Supplementary Table 1. A full list of cancer genes. Tumour Tumour Other Gene Gene full Entrez Chr Somat Germli Cancer Tissue Molecular Mut Translocati Other Chr Types Types Germline Syn Symbol name Gene ID Band ic ne Synd Type Genetics Types on Partner Synd (Somatic) (Germline) Mut Abl-interactor 10p11. ABI1; E3B1; ABI-1; ABI1 10006 10 yes AML L Dom T MLL 1 2 SSH3BP1; 10006 V-abl Abelson ABL1; p150; ABL; c- murine BCR; CML; ALL; ABL; JTK7; bcr/abl; v- ABL1 leukemia viral 25 9 9q34.1 yes L Dom T; Mis ETV6; T-ALL abl; P00519; 25; oncogene NUP214 ENSG00000097007 homolog 1 C-abl ABL2; ARG; RP11- oncogene 2; 1q24- 177A2_3; ABLL; ABL2 non-receptor 27 1 yes AML L Dom T ETV6 q25 ENSG00000143322; tyrosine P42684; 27 kinase Acyl-coa 2181; ASPM; synthetase PRO2194; ACS3; ACSL3 long-chain 2181 2 2q36 yes Prostate E Dom T ETV1 FACL3; O95573; family ENSG00000123983; member 3 ACSL3 CASC5; AF15Q14; AF15q14 Q8NG31; D40; AF15Q14 57082 15 15q14 yes AML L Dom T MLL protein ENSG00000137812; 57082 ALL1-fused MLLT11; Q13015; gene from AF1Q; AF1Q 10962 1 1q21 yes ALL L Dom T MLL chromosome ENSG00000213190; 1q 10962 SH3 protein Q9NZQ3; AF3P21; interacting WISH; ORF1; with Nck; 90 AF3p21 51517 3 3p21 yes ALL L Dom T MLL WASLBP; SPIN90; kda (ALL1 ENSG00000213672; fused gene NCKIPSD; 51517 from 3p21) 27125; Q9UHB7; ALL1 fused MCEF; AF5Q31; AF5q31 gene from 27125 5 5q31 yes ALL L Dom T MLL ENSG00000072364; 5q31 AFF4 KIAA0803; AKAP350; CG-NAP; MU-RMS- A kinase 40_16A; PRKA9; (PRKA) 7q21- Papillary AKAP9 10142 7 yes E Dom T BRAF YOTIAO; HYPERION; anchor protein q22 thyroid AKAP450; Q99996; (yotiao) 9 ENSG00000127914; 10142; AKAP9 P31749; AKT1_NEW; 207; V-akt murine Breast; ENSG00000142208; thymoma viral 14q32. colorectal; AKT1 207 14 yes E Dom Mis AKT; MGC99656; oncogene 32 ovarian; PKB; PKB-ALPHA; homolog 1 NSCLC PRKBA; RAC; RAC- ALPHA V-akt murine AKT2; PRKBB; thymoma viral 19q13. Ovarian; P31751; RAC-BETA; AKT2 208 19 yes E Dom A oncogene 1-q13.2 pancreatic ENSG00000105221; homolog 2 208; PKBBETA Aldehyde ALDH2; ALDHI; dehydrogenase ALDM; MGC1806; 12q24. ALDH2 2 family 217 12 yes Leiomyoma M Dom T HMGA2 P05091; ALDH-E2; 2 (mitochondrial ENSG00000111275; ) 217 NPM1; TPM3; TFG; TPM4; ALCL; ATIC; Anaplastic Familial ENSG00000171094; NSCLC; CLTC; ALK lymphoma 238 2 2p23 yes yes Neuroblastoma neuroblast L; E; M Dom T; Mis; A CD246; TFG/ALK; neuroblasto MSN; kinase (Ki-1) oma Q9UM73; ALK; 238 ma ALO17; CARS; EML4; KIF5B; C2orf22 57674; KIAA1618 17q25. ENSG00000173821; ALO17 57674 17 yes ALCL L Dom T ALK protein 3 C17orf27; KIAA1554; Q63HN8; RNF213 AMER1; RP11- APC 