Supplementary Table 2: Mutation List for confirmation phase List of mutation events with associated references occurring in melanoma considered for confirmation phase.

Gene Mutation Occurrence Reference Validation Final AKT1 E17K 1/202 (0.5%) 1 Y AKT3 E17K 3/202 (1.5%) 1 Y Y CXCR4 V160I 1/18 (5.5%) 2 Y Y EPHA3 G228R 1/24 (4.1%) 3 Y OBSCN E4574K 1/24 (4.1%) 3 TECTA P802S 1/24 (4.1%) 3 FAS A241T 1/44 (2.2%) 4 FAS N250S 1/44 (2.2%) 4 FAS V251I 1/44 (2.2%) 4 GNAQ Q209L 26/75 (35%) 5 Y Y GNAQ Q209L 66/134 (49.2%) 6 Y Y MITF L142F 1/26 (3.8%) 7 MITF E87R 1/50 (2%) 7 MITF L135V 1/50 (2%) 7 MITF G244R 1/50 (2%) 7 MITF D380N 1/50 (2%) 7 SOX10 Q125X 1/50 (2%) 7 SOX10 R43Q 1/55 (1.8%) 7 SOX10 A361V 1/55 (1.8%) 7 SOX10 H414Y 1/55 (1.8%) 7 SOX10 A424V 1/55 (1.8%) 7 SOX10 G413S-D 2/55 (3.6%) 7 MEK1 G171T 3% (1/37) 8 MEK1 K57N 3% (1/37) 8 Y MEK1 P124L - 9 Y Y MEK1 Q56P - 9 Y Y MMP2 A526T 1/24 (4.1%) 10 MYO18B P606L 1/24 (4.1%) 10 MMP11 A235V 1/79 (1.7%) 11 MMP11 R70L-R 1/79 (1.7%) 11 MMP14 E183E 1/79 (1.7%) 11 MMP14 V555A 1/79 (1.7%) 11 MMP2 I128I 1/79 (1.7%) 11 MMP2 P84L 1/79 (1.7%) 11 MMP2 D622G 1/79 (1.7%) 11 MMP24 D507N 1/79 (1.7%) 11 MMP24 G240R 1/79 (1.7%) 11 MMP24 K216K 1/79 (1.7%) 11 MMP24 P521Q 1/79 (1.7%) 11 MMP24 W163X 1/79 (1.7%) 11 MMP27 A125V/LOH 1/79 (1.7%) 11 MMP27 D407N 1/79 (1.7%) 11 MMP27 E25K 1/79 (1.7%) 11 MMP27 E65K/LOH 1/79 (1.7%) 11 MMP27 M406I 1/79 (1.7%) 11 MMP27 W106X/LOH 1/79 (1.7%) 11 MMP27 W349X 1/79 (1.7%) 11 MMP28 G243A 1/79 (1.7%) 11 MMP28 G313R 1/79 (1.7%) 11 MMP28 Q312H 1/79 (1.7%) 11 MMP28 Q363Q 1/79 (1.7%) 11 MMP8 E138Q/LOH 1/79 (1.7%) 11 MMP8 E314K 1/79 (1.7%) 11 MMP8 G104R/LOH 1/79 (1.7%) 11 MMP8 K87N/LOH 1/79 (1.7%) 11 MMP8 P78S/LOH 1/79 (1.7%) 11 MMP8 S50F/LOH 1/79 (1.7%) 11 DDR1 S372F 1/80 (1.25%) 12 DDR1 R570Q 1/80 (1.25%) 12 EPHA10 E124K 1/80 (1.25%) 12 Y Y EPHA10 G790E 1/80 (1.25%) 12 EPHA10 G843A 1/80 (1.25%) 12 Y EPHA6 T307S 1/80 (1.25%) 12 Y EPHA6 R494M 1/80 (1.25%) 12 Y EPHA6 E537K 1/80 (1.25%) 12 Y EPHA6 K655I 1/80 (1.25%) 12 Y EPHA6 E680K 1/80 (1.25%) 12 Y EPHB1 R79W 1/80 (1.25%) 12 Y EPHB1 D771N 1/80 (1.25%) 12 Y EPHB1 G811E 1/80 (1.25%) 12 Y EPHB1 W919X 1/80 (1.25%) 12 EPHB2 E109K 1/80 (1.25%) 12 Y EPHB2 A205V 1/80 (1.25%) 12 Y EPHB2 D318N 1/80 (1.25%) 12 EPHB2 T512I 1/80 (1.25%) 12 EPHB2 P887L 1/80 (1.25%) 12 Y EPHB6 S131F 1/80 (1.25%) 12 EPHB6 S152F 1/80 (1.25%) 12 EPHB6 G404S 1/80 (1.25%) 12 Y Y EPHB6 R679Q 1/80 (1.25%) 12 Y Y EPHB6 A688G 1/80 (1.25%) 12 Y EPHB6 R704W 1/80 (1.25%) 12 Y ERBB4 L39F 1/80 (1.25%) 12 ERBB4 Y111H 1/80 (1.25%) 12 ERBB4 M313I 1/80 (1.25%) 12 ERBB4 E317K 