Table 1.
Summary of point mutations and small indels identified in the primary tumor, brain metastasis, and xenograft.
| Chr | Start | Allele Change | Gene | Amino Acid Change | Mutant Allele Frequency | Copy Number | Enrichment FDR | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| N | T | M | X | T | M | X | M | X | |||||
| 1 | 26062702 | G>A | PAQR7 | p.A72 | 0.17% | 5.78% | 34.55% | 13.70% | 2 | 2 | 2 | 9.00e-4 | 0.011 |
| 1 | 26646672 | G>A | DHDDS | p.R159H | 0.14% | 21.12% | 40.24% | 88.29% | 2 | 2 | 2 | 5.73e-5 | 2.46e-5 |
| 1 | 43684654 | G>A | KIAA0467 | p.G2119R | 0.13% | 7.00% | 40.02% | 84.84% | 2 | 2 | 2 | 0.001 | 5.98e-5 |
| 1 | 45068225 | C>G | PTCH2 | p.W293S | 0.02% | 13.70% | 36.03% | 43.61% | 2 | 2 | 2 | 0.085 | 0.381 |
| 1 | 152723308 | delGCAACTTTTCATT | SHE | p.LPFKG476in_frame_delW | 0.19% | 19.28% | 21.33% | 7.69% | 4.61 | 5.34 | 6.92 | 0.820 | 0.065 |
| 1 | 226395989 | C>A | GUK1 | p.P11Q | 0.01% | 36.29% | 33.12% | 40.17% | 3.66 | 3.96 | 4.64 | 0.374 | 0.365 |
| 1 | 242935580 | A>T | PPPDE1 | p.T151S | 0.12% | 3.39% | 48.57% | 11.47% | 3.45 | 3.71 | 4.38 | 0.012 | 0.063 |
| 2 | 24994872 | G>A | ADCY3 | p.H163 | 0.06% | 7.10% | 37.49% | 48.71% | 3.17 | 3.24 | 3.78 | 0.007 | 0.029 |
| 2 | 56273320 | delG | CCDC85A | p.E161fs | 0.16% | 1.71% | 17.11% | 28.78% | 2.9 | 3.24 | 3.34 | 0.002 | 0.006 |
| 2 | 197349569 | G>C | GTF3C3 | p.R474G | 0.11% | 29.42% | 37.75% | 11.08% | 1.4 | 1.31 | 1.24 | 0.316 | 0.065 |
| 2 | 229835724 | C>T | PID1 | p.S14 | 0.11% | 8.95% | 38.89% | 66.13% | 2 | 2 | 1.36 | 0.001 | 0.166 |
| 2 | 241641282 | C>T | SNED1 | p.T708I | 0.04% | 0.32% | 36.52% | 2.30% | 2 | 2 | 2 | 1.58e-4 | 0.719 |
| 3 | 10236363 | G>T | IRAK2 | e8-1 | 0.38% | 48.37% | 52.69% | 53.33% | 2 | 2 | 2 | 0.156 | 0.762 |
| 3 | 139505123 | G>A | TXNDC6 | p.R221W | 0.29% | 39.50% | 58.62% | 15.81% | 2 | 2 | 2 | 0.039 | 0.012 |
| 3 | 150728323 | A>C | WWTR1 | p.F299V | 0.03% | 6.87% | 28.14% | 9.53% | 2 | 2 | 2 | 1.43e-4 | 0.020 |
| 4 | 40051165 | C>A | CHRNA9 | p.D437E | 0.10% | 28.38% | 36.82% | 90.26% | 2 | 2 | 2 | 0.073 | 9.67e-5 |
| 4 | 40134827 | delG | RBM47 | p.I280fs | 0.05% | 8.62% | 79.15% | 79.74% | 2 | 2 | 2 | 0.030 | 0.124 |
| 4 | 82232630 | C>T | PRKG2 | p.R709 | 0.11% | 6.99% | 82.99% | 91.51% | 2 | 2 | 2 | 0.083 | 0.094 |
| 5 | 135422725 | G>A | TGFBI | p.E576K | 0.17% | 89.09% | 37.58% | 18.45% | 2 | 2 | 2 | 3.34e-6 | 3.23e-5 |
| 5 | 169466048 | C>T | FOXI1 | p.S170F | 0.15% | 69.28% | 78.33% | 93.61% | 2 | 2 | 2 | 0.473 | 0.009 |
| 7 | 100463999 | G>C | MUC17 | p.S861T | 1.69% | 9.22% | 1.46% | 14.43% | 2 | 2.76 | 4.04 | 0.073 | 0.816 |
| 7 | 128284099 | C>T | FLNC | p.N2483 | 0.11% | 0.17% | 18.21% | 0.16% | 2.54 | 2.8 | 2.93 | 0.002 | 0.193 |
| 7 | 148400407 | G>A | ZNF786 | p.F130 | 0.13% | 13.61% | 62.86% | 81.04% | 2.51 | 2.85 | 3.54 | 3.01e-4 | 3.23e-5 |
| 8 | 3232441 | C>A | CSMD1 | p.A409S | 0.04% | 29.75% | 54.22% | 65.18% | 2 | 2 | 2 | 0.355 | 0.141 |
