Research Article
A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome Sequencing
Table 3
Coding mutations in the HPV-positive tumor.
| Chr | Position | Reference allele | Tumor allele | Zygosity | dbSNP ID | Region | Type | Gene | Transcript name | Exon | CDS position | Protein change | Stansky* | Agrawal** |
| 19 | 15789140 | A | G | Homo | rs609290 | Exonic | Nonsynonymous | CYP4F12 | NM_023944 | 3 | c.A268G | p.I90V | Yes | | 10 | 88946876 | G | A | Hetero | | Exonic | Nonsynonymous | FAM35A | NM_019054 | 8 | c.G2227A | p.D743N | | | 3 | 51930850 | T | C | Homo | rs57859638 | Exonic | Nonsynonymous | IQCF1 | NM_152397 | 3 | c.A169G | p.K57E | | | 7 | 20180717 | C | G | Homo | rs3735615 | Exonic | Nonsynonymous | MACC1 | NM_182762 | 7 | c.G2411C | p.R804T | Yes | | 14 | 64882380 | A | G | Hetero | rs1950902 | Exonic | Nonsynonymous | MTHFD1 | NM_005956 | 6 | c.A401G | p.K134R | | | 7 | 100634194 | C | G | Hetero | | Exonic | Nonsynonymous | MUC12 | NM_001164462 | 2 | c.C350G | p.A117G | | | 19 | 9006667 | A | G | Homo | rs75101943 | Exonic | Nonsynonymous | MUC16 | NM_024690 | 44 | c.T39581C | p.I13194T | Yes | | 19 | 9074122 | T | G | Homo | | Exonic | Nonsynonymous | MUC16 | NM_024690 | 3 | c.A13324C | p.T4442P | Yes | | 3 | 195517753 | C | T | Hetero | | Exonic | Nonsynonymous | MUC4 | NM_018406 | 2 | c.G698A | p.G233E | Yes | | 11 | 1017381 | G | C | Hetero | rs34912894 | Exonic | Nonsynonymous | MUC6 | NM_005961 | 61 | c.C5420G | p.T1807S | Yes | | 19 | 50865535 | A | G | Homo | rs676314 | Exonic | Nonsynonymous | NAPSA | NM_004851 | 2 | c.T119C | p.I40T | | | 4 | 170345835 | G | C | Homo | | Exonic | Nonsynonymous | NEK1 | NM_001199397 | 31 | c.C3091G | p.Q1031E | | | 17 | 3195485 | C | T | Hetero | | Exonic | Nonsynonymous | OR3A1 | NM_002550 | 1 | c.G392A | p.R131Q | | | 3 | 98073075 | A | G | Hetero | | Exonic | Nonsynonymous | OR5K4 | NM_001005517 | 1 | c.A378G | p.I126M | Yes | | 5 | 140590766 | A | G | Homo | rs2910006 | Exonic | Nonsynonymous | PCDHB12 | NM_018932 | 1 | c.A2287G | p.K763E | | | 12 | 27787878 | G | A | Hetero | | Exonic | Nonsynonymous | PPFIBP1 | NM_001198916 | 4 | c.G100A | p.D34N | | | 15 | 43827261 | G | C | Hetero | | Exonic | Nonsynonymous | PPIP5K1 | NM_001190214 | 30 | c.C3832G | p.H1278D | | | 1 | 12853378 | T | G | Hetero | rs112330886 | Exonic | Nonsynonymous | PRAMEF1 | NM_023013 | 2 | c.T2G | p.M1R | Yes | | X | 135956575 | G | A | Hetero | rs78646793 | Exonic | Nonsynonymous | RBMX | NM_002139 | 9 | c.C902T | p.P301L | | | 6 | 33272855 | G | C | Homo | rs2071888 | Exonic | Nonsynonymous | TAPBP | NM_172208 | 4 | c.C779G | p.T260R | | | 12 | 11183046 | C | T | Hetero | | Exonic | Nonsynonymous | TAS2R31 | NM_176885 | 1 | c.G889A | p.V297M | | | 12 | 11213969 | A | G | Hetero | rs2599402 | Exonic | Nonsynonymous | TAS2R46 | NM_176887 | 1 | c.T925C | p.S309P | Yes | | 3 | 100084425 | T | G | Homo | | Exonic | Nonsynonymous | TOMM70A | NM_014820 | 12 | c.A1810C | p.K604Q | Yes | | 9 | 135277007 | C | T | Homo | rs3739916 | Exonic | Nonsynonymous | TTF1 | NM_007344 | 2 | c.G1202A | p.R401Q | | Yes | 19 | 38378659 | A | T | Homo | | Exonic | Nonsynonymous | WDR87 | NM_031951 | 6 | c.T5535A | p.N1845K | | | 9 | 74975645 | C | G | Hetero | | Exonic | Nonsynonymous | ZFAND5 | NM_001102421 | 2 | c.G50C | p.G17A | | | 12 | 133732818 | C | T | Hetero | | Exonic | Nonsynonymous | ZNF10 | NM_015394 | 5 | c.C986T | p.S329F | | | 19 | 44933706 | C | T | Hetero | rs57014690 | Exonic | Nonsynonymous | ZNF229 | NM_014518 | 6 | c.G1250A | p.S417N | Yes | | 19 | 57089050 | C | T | Hetero | rs4801177 | Exonic | Nonsynonymous | ZNF470 | NM_001001668 | 6 | c.C1253T | p.T418I | Yes | | 19 | 52618497 | A | T | Hetero | | Exonic | Nonsynonymous | ZNF616 | NM_178523 | 4 | c.T1920A | p.N640K | Yes | | 2 | 71654175 | G | A | Homo | rs1804020 | Exonic | Nonsynonymous | ZNF638 | NM_001252612 | 24 | c.G5176A | p.V1726M | | | 7 | 57528923 | G | C | Hetero | | Exonic | Nonsynonymous | ZNF716 | NM_001159279 | 4 | c.G756C | p.W252C | | |
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Chr: chromosome, *mutations present in Stransky et al., Science 2011 [7], **mutations present in Agrawal et al., Science 2011 [6], Homo: homozygous, Hetero: heterozygous.
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