1/80 (1.25%) 12 Y ERBB4 S341L 1/80 (1.25%) 12 Y ERBB4 R393W 1/80 (1.25%) 12 Y Y ERBB4 P409L 1/80 (1.25%) 12 Y ERBB4 R491K 1/80 (1.25%) 12 Y ERBB4 E542K 1/80 (1.25%) 12 ERBB4 R544W 1/80 (1.25%) 12 Y ERBB4 E563K 1/80 (1.25%) 12 Y ERBB4 D609N 1/80 (1.25%) 12 Y ERBB4 P700S 1/80 (1.25%) 12 Y ERBB4 E836K 1/80 (1.25%) 12 Y ERBB4 E872K 1/80 (1.25%) 12 ERBB4 G936R 1/80 (1.25%) 12 Y ERBB4 P1033S 1/80 (1.25%) 12 Y ERBB4 R1174Q 1/80 (1.25%) 12 ERBB4 S1246N 1/80 (1.25%) 12 FER Y532H 1/80 (1.25%) 12 Y FER G580D 1/80 (1.25%) 12 Y FLT1 R281Q 1/80 (1.25%) 12 Y FLT1 S287F 1/80 (1.25%) 12 Y FLT1 W589X 1/80 (1.25%) 12 FLT1 P814S 1/80 (1.25%) 12 Y FLT1 E943K 1/80 (1.25%) 12 Y FLT1 D1081N 1/80 (1.25%) 12 Y FLT1 E1223K 1/80 (1.25%) 12 Y MATK W416X 1/80 (1.25%) 12 MET C610Y 1/80 (1.25%) 12 MET N1059S 1/80 (1.25%) 12 MET R1188Q 1/80 (1.25%) 12 Y Y NTRK1 M349I 1/80 (1.25%) 12 NTRK1 R547G 1/80 (1.25%) 12 PDGFRA A191T 1/80 (1.25%) 12 Y PDGFRA E459K 1/80 (1.25%) 12 Y PDGFRA S890F 1/80 (1.25%) 12 Y PDGFRA P937L 1/80 (1.25%) 12 Y PDGFRA D1024N 1/80 (1.25%) 12 PTK2B A494V 1/80 (1.25%) 12 Y PTK2B W273X 1/80 (1.25%) 12 Y PTK2B G414E 1/80 (1.25%) 12 Y Y PTK2B R429C 1/80 (1.25%) 12 Y Y PTK2B E494K 1/80 (1.25%) 12 PTK2B E792K 1/80 (1.25%) 12 Y PTK2B R918Q 1/80 (1.25%) 12 Y PTK2B E938K 1/80 (1.25%) 12 Y PTK6 W210X 1/80 (1.25%) 12 Y PTK7 P352S 1/80 (1.25%) 12 Y ROR2 V391A 1/80 (1.25%) 12 Y ROR2 S557L 1/80 (1.25%) 12 Y ROR2 A793S 1/80 (1.25%) 12 Y Y ROR2 E47K 1/80 (1.25%) 12 TIE1 S54L 1/80 (1.25%) 12 Y TIE1 T89M 1/80 (1.25%) 12 Y TIE1 D98N 1/80 (1.25%) 12 TIE1 G533E 1/80 (1.25%) 12 Y TIE1 P1094L 1/80 (1.25%) 12 EPHA10 V79M/A 2/80 (2.5%) 12 EPHA10 G217S/D 2/80 (2.5%) 12 EPHB2 E615K 2/80 (2.5%) 12 Y ERBB4 E452K 2/80 (2.5%) 12 Y Y GNA11 R183C N/A 13 Y Y GNA11 Q209L N/A 13 Y Y GNAQ R183C N/A 13 Y Y STK11 Y49D 1/144 (0.7%) COSMIC STK11 G135R 1/144 (0.7%) COSMIC PIK3CA D538N 1/181 (0.6%) COSMIC PIK3CA H1047R 1/181 (0.6%) COSMIC NRAS E49K 1/2965 (0.04%) COSMIC NRAS G60E 1/2965 (0.04%) COSMIC NRAS Y64N 1/2965 (0.04%) COSMIC NRAS S65C 1/2965 (0.04%) COSMIC KIT K550N 1/340 (0.3%) COSMIC KIT Y553N 1/340 (0.3%) COSMIC KIT V569G 1/340 (0.3%) COSMIC KIT R634W 1/340 (0.3%) COSMIC KIT A829P 1/340 (0.3%) COSMIC KIT I841V 1/340 (0.3%) COSMIC ADAM28 D470N 1/4 (25%) COSMIC ADAM29 G589E 1/4 (25%) COSMIC ALDH2 R51K 1/4 (25%) COSMIC ALPK3 G1364E 1/4 (25%) COSMIC Y ANAPC5 L551V 1/4 (25%) COSMIC APBB1IP Q464K 1/4 (25%) COSMIC ARL4C G71S 1/4 (25%) COSMIC BAI3 D755N 1/4 (25%) COSMIC BCL11A S554F 1/4 (25%) COSMIC CAMK1 P217S 1/4 (25%) COSMIC Y CARD6 L638F 1/4 (25%) COSMIC CCR1 L351F 