403E24_2; WTX; membrane Wilms F; D; N; AMER1 139285 X Xq11.2 yes O Rec FLJ39827; recruitment tumour Mis ENSG00000184675; protein 1 FAM123B; 139285 Colorectal; Colorectal; Adenomat pancreatic; pancreatic; ous 324; DP2; DP2_5; DP3; Adenomatous desmoid; desmoid; polyposis D; Mis; GS; FPC; FAP; APC polyposis of 324 5 5q21 yes yes E; M; O Rec hepatoblasto hepatoblastom coli; N; F; S ENSG00000134982; the colon gene ma; glioma; a; glioma; Turcot P25054; APC other CNS other CNS syndrome 23365; Q9NZN5; RHO guanine PRO2792; nucleotide ARHGE 11q23. DKFZp686O2372; exchange 23365 11 yes AML L Dom T MLL F12 3 LARG; KIAA0382; factor (GEF) ENSG00000196914; 12 (LARG) ARHGEF12 RAS homolog RHOH; TTF; RhoH; gene family; ARHH; ARHH 399 4 4p13 yes NHL L Dom T BCL6 member H ENSG00000168421; (TTF) 399 8289; BAF250; BAF250a; P270; RP1- AT rich Clear cell 50O24_1; B120; interactive ovarian Mis; N; ARID1A 8289 1 1p35.3 yes E Rec BM029; C1orf4; domain 1A carcinoma; F; S; D SMARCF1; (SWI-like) RCC ENSG00000117713; ARID1A 196528; ENSG00000189079; AT rich Hepatocellul BAF200; ARID2 interactive 196528 12 12q12 yes ar E Rec N; S; F DKFZp686G052; domain 2 carcinoma DKFZp779P0222; FLJ30619; KIAA1557; p200; Q68CP9; ARID2 Aryl ARNT; HIF1BETA; hydrocarbon TANGO; HIF1B; HIF- ARNT receptor 405 1 1q21 yes AML L Dom T ETV6 1beta; P27540; nuclear ENSG00000143437; translocator 405 Alveolar soft part sarcoma Alveolar 79058; Q9BZE9; ASPSCR chromosome 79058 17 17q25 yes soft part M Dom T TFE3 ENSG00000169696; 1 region; sarcoma ASPSCR1 candidate 1 171023; KIAA0978; MGC117280; Additional sex 20q11. MDS; ASXL1 171023 20 yes L Rec F; N; Mis MGC71111; Q8IXJ9; combs like 1 1 CMML ENSG00000171456; ASXL1 Malignant melanoma Activating of soft parts; 466; TREB36; P18846; EWSR1; ATF1 transcription 466 12 12q13 yes angiomatoid E; M Dom T ENSG00000123268; FUS factor 1 fibrous ATF1 histiocytom a 5- Aminoimidaz ole-4- P31939; IMPCHASE; carboxamide PURH; AICARFT; ATIC ribonucleotide 471 2 2q35 yes ALCL L Dom T ALK ENSG00000138363; formyltransfer 471; ATIC ase/IMP cyclohydrolas e 472; TELO1; ATA; ATC; ATDC; Leukaemia; MGC74674; Q13315; Ataxia Ataxia- 11q22. lymphoma; D; Mis; AT1; ATM telangiectasia 472 11 yes yes T-PLL telangiecta L; O Rec 3 medulloblasto N; F; S DKFZp781A0353; mutated sia ma; glioma ATE; ATD; TEL1; ENSG00000149311; ATM ATPase; Adrenal Na+/K+ P05023; ATP1A1; 476; aldosterone ATP1A1 transporting; 476 1 p21 yes E Dom Mis; O ENSG00000163399; producing alpha 1 MGC3285; MGC51750 adenoma polypeptide ATPase; Ca++ Adrenal ATP2B3; PMCA3; transporting; aldosterone ATP2B3 492 X q28 yes