRAS (32%), EGFR (18%) | LRP1B (9%), PTPRD (5%) | CG→AT (43% versus 13%)§ | 29 |
| Clear cell RCC (n = 101) | 3,544 | 515 | 319 | NA | VHL (55%) | SETD2 (3%), KDM5C (3%) | CG→TA (∼40%) | 107 |
| Clear cell RCC (n = 7) | 20,921 | 156 | 108 | 16 | NA | PBRM1 (41%) | CG→TA (31%), AT→GC (22%) | 108 |
| Ovarian clear cell (n = 8) | ∼18,000 | 258 | 253 | 20‖ | PIK3CA (40%), PPP2R1A (7%), KRAS (5%) | ARID1A (57%) | CG→TA (49%) | 109 |
| Medulloblastoma (childhood) (n = 21)¶ | 21,039 | 202 | 196 | 11 | PTCH1 (30%), TP53 (7.6%) | MLL2 (10.6%), MLL3 (2%) | CG→TA (55%), CG→AT (21%) | 110 |
| Whole-genome sequencing | ||||||||
| Acute myeloid leukaemia (n = 1) | NA | 500–1,000 | 10 | 10 | NPM1 (28%), FLT3 (24%) | DNMT3A (22%) | NA | 41,111 |
| Acute myeloid leukaemia (n = 1) | NA | ∼750 | 64# | 12 | FLT3 (27%), NPM1 (23%), NRAS (11%) | IDH1 (16%) | NA | 112 |
| Lobular breast (n = 1) | NA | NA | NA | 32 | CDH1 (∼60%) | HAUS3 (∼1%) | CG→TA (54%) | 113 |
| Basal-like breast (n = 3) | NA | 27,173 | ∼200 | NA | TP53 (65%) | CHGB (NA) | CG→TA (55%) | 35,114 |
| Non-small-cell lung (n = 1) | NA | >50,000 | NA | >302 | KRAS (∼30%) | MIR598 (NA) | CG→AT (46%) | 35 |
| Small-cell lung (n = 1) | NA | 22,910 | 105 | NA | TP53 (85%), RB1 (80%) | CHD7 (NA) | CG→AT (∼36%) | 36 |
| Melanoma (n = 1) | NA | 33,345 | 195 | NA | BRAF (∼70%), TP53 (∼50%) | SPDEF (NA) | CG→TA (∼66%) | 31 |
| Prostate (n = 7) | NA | 3,866 | NA | 20 | SPOP (28%) | SPTA1 (28%) | AT→GC (32%) | 115 |
| Multiple myeloma (n = 38) | NA | 7,450 | NA | 35 | KRAS (26%), NRAS (24%) | FAM46C (13%) | CG→TA (47%), AT→TA (13%) | 116 |
APC, adenomatous polyposis coli; ARID1A, AT-rich interactive domain 1A; ATRX, alpha thalassaemia/mental retardation syndrome X-linked; CDH1, E-cadherin; CDKN2A, cyclin-dependent kinase inhibitor 2A; CHD, chromodomain helicase DNA binding protein; CHGB, chromogranin B; DAXX, death-domain associated protein; DNMT3A, DNA methyltransferase 3α; EGFR, epidermal growth factor receptor; FLT3, FMS-related tyrosine kinase 3; HAUS3, HAUS augmin-like complex, subunit 3; IDH1, isocitrate dehydrogenase 1; KDM5C, lysine (K)-specific demethylase 5C (which encodes JARID1C); LRP1B, low density lipoprotein receptor-related protein 1B; MEN1, multiple endocrine neoplasia 1; MIR598, microRNA-598; MLL, mixed-lineage leukaemia; MSI, microsatellite instability; MSS, microsatellite stable; NA, not applicable; non-syn., non-synonymous; NPM1, nucleophosmin; PBRM1, polybromo 1; PIK3CA, PI3K, catalytic, α-polypeptide; PPP2R1A, protein phosphatase 2, regulatory subunit A, α; PTCH1, patched 1; PTPRD, protein tyrosine phosphatase, receptor type, D; RB1, retinoblastoma 1; RCC, renal cell carcinoma; SETD2, SET domain containing 2; SPDEF, SAM pointed domain containing ETS transcription factor; SPOP, speckle-type POZ protein; SPTA1, spectrin, α, erythrocytic 1; TGM3, transglutaminase 3; VHL, von Hippel-Lindau tumour suppressor.
Where possible, values are taken from follow-up studies or are prevalence frequencies of the same study (excludes discovery samples).
Number of genes containing at least one non-synonymous point mutation.
Values for tumours from smokers versus never-smokers, respectively.
One treated sample with 125 mutations is excluded from this calculation, as done by the original authors.
Excluding cell line sample.
Somatic point mutations in conserved or regulatory portions of the genome.