Supplementary Table S1. Summary of the six next-generation sequencing (NGS) studies containing 241 paired melanoma tumor/normal samples Study NGS # paired tumor-normal Tumor subtype Reference ID technology samples 1 Whole genome 25 23 cutaneous, 2 acral Berger et al., 2012 (1) 95 cutaneous, 5 acral, 2 mucosal, 1 uveal, and 18 2 Whole exome 121 Hodis et al., 2012 (2) unknown 61 cutaneous, 14 acral, 7 mucosal, 5 uveal, and 12 Krauthammer et al., 2012 3 Whole exome 99* unknown (3) 4 Whole exome 7 7 cutaneous Nikolaev et al., 2012 (4) 5 Whole exome 8 8 cutaneous Stark et al., 2012 (5) 6 Whole exome 14 14 cutaneous Wei et al., 2011 (6) 187 cutaneous, 19 acral, 9 mucosal, 6 uveal, and 30 Total 241# unknown *48 tumor samples without normal samples were excluded from our study. #23 paired samples in Berger et al. (2012) were used in Hodis et al. (2012). In addition, there were 10 samples without any mutations in Krauthammer et al. (2012). These samples were excluded in our analysis. 1 Supplementary Table S2. Summary of known driver mutations detected in the 241 melanoma samples Mutation* Type # samples BRAF GNAQ GNA11 KIT NRAS present Acral 17 3 1 0 0 0 2 Mucosal 7 2 1 0 0 0 1 Uveal 6 3 0 0 3 0 0 Cutaneous 182 138 99 0 0 1 38 Unknown 29 26 20 0 0 0 6 Total 172 121 241 0 (0%) 3 (1.2%) 1 (0.4%) 47 (19.5%) (frequency) (71.3%) (50.2%) *Includes the somatic point mutations identified by the Vanderbilt melanoma SNaPshot assay and known to be functional and actionable (7). 2 Supplementary Table S3. Mutated genes significantly associated with BRAF-mutated samples (frequency≥ 10% and p-value < 0.05) in the Hodis et al. study # samples with BRAF # samples without mutation BRAF mutation Frequency Frequency p- Gene (N = 76) (%) (N = 45) (%) value PIK3C2G 9 11.8 0 0% 0.013 Supplementary Table S4. Mutated genes significantly associated with NRAS-mutated samples (frequency≥ 10% and p-value < 0.05) in the Hodis et al. study # samples with NRAS # samples without mutation NRAS mutation Frequency Frequency p- Gene (N = 31) (%) (N = 90) (%) value PIK3R4 5 16.1 1 1.1 0.004 PI4KA 6 19.4 4 4.4 0.018 PPP6C 6 19.4 5 5.6 0.031 TRPM6 10 32.3 13 14.4 0.031 KALRN 8 25.8 9 10.0 0.034 TSC2 4 12.9 2 2.2 0.037 Genes were ordered by p-values 3 Supplementary Table S5. Mutated genes significantly associated with BRAF-mutated samples (frequency≥ 10% and p-value < 0.05) in the Krauthammer et al. study # samples with BRAF # samples without BRAF mutation mutation Frequency Frequency p- Gene (N = 34) (%) (N = 55) (%) value STK33 4 11.8 0 0 0.019 NF1 7 20.6 3 5.5 0.034 Genes were ordered by p-values Supplementary Table S6. Mutated genes significantly associated with NRAS-mutated samples (frequency≥ 10% and p-value < 0.05) in the Krauthammer et al. study # samples with NRAS # samples without mutation NRAS mutation Frequency Frequency p- Gene (N = 19) (%) (N = 70) (%) value TTN 10 52.6 19 27.1 0.036 ALPK1 2 10.5 0 0 0.044 MAPK14 2 10.5 0 0 0.044 Genes were ordered by p-values. 