E Dom O ENSG00000067842; plasma producing 492 membrane 3 adenoma ATR-X P46100; Alpha Pancreatic (alpha ATRX_ENST00000373 thalassemia/m neuroendocr thalassem 344; 546; ATR2; ental ATRX 546 X Xq21.1 yes ine tumours; E Rec Mis; F; N yes ia/mental MGC2094; MRXHF1; retardation paediatric retardatio RAD54; RAD54L; syndrome X- GBM n) SFM1; SHS; XH2; linked syndrome XNP; ZNF-HX Colorectal; endometrial; prostate and hepatocellul 8312; LA16c-314G4_3; ar 16p13. D; Mis; MGC52315; AXIN; AXIN1 Axin 1 8312 16 yes yes carcinomas; E; O Rec 3 N; F; S ENSG00000103126; hepatoblasto O15169; AXIN1 ma; sporadic medulloblast oma BRCA1 8314; associated Uveal DKFZp686N04275; protein-1 melanoma; Mesothelioma; FLJ37180; HUCEP-13; 3p21.3 N; Mis; BAP1 (ubiquitin 8314 3 yes breast; uveal E Rec hucep-6; KIAA0272; 1-p21.2 F; S; O carboxy- NSCLC; melanoma ENSG00000163930; terminal RCC BAP1; FLJ35406; hydrolase) Q92560 BCL10; CIPER; CLAP; B-cell mE10; CARMEN; c- BCL10 CLL/lymphom 8915 1 1p22 yes MALT L Dom T IGH@ E10; a 10 ENSG00000142867; 8915 KIAA1809; BCL11A-L; FLJ10173; EVI9; B-cell Q9H165; BCL11A-XL; BCL11A CLL/lymphom 53335 2 2p13 yes B-CLL L Dom T IGH@ BCL11A-S; CTIP1; a 11A FLJ34997; ENSG00000119866; 53335; BCL11A BCL11B; RIT1; CTIP- B-cell 14q32. 2; Q9C0K0; hRIT1- BCL11B CLL/lymphom 64919 14 yes T-ALL L Dom T TLX3 1 alpha; CTIP2; 64919; a 11B (CTIP2) ENSG00000127152 B-cell BCL2; Bcl-2; 18q21. BCL2 CLL/lymphom 596 18 yes NHL; CLL L Dom T IGH@ ENSG00000171791; 3 a 2 596 BCL3; P20749; BCL4; B-cell D19S37; BCL3 CLL/lymphom 602 19 19q13 yes CLL L Dom T IGH@ ENSG00000069399; a 3 602 B-cell BCL5 CLL/lymphom 603 17 17q22 yes CLL L Dom T MYC a 5 IG loci; ZNFN1A1; LCP1; PIM1; TFRC; CIITA; BCL6A; BCL5; ZNF51; B-cell NACA; LAZ3; P41182; BCL6 CLL/lymphom 604 3 3q27 yes NHL; CLL L Dom T; Mis HSPCB; ZBTB27; a 6 HSPCA; ENSG00000113916; HIST1H4I; 604; BCL6 IL21R; POU2AF1; ARHH; EIF4A2; SFRS3 B-cell BCL7A; BCL7; 12q24. BCL7A CLL/lymphom 605 12 yes BNHL L Dom T MYC ENSG00000110987; 1 a 7A 605 607; LGS; B-cell IGH@; MGC131591; BCL9 CLL/lymphom 607 1 1q21 yes B-ALL L Dom T IGL@ ENSG00000116128; a 9 BCL9 ANOP2; MGC71031; FLJ20285; Retinoblasto oculo- MGC131961; ma; AML; facio- BCL6 F; N; S; KIAA1575; MCOPS2; BCOR 54880 X Xp11.4 yes APL Rec RARA yes cardio- corepressor T MAA2; (translocatio dental ENSG00000183337; n) genetic BCOR; 54880; FLJ38041 P11274; FLJ16453; PHL; ALL; D22S662; ABL1; Breakpoint 22q11. CML; ALL; CML; D22S11; BCR1; BCR 613 22 yes L Dom T FGFR1; cluster region 21 AML BCR; JAK2 ENSG00000186716; 613 201163; BHD; FLCL; Folliculin; Renal; Birt-Hogg- MGC17998; Birt-Hogg- 