Table 1. “Best GBM-related mutations” from coding regions of SD01 and TCGA samples.
| Gene | Sample | AA change | FATHMM score | SIFT score | AF (Tumor) | Coverage (Tumor) |
|---|---|---|---|---|---|---|
| EGFR | SD01 RNA-seq only | A702S | −0.97 (CANCER) | 0.01 (Del) | 0.015 | 852 |
| EGFR | SD01 Intersection | A289V | −1.04 (CANCER) | 0.002 (Del) | 0.072 | 125 |
| EGFR | GBM01 Intersection | G63R | −1.93 (CANCER) | 0.0 (Del) | 0.175 | 296 |
| TP53 | GBM01 Intersection | G105R | −10.02 (CANCER) | 0.0 (Del) | 0.44 | 50 |
| TP53 | GBM02 RNA-seq only | I254S | −9.48 (CANCER) | 0.0 (Del) | 0.949 | 390 |
| TSC2 | GBM02 RNA-seq only | V296fs | 71% (pathogenic) | 85.8% (Dam) | 0.137 | 55 |
| PTEN | GBM02 Intersection | D107Y | −3.06 (CANCER) | 0.0 (Del) | 0.69 | 92 |
| PTEN | GBM03 Intersection | R173H | −6.42 (CANCER) | 0.0 (Del) | 0.331 | 173 |
| PTEN | GBM04 Intersection | D326fs | 88% (pathogenic) | 85.8% (Dam) | 0.393 | 146 |
| PTEN | GBM07 WXS only | R130Q | −5.84 (CANCER) | 0.0 (Del) | 0.713 | 190 |
| NF1 | GBM10 WXS only | C622F | −0.83 (CANCER) | 0.01 (Del) | 0.403 | 389 |
Notes:
All variants shown were included in COSMIC and in a set of 29 GBM-related genes but not dbSNP. All variants are deleterious based on scoring by SIFT and FATHMM with cancer weights. For SIFTindel and FATHMM indels, the score is given as a confidence score of the prediction. AF (Allele Fraction, tumor) shows the proportion of altered reads in tumor samples, with Coverage (tumor) being the total number of reads at the variant position.