| 8 | 8477326 | C>T | ENSG00000222487 | NULL | 0.11% | 9.61% | 28.43% | 13.74% | 2 | 2 | 2.67 | 0.120 | 0.787 |
| 9 | 5040714 | T>C | JAK2 | p.I166T | 0.09% | 61.63% | 21.93% | 47.40% | 2.83 | 2.67 | 2.84 | 0.246 | 0.999 |
| 9 | 107137789 | G>A | SLC44A1 | p.A132T | 0.08% | 2.59% | 76.14% | 85.31% | 2 | 1.29 | 1.19 | 1.43e-4 | 1.05e-4 |
| 10 | 14603968 | C>T | FAM107B | p.R237Q | 2.65% | 13.53% | 63.25% | 97.88% | 3.7 | 4.04 | 4.76 | 3.29e-6 | 8.54e-8 |
| 10 | 30789749 | C>T | MAP3K8 | p.P461L | 0.11% | 13.33% | 31.72% | 77.47% | 3.44 | 3.71 | 4.21 | 0.002 | 9.67e-5 |
| 10 | 79240899 | G>A | DLG5 | p.D1474 | 0.07% | 32.94% | 76.10% | 74.72% | 2 | 2 | 2 | 6.12e-5 | 0.011 |
| 11 | 12496610 | insATGGAG | PARVA | p.338in_frame_insDG | 0.00% | 1.41% | 10.75% | 10.58% | 2 | 2 | 2 | 0.347 | 0.365 |
| 11 | 48128224 | A>T | PTPRJ | p.K1017N | 0.20% | 1.25% | 32.08% | 57.23% | 2 | 2 | 2.99 | 3.48e-4 | 2.20e-4 |
| 11 | 102687902 | G>A | DYNC2H1 | p.R3867Q | 0.06% | 12.81% | 25.78% | 15.69% | 2 | 2 | 2 | 0.002 | 0.023 |
| 12 | 31122692 | T>G | DDX11 | p.V33G | 0.02% | 44.35% | 40.39% | 57.88% | 1.49 | 1.37 | 1.24 | 0.316 | 0.386 |
| 13 | 76628331 | G>A | MYCBP2 | p.Q2222* | 0.10% | 87.84% | 43.76% | 36.95% | 2 | 2 | 2 | 0.004 | 0.003 |
| 13 | 100688137 | A>T | NALCN | p.D468E | 0.16% | 18.60% | 87.66% | 1.65% | 2 | 2.74 | 2.92 | 0.004 | 0.216 |
| 14 | 19285546 | G>T | OR4Q3 | p.L40 | 0.22% | 36.94% | 40.31% | 32.28% | 2 | 2 | 2 | 0.313 | 0.107 |
| 16 | 66569387 | T>G | DPEP3 | p.R262S | 0.84% | 45.61% | 39.43% | 76.59% | 2 | 2.9 | 3.02 | 0.293 | 6.93e-4 |
| 16 | 82828230 | C>A | KCNG4 | p.G121 | 0.04% | 4.15% | 26.82% | 69.89% | 2.43 | 3.09 | 3.49 | 0.083 | 0.259 |
| 17 | 7519157 | insG | TP53 | p.Q167fs | 4.61% | 79.40% | 62.62% | 97.96% | 2 | 2 | 2 | 0.085 | 0.003 |
| 17 | 32904736 | C>T | TADA2L | p.R339W | 0.12% | 17.49% | 59.92% | 79.47% | 2 | 2 | 2 | 0.002 | 0.002 |
| 19 | 12363315 | G>A | ZNF799 | p.H299 | 0.17% | 2.05% | 26.23% | 11.81% | 2 | 2 | 3.06 | 0.062 | 0.618 |
| 19 | 16006577 | insA | ENSG00000167459 | p.I38fs | 4.82% | 26.53% | 48.47% | 37.74% | 2 | 2 | 3.06 | 0.286 | 0.809 |
| 20 | 5851563 | G>A | CHGB | p.R258Q | 0.14% | 35.64% | 45.50% | 54.87% | 2.57 | 2.86 | 3.64 | 0.057 | 0.005 |
| 21 | 45015744 | G>A | UBE2G2 | p.I158 | 0.12% | 21.57% | 26.72% | 20.89% | 2 | 2 | 2 | 0.522 | 0.728 |
| X | 15731812 | C>G | ZRSR2 | p.A95G | 1.01% | 64.01% | 58.66% | 72.08% | 2.51 | 2.77 | 2.99 | 0.137 | 0.969 |
| X | 43893087 | C>G | EFHC2 | e15-1 | 0.01% | 9.88% | 23.15% | 7.35% | 2 | 2.68 | 2.82 | 0.114 | 0.381 |
| X | 46318872 | insA | CHST7 | p.T188fs | 0.19% | 3.67% | 54.36% | 38.84% | 2 | 2.68 | 2.82 | 0.073 | 0.058 |
| X | 105040331 | C>A | NRK | p.A681E | 0.12% | 4.08% | 30.84% | 52.45% | 2 | 2 | 2 | 0.085 | 0.017 |
| X | 129374039 | A>G | RBMX2 | p.K169E | 0.30% | 11.88% | 38.36% | 69.46% | 2 | 2.65 | 2.77 | 0.002 | 0.003 |
*
Gene sets from Ensembl build 54 and Genbank (downloaded in May 2009) were used for annotation of mutations. T: primary tumor; M: metastasis; X: xenograft.