17p11. fibrofolliculom BHD 201163 17 yes Dube E; M Rec? Mis. N; F MGC23445; Dube 2 as; syndrome ENSG00000154803; syndrome trichodiscomas FLCN BIRC3; AIP1; HAIP1; hiap-1; RNF49; Baculoviral CLL; D; F; N; MALT2; cIAP2; API2; BIRC3 IAP repeat- 330 11 11q22 yes MALT; L Dom MALT1 T; Mis Q13489; HIAP1; containing 3 MCL; MM ENSG00000023445; 330; CIAP2; MIHC RECQL3; Leukaemia; MGC131620; BS; lymphoma; MGC126616; Bloom 15q26. Bloom BLM 641 15 yes skin squamous L; E Rec Mis; N; F RECQL2; RECQ2; syndrome 1 syndrome cell; other MGC131618; tumour types ENSG00000197299; BLM; 641 Bone 657; ACVRLK3; morphogeneti 10q22. gastrointestinal Juvenile CD292; ALK3; P36894; BMPR1A c protein 657 10 yes E Rec Mis; N; F 3 polyps polyposis ENSG00000107779; receptor; type BMPR1A IA Melanoma; colorectal; papillary thyroid; P15056; MGC126806; V-raf murine Cardio- borderline BRAF1; B-raf 1; sarcoma viral AKAP9; facio- BRAF 673 7 7q34 yes ovarian; E Dom Mis; T; O yes RAFB1; MGC138284; oncogene KIAA1549 cutaneous NSCLC; ENSG00000157764; homolog B1 syndrome cholangioca 673; BRAF; B-raf1 rcinoma; pilocytic astrocytoma IRIS; BRCAI; PSCP; Familial Hereditary D; Mis; RNF53; BRCC1; BRCA1 breast/ovarian 672 17 17q21 yes yes Ovarian Breast; ovarian breast/ovar E Rec N; F; S ENSG00000012048; cancer gene 1 ian cancer 672; BRCA1 Breast; BRCA2; FAD; RP11- ovarian; 298P3_4; FANCB; Familial Breast; Hereditary pancreatic; D; Mis; BRCC2; FANCD1; BRCA2 breast/ovarian 675 13 13q12 yes yes ovarian; breast/ovar L; E Rec leukaemia N; F; S FANCD; FAD1; FACD; cancer gene 2 pancreatic ian cancer (FANCB; ENSG00000139618; FANCD1) 675 Lethal 8019; KIAA0043; midline Bromodomain RING3L; ORFX; BRD3 8019 9 9q34 yes carcinoma E Dom T C15orf55 containing 3 Q15059; BRD3; of young ENSG00000169925 people Lethal 23476; MCAP; midline Bromodomain 19p13. O60885; CAP; HUNKI; BRD4 23476 19 yes carcinoma E Dom T C15orf55 containing 4 1 ENSG00000141867; of young BRD4 people Fanconi 83990; MGC126521; BRCA1 anaemia J; OF; MGC126523; interacting AML; breast Q9BX63; FLJ90232; BRIP1 protein C- 83990 17 17q22 yes leukaemia; L; E Rec F; N; Mis cancer FANCJ; BACH1; terminal breast susceptibli ENSG00000136492; helicase 1 ty BRIP1 B-cell BTG1; P62324; translocation BTG1 694 12 12q22 yes BCLL L Dom T MYC ENSG00000133639; gene 1; anti- 694 proliferative BUB1 BUB1B; Bub1A; budding Mosaic hBUBR1; O60566; uninhibited by Rhabdomyosar Mis; N; BUB1B 701 15 15q15 yes variegated M Rec BUB1beta; SSK1; benzimidazole coma F; S aneuploidy ENSG00000156970; s 1 homolog 701; BUBR1; MAD3L beta (yeast) Chromosome 12 open 12q14.