1/4 (25%) COSMIC CCR1 M1I 1/4 (25%) COSMIC CD40 G266D 1/4 (25%) COSMIC CLIC2 R201C 1/4 (25%) COSMIC CNTN5 G195E 1/4 (25%) COSMIC COPS7B P7L 1/4 (25%) COSMIC CXCR7 S15L 1/4 (25%) COSMIC DDX3X A502T 1/4 (25%) COSMIC DKK2 S222F 1/4 (25%) COSMIC DYRK1B Q275R 1/4 (25%) COSMIC Y EDIL3 Q187K 1/4 (25%) COSMIC EPHA7 G232R 1/4 (25%) COSMIC Y EPHB4 P346L 1/4 (25%) COSMIC ETV5 Y445C 1/4 (25%) COSMIC FBXO43 S543L 1/4 (25%) COSMIC FGD1 R636W 1/4 (25%) COSMIC Y FZD7 P285S 1/4 (25%) COSMIC GLI1 S1094F 1/4 (25%) COSMIC GNB4 P107L 1/4 (25%) COSMIC GRIN2B G1449E 1/4 (25%) COSMIC HECW1 I120S 1/4 (25%) COSMIC HECW1 R817Q 1/4 (25%) COSMIC HRB G340R 1/4 (25%) COSMIC IL16 S391F 1/4 (25%) COSMIC IRX2 T179>I 1/4 (25%) COSMIC ITGAD G813R 1/4 (25%) COSMIC ITK R19K 1/4 (25%) COSMIC Y LOC347421 D649N 1/4 (25%) COSMIC LOC347475 I67V 1/4 (25%) COSMIC LOC402569 D41N 1/4 (25%) COSMIC MADD S1620F 1/4 (25%) COSMIC MAP7D3 R339C 1/4 (25%) COSMIC MCM2 R825W 1/4 (25%) COSMIC MGC39900 K12N 1/4 (25%) COSMIC NEK10 E379K 1/4 (25%) COSMIC Y Y NOVA1 A256D 1/4 (25%) COSMIC OBSCN A4234T 1/4 (25%) COSMIC OC90 K231E 1/4 (25%) COSMIC PDGFRA E996K 1/4 (25%) COSMIC Y Y PIB5PA M394I 1/4 (25%) COSMIC PKN1 R185C 1/4 (25%) COSMIC Y PLCH2 L286F 1/4 (25%) COSMIC PLEKHA7 G207E 1/4 (25%) COSMIC PPP1R9A P452S 1/4 (25%) COSMIC PPP6C H114Y 1/4 (25%) COSMIC PRKCI P109L 1/4 (25%) COSMIC Y PTCHD2 V1209M 1/4 (25%) COSMIC PTPN22 E382>K 1/4 (25%) COSMIC PTPRC E200K 1/4 (25%) COSMIC PTPRC E228K 1/4 (25%) COSMIC PTPRK R1294Q 1/4 (25%) COSMIC PTPRT S492F 1/4 (25%) COSMIC RASGRF2 L568F 1/4 (25%) COSMIC REST P752T 1/4 (25%) COSMIC ROCK2 S1194P 1/4 (25%) COSMIC Y RPS6KA2 E311K 1/4 (25%) COSMIC SATB1 E505K 1/4 (25%) COSMIC SERPINA2 K383Q 1/4 (25%) COSMIC SERPINA6 R282L 1/4 (25%) COSMIC SMARCAD1 V888D 1/4 (25%) COSMIC SMARCC2 E614K 1/4 (25%) COSMIC SMG5 P549L 1/4 (25%) COSMIC SNTB1 L301P 1/4 (25%) COSMIC SNTB1 R401Q 1/4 (25%) COSMIC SPDEF D283H 1/4 (25%) COSMIC STK19 D89N 1/4 (25%) COSMIC TNFRSF8 P215S 1/4 (25%) COSMIC TP63 M499I 1/4 (25%) COSMIC TRIM60 R271T 1/4 (25%) COSMIC TTBK1 P855S 1/4 (25%) COSMIC TTN A1301T 1/4 (25%) COSMIC TTN E18435K 1/4 (25%) COSMIC TTN E5659K 1/4 (25%) COSMIC WNT6 G307S 1/4 (25%) COSMIC ZNF217 P651S 1/4 (25%) COSMIC ZNF280C H379>Y 1/4 (25%) COSMIC CTNNB1 S33C 1/414 (0.2%) COSMIC BRAF K439Q 1/4417 (0.02%) COSMIC BRAF R444W 1/4417 (0.02%) COSMIC BRAF G464R 1/4417 (0.02%) COSMIC BRAF S467L 1/4417 (0.02%) COSMIC BRAF K475M 1/4417 (0.02%) COSMIC BRAF N581I 1/4417 (0.02%) COSMIC BRAF L584F 1/4417 (0.02%) COSMIC BRAF E586K 1/4417 (0.02%) COSMIC BRAF G596S 1/4417 (0.02%) COSMIC