4 Supplementary Table S7. Mutated genes significantly associated with BRAF-mutated samples identified by the meta-analysis but not significantly BRAF-associated in the Hodis et al. study (corresponds with Table 1) # samples with BRAF # samples without BRAF mutation mutation Frequency Frequency p- Gene (N = 76) (%) (N = 45) (%) value TTN 63 82.9 34 75.6 0.227 TP53 17 22.4 5 11.1 0.093 COL1A1 10 13.2 5 11.1 0.490 Supplementary Table S8. Mutated genes significantly associated with NRAS-mutated samples identified by the meta-analysis but some of them not significantly NRAS-associated in the Hodis et al. study (corresponds with Table 2) Gene # samples with NRAS Frequency # samples without NRAS Frequency p- mutation (%) mutation (%) value (N = 31) (N = 90) TTN 27 87.1 70 77.8 0.197 PPP6C 6 19.4 5 5.6 0.031 KALRN 8 25.8 9 10.0 0.034 PIK3R4 5 16.1 1 1.1 0.004 TRPM6 10 32.3 13 14.4 0.031 GUCY2C 4 12.9 5 5.6 0.170 PRKAA2 5 16.1 6 6.7 0.114 5 Supplementary Table S9. Mutated genes significantly associated with BRAF-mutated samples as identified by the meta-analysis but not significantly BRAF-associated in the Krauthammer et al. study (corresponds with Table 1) # samples with BRAF # samples without BRAF mutation mutation Frequency Frequency p- Gene (N = 34) (%) (N = 55) (%) value TTN 12 35.3 17 30.9 0.420 TP53 6 17.6 5 9.1 0.194 COL1A1 2 5.9 1 1.8 0.324 Supplementary Table S10. Mutated genes significantly associated with NRAS-mutated samples as identified by the meta-analysis but most of them not significantly NRAS- associated in the Krauthammer et al. study (corresponds with Table 2) Gene # samples with NRAS Frequency # samples without NRAS Frequency p- mutation (%) mutation (%) value (N = 19) (N = 70) TTN 10 52.6 19 27.1 0.036 PPP6C 3 15.8 5 7.1 0.226 KALRN 5 26.3 11 15.7 0.227 PIK3R4 1 5.3 2 2.9 0.518 TRPM6 3 15.8 10 14.3 0.559 GUCY2C 2 10.5 2 2.9 0.199 PRKAA2 2 10.5 3 4.3 0.289 6 Supplementary Table S11. Meta-analysis defined mutated genes associated with BRAF- mutated samples (frequency≥ 10%, p-value < 0.05 is shown in red) by histological subtype # samples with # samples without Type BRAF mutation (N BRAF mutation (N = Gene = Total number) Frequency Total number) Frequency p-value TTN Total 84 (N = 130) 64.6% 54 (N = 111) 48.7% 0.009 Acral 0 (N = 1) 0.0% 0 (N = 16) 0.0% 1.000 Mucosal 1 (N = 1) 100% 0 (N = 6) 0.0% 0.143 Uveal 0 (N = 0) 0.0% 1 (N = 6) 16.7% 1.000 Cutaneous 69 (N = 108) 63.9% 48 (N = 74) 64.9% 0.614 Unknown 14 (N = 20) 70.0% 5 (N = 9) 55.6% 0.364 TP53 Total 28 (N = 130) 21.5% 11 (N = 111) 9.9% 0.011 Acral 0 (N = 1) 0.0% 0 (N = 16) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 0 (N = 6) 0.0% 1.000 Uveal 0 (N = 0) 0.0% 0 (N = 6) 0.0% 