Table 1. Somatic missense mutations identified in the samples analyzed.
| Tissue Sample (Date collected) |
Blood (Jan. 2010) |
Primary Tumor (Feb. 2010) |
Level IV Lymph Node Metastasis (Apr. 2010) |
Lung Metastasis (Apr. 2010) |
Cervical Lymph Node Metastasis (Oct. 2012) |
|---|---|---|---|---|---|
| Total Variations | 1114 | 1479 | 3127 | 8111 | 1252 |
| Population Frequency Filter (MAF<0.005) | |||||
| -1000GP_EU | 150 | 529 | 2171 | 7123 | 294 |
| - ExAC_NFE | 69 | 443 | 2089 | 7031 | 208 |
| - ESP6500_Eur | 69 | 443 | 2088 | 7031 | 206 |
| ClinVar | 66 | 439 | 2079 | 7019 | 206 |
| Quality Filters | |||||
| -DP>100 | 48 | 214 | 1422 | 5699 | 137 |
| - GQ>30 | 44 | 75 | 311 | 482 | 84 |
| - SAF/SAR≠ 0 | 39 | 67 | 236 | 474 | 72 |
| - HRUN<6 | 37 | 61 | 232 | 458 | 60 |
| - AF>10% | 37 | 54 | 143 | 255 | 55 |
| Functional Filters | |||||
| - Exonic* | 10 | 15 | 32 | 30 | 14 |
| - Somatic Variants | - | 5 | 22 | 22 | 4 |
| - Somatic variants found in all tissues | 1 | 1 | 1 | 1 |
AF: Allele frequency; DP: Depth of Coverage (total read depth at the locus); GQ: Genotype Quality (Phred-scaled marginal (or unconditional) probability of the called genotype); HRUN: Run length (the number of consecutive repeats of alternate allele in the reference genome); SAF/SAR: (Alternative allele observation on the forward strand / Alternative allele observation on the reverse strand).
* Exonic variants included nonsynonymous, stop-gain, stop-loss, splice-site variants and frameshift indels.