BRAF T599I 1/4417 (0.02%) COSMIC BRAF S607P 1/4417 (0.02%) COSMIC BRAF Q609R 1/4417 (0.02%) COSMIC BRAF F610S 1/4417 (0.02%) COSMIC BRAF E611D 1/4417 (0.02%) COSMIC BRAF W619R 1/4417 (0.02%) COSMIC BRAF I617T 1/4417 (0.05%) COSMIC MLL2 P4236S 1/7 (14.3%) COSMIC HRAS G13D 1/887 (0.1%) COSMIC APC Q1477H 1/95 (1%) COSMIC KRAS G13D 1/961 (0.1%) COSMIC BRAF G469E-R-S-V 10/4417 (0.23%) COSMIC/ONCO Y Y KIT K642E 11/340 (3.2%) COSMIC Y Y NRAS A18T 12/2965 (0.5%) COSMIC Y BRAF K601E-I-K-N 12/4417 (0.27%) COSMIC Y Y BRAF L597L-Q-R-S-V 13/4417 (0.29%) COSMIC/ ONCO Y Y CTNNB1 S37F-P-Y 14/414 (3.4%) COSMIC Y KRAS G12D-R-V 16/961 (1.6%) COSMIC Y Y BRAF V600-D-E-G-K-M-R 1745/4417 (39.51%) COSMIC/ ONCO Y Y STK11 D194Y 2/144 (1.4%) COSMIC EGFR p.P753S 2/243 (0.8%) COSMIC KIT W557R 2/340 (0.6%) COSMIC Y Y KIT V559A 2/340 (0.6%) COSMIC Y Y KIT D816H 2/340 (0.6%) COSMIC Y CTNNB1 D32E-G 2/414 (0.5%) COSMIC BRAF I582M 2/4417 (0.05%) COSMIC BRAF D587E-N 2/4417 (0.05%) COSMIC BRAF L588P-R 2/4417 (0.05%) COSMIC BRAF A598T-V 2/4417 (0.05%) COSMIC BRAF G606E 2/4417 (0.05%) COSMIC BRAF H608R 2/4417 (0.05%) COSMIC BRAF G615R 2/4417 (0.05%) COSMIC BRAF S616P 2/4417 (0.05%) COSMIC HRAS G12V 2/887 (0.2%) COSMIC PIK3CA E545K 3/181 (1.7%) COSMIC Y BRAF W604G-S 3/4417 (0.07%) COSMIC BRAF S614P 3/4417 (0.07%) COSMIC Y BRAF L618S 3/4417 (0.07%) COSMIC KIT D820Y 4/340 (1.2%) COSMIC Y Y CTNNB1 S45F-P-Y 4/414 (9.6%) COSMIC Y Y BRAF F595L-S 4/4417 (0.09%) COSMIC Y NRAS G13A-D-R-V 41/2965 (1.5%) COSMIC Y Y NRAS G12A-C-D-N-R-S-V 46/2965 (1.5%) COSMIC Y Y KRAS Q61H-L-R 5/961 (0.5%) COSMIC Y Y NRAS Q61E-H-K-L-P-R 515/2965 (17.4%) COSMIC/ ONCO Y Y STK11 Q170X 6/144 (4.2%) COSMIC Y BRAF I592M-V 6/4417 (0.14%) COSMIC BRAF D594E-G-N-V 6/4417 (0.14%) COSMIC BRAF G466A-R-E-V 8/4417 (0.18%) COSMIC Y Y BRAF S605F-G-N-R 8/4417 (0.18%) COSMIC HRAS Q61H-K-L-R 8/887 (0.9%) COSMIC Y KIT L576P 9/340 (2.6%) COSMIC Y Y MET T1010I 1/44 (2.3%) ONCO Y Y PIK3CA H701P 1/44 (2.3%) ONCO Y PIK3CA R88Q 1/44 (2.3%) ONCO Y Y CDK4 R24C/H 2/44 (5%) ONCO Y Y

REFERENCES

1 Davies, M.A., et al., A novel AKT3 mutation in melanoma tumours and cell lines. Br J Cancer, 2008. 99(8): p. 1265-8. 2 Ierano, C., et al., A point mutation (G574A) in the chemokine receptor CXCR4 detected in human cancer cells enhances migration. Cell Cycle, 2009. 8(8): p. 1228-37. 3 Balakrishnan, A., et al., Novel somatic and germline mutations in cancer candidate in glioblastoma, melanoma, and pancreatic carcinoma. Cancer Res, 2007. 67(8): p. 3545-50. 4 Shin, M.S., et al., Alterations of Fas (Apo-1/CD95) in cutaneous malignant melanoma. Am J Pathol, 1999. 