Table 1.
Clinically informative mutations in HPV-positive and negative disease
| Sample | Position | Mutation | Ref | Var | (%) Var | # Reads | COSMIC ID | TCGA_HNSCC dataa | Provisional |
|---|---|---|---|---|---|---|---|---|---|
| HPV−_1 | chr3:178936091 | PIK3CA c.1633G>A, p.E545K | G | A | 18.99 | 4,255 | COSM763 | (21) specimens | |
| HPV−_1 | chr7:116411990 | MET c.3029C>T, p.T1010I | C | T | 43.33 | 4,133 | COSM707 | (0) likely SNP | |
| HPV−_3 | chr17:7,577,106 | TP53 c.832C>A, p.P278T | G | T | 40.66 | 2,688 | COSM368635 | (0), but (3) p.T278S | |
| HPV+_1 | chr4:1803568 | FGFR3 c.746C>G, p.S249C | C | G | 17.98 | 1,424 | COSM715 | (1) TCGA-CR-6481 (OPSCC, HPV+) | |
| HPV+_3 | chr4:1803564 | FGFR3 c.742C>T, p.R248C | C | T | 16.98 | 2,091 | COSM714 | (0) specimens | |
| HPV+_3 | chr13:49027168 | RB1 c.1735C>T, p.R579a | C | T | 18.78 | 1,347 | COSM892 | (0), but (8) inactivating mutations | |
| HPV+_4 | chr3:178916876 | PIK3CA c.263G>A, p.R88Q | G | A | 44.92 | 2,560 | COSM746 | (1) TCGA-CR-6471 | |
Using the AmpliSeq Cancer Panel (v1), we identified clinically informative mutations in 50 % (2/4) of the HPV-negative tumors and (3/4) 75 % of the HPV-positive tumors. Specific mutations were compared to the HNSCC TCGA dataset queried using cBioPortal. The numbers of specific mutations which were also found in the TCGA dataset are shown in brackets, and the TCGA case number is shown for tumors where only one tumor shared the same mutation
aProvisional TCGA HNSCC dataset (516 tumors) viewed using cBioPortal July 2014