1.000 Cutaneous 22 (N = 108) 20.4% 11 (N = 74) 14.9% 0.228 Unknown 6 (N = 20) 30.0% 0 (N = 9) 0.0% 0.082 COL1A1 Total 17 (N = 130) 13.1% 6 (N = 111) 5.4% 0.034 Acral 0 (N = 1) 0.0% 0 (N = 16) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 0 (N = 6) 0.0% 1.000 Uveal 0 (N = 0) 0.0% 0 (N = 6) 0.0% 1.000 Cutaneous 14 (N = 108) 13.0% 6 (N = 74) 8.1% 0.217 Unknown 3 (N = 20) 15.0% 0 (N = 9) 0.0% 0.312 Genes were ordered by p-values. 7 Supplementary Table S12. Meta-analysis defined mutated genes associated with NRAS- mutated samples (frequency≥ 10%, p-value < 0.05 is shown in red) by histological subtype Gene Type # samples with Frequency # samples without Frequency p-value NRAS NRAS mutation mutation (N = (N = Total Total number) number) TTN Total 37 (N = 51) 72.6% 101 (N = 190) 53.2% 0.009 Acral 0 (N = 2) 0.0% 0 (N = 15) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 1 (N = 6) 16.7% 1.000 Uveal 1 (N = 1) 100% 0 (N = 5) 0.0% 0.167 Cutaneous 32 (N = 41) 78.0% 85 (N = 141) 60.3% 0.026 Unknown 4 (N = 6) 66.7% 15 (N =23) 65.2% 0.669 PPP6C Total 9 (N = 51) 17.7% 11 (N = 190) 5.8% 0.011 Acral 0 (N = 2) 0.0% 0 (N = 15) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 1 (N = 6) 16.7% 1.000 Uveal 0 (N = 1) 0.0% 0 (N = 5) 0.0% 1.000 Cutaneous 8 (N = 41) 19.5% 9 (N = 141) 6.4% 0.017 Unknown 1 (N = 6) 16.7% 1 (N =23) 4.3% 0.002 KALRN Total 14 (N = 51) 27.5% 24 (N = 190) 12.6% 0.012 Acral 0 (N = 2) 0.0% 1 (N = 15) 6.7% 1.000 Mucosal 0 (N = 1) 0.0% 0 (N = 6) 0.0% 1.000 Uveal 0 (N = 1) 0.0% 0 (N = 5) 0.0% 1.000 Cutaneous 12 (N = 41) 29.3% 21 (N = 141) 14.9% 0.034 Unknown 2 (N = 6) 33.3% 2 (N =23) 8.7% 0.180 PIK3R4 Total 6 (N = 51) 11.8% 5 (N = 190) 2.6% 0.013 Acral 0 (N = 2) 0.0% 0 (N = 15) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 0 (N = 6) 0.0% 1.000 8 Uveal 0 (N = 1) 0.0% 0 (N = 5) 0.0% 1.000 Cutaneous 5 (N = 41) 12.2% 5 (N = 141) 3.5% 0.048 Unknown 1 (N = 6) 16.7% 0 (N =23) 0.0% 0.207 TRPM6 Total 14 (N = 51) 27.5% 26 (N = 190) 13.7% 0.020 Acral 0 (N = 2) 0.0% 0 (N = 15) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 0 (N = 6) 0.0% 1.000 Uveal 0 (N = 1) 0.0% 0 (N = 5) 0.0% 1.000 Cutaneous 13 (N = 41) 31.7% 23 (N = 141) 16.3% 0.028 Unknown 1 (N = 6) 16.7% 3 (N =23) 13.0% 0.627 GUCY2C Total 7 (N = 51) 13.7% 8 (N = 190) 4.2% 0.021 Acral 0 (N = 2) 0.0% 0 (N = 15) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 0 (N = 6) 0.0% 1.000 Uveal 0 (N = 1) 0.0% 0 (N = 5) 0.0% 1.000 Cutaneous 6 (N = 41) 14.6% 7 (N = 141) 5.0% 0.045 Unknown 1 (N = 6) 16.7% 1 (N =23) 4.3% 0.377 PRKAA2 Total 7 (N = 51) 13.7% 10 (N = 190) 5.3% 0.043 Acral 0 (N = 2) 0.0% 0 (N = 15) 0.0% 1.000 Mucosal 0 (N = 1) 0.0% 0 (N = 6) 0.0% 1.000 Uveal 0 (N = 1) 0.0% 0 (N = 5) 0.0% 1.000 Cutaneous 6 (N = 41) 14.6% 10 (N = 141) 7.1% 0.120 Unknown 1 (N = 6) 16.7% 0 (N =23) 0.0% 0.207 Genes were ordered by p-values.