154(6): p. 1785-91. 5 Van Raamsdonk, C.D., et al., Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi. Nature, 2009. 457(7229): p. 599-602 6 Onken, M.D., et al., Oncogenic mutations in GNAQ occur early in uveal melanoma. Invest Ophthalmol Vis Sci, 2008. 49(12): p. 5230-4. 7 Cronin, J.C., et al., Frequent mutations in the MITF pathway in melanoma. Pigment Cell Melanoma Res, 2009. 22(4): p. 435-44. 8 Murugan, A.K., et al., MEK1 mutations, but not ERK2 mutations, occur in melanomas and colon carcinomas, but none in thyroid carcinomas. Cell Cycle, 2009. 8(13): p. 2122-4. 9 Emery, C.M., et al., MEK1 mutations confer resistance to MEK and B-RAF inhibition. Proc Natl Acad Sci U S A, 2009. 106(48): p. 20411-6. 10 Bleeker, F.E., et al., Mutational profiling of cancer candidate genes in glioblastoma, melanoma and pancreatic carcinoma reveals a snapshot of their genomic landscapes. Hum Mutat, 2009. 30(2): p. E451-9. 11 Palavalli, L.H., et al., Analysis of the matrix family reveals that MMP8 is often mutated in melanoma. Nat Genet, 2009. 41(5): p. 518-20. 12 Prickett, T.D., et al., Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4. Nat Genet, 2009. 41(10): p. 1127-32. 13 Van Raamsdonk, C.D., et al., Mutations in GNA11 in uveal melanoma. N Engl J Med, 2010. 363(23): p. 2191-9. COSMIC Forbes, S.A., et al., The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet, 2008. Chapter 10: p. Unit 10 11- Accessed January 2010 ONCO Mutation identified from screening the OncoCarta Panel against 40 stage III melanoma cell lines

Ierano, C., et al., A point mutation (G574A) in the chemokine receptor CXCR4 detected in human cancer cells enhances migration. Cell Cycle, 2009. 8(8): p. 1228-37. Balakrishnan, A., et al., Novel somatic and germline mutations in cancer candidate genes in glioblastoma, melanoma, and pancreatic carcinoma. Cancer Res, 2007. 67(8): p. 3545-50.

Murugan, A.K., et al., MEK1 mutations, but not ERK2 mutations, occur in melanomas and colon carcinomas, but none in thyroid carcinomas. Cell Cycle, 2009. 8(13): p. 2122-4. Bleeker, F.E., et al., Mutational profiling of cancer candidate genes in glioblastoma, melanoma and pancreatic carcinoma reveals a snapshot of their genomic landscapes. Hum Mutat, 2009. 30(2): p. E451-9. Palavalli, L.H., et al., Analysis of the family reveals that MMP8 is often mutated in melanoma. Nat Genet, 2009. 41(5): p. 518-20.

Forbes, S.A., et al., The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet, 2008. Chapter 10: p. Unit 10 11- Accessed January 2010