Table 5.
Performance of the platform on FFPE samples from the 2016 EMQN Oncogene Panel Testing External Quality Assessment Scheme. All variants were correctly detected. Percentages show the frequencies of the variants present as reported by EMQN (quantitated by ddPCR) and the frequencies of the same variants as determined by the developed NGS platform. Sample #4 was mildly formalin compromised. Analyses of these samples were performed with v6
| Variants present in each sample | Estimated frequencies | |
|---|---|---|
| EMQN (ddPCR) (%) | NGS platform (%) | |
| FFPE sample #1 | ||
| BRAF (NM_004333.4) c.1799T>A; p.V600E | 16 | 19.24 |
| KRAS (NM_004985.3) c.38G>A; p.G13D | 16 | 16.97 |
| PIK3CA (NM_006218.2) c.3140A>G; p.H1047R | 17 | 15.12 |
| FFPE sample #2 | ||
| BRAF (NM_004333.4) c.1799T>A; p.V600E | 66.70 | 67.62 |
| EGFR (NM_005228.3) c.2155G>A; p.G719S | 1.10 | 0.72 |
| EGFR (NM_005228.3) c.2235_2249del15; p.E746_A750del | 0.90 | 0.28 |
| EGFR (NM_005228.3) c.2369C>T; p.T790M | 1.20 | 2.11 |
| EGFR (NM_005228.3) c.2573T>G; p.L858R | 1.30 | 0.95 |
| EGFR (NM_005228.3) c.2582T>A; p.L861Q | 0.70 | 0.95 |
| PIK3CA (NM_006218.2) c.3140A>G; p.H1047R | 50 | 46.87 |
| FFPE sample #3 | ||
| BRAF (NM_004333.4) c.1799T>A; p.V600E | 12 | 12.88 |
| EGFR (NM_005228.3) c.2155G>A; p.G719S | 23.60 | 22.44 |
| EGFR (NM_005228.3) c.2235_2249del15; p.E746_A750del | 1.70 | 0.72 |
| EGFR (NM_005228.3) c.2369C>T; p.T790M | 1.02 | 1.33 |
| EGFR (NM_005228.3) c.2573T>G; p.L858R | 3.40 | 3.82 |
| KIT (NM_000222.2) c.2447A>T; p.D816V | 9 | 9.75 |
| KRAS (NM_004985.3) c.35G>A; p.G12D | 5.90 | 7.97 |
| KRAS (NM_004985.3) c.38G>A; p.G13D | 15 | 13.55 |
| NRAS (NM_002524.4) c.181C>A; p.Q61K | 12 | 8.55 |
| PIK3CA (NM_006218.2) c.1633G>A; p.E545K | 7.80 | 9.98 |
| PIK3CA (NM_006218.2) c.3140A>G; p.H1047R | 18 | 18.36 |
| FFPE sample #4 (formalin compromised) | ||
| BRAF (NM_004333.4) c.1799T>A; p.V600E | 9.40 | 4.09 |
| EGFR (NM_005228.3) c.2155G>A; p.G719S | 26.50 | 15.87 |
| EGFR (NM_005228.3) c.2235_2249del15; p.E746_A750del | 2.30 | 1.50 |
| EGFR (NM_005228.3) c.2369C>T; p.T790M | 0.85 | 0.90 |
| EGFR (NM_005228.3) c.2573T>G; p.L858R | 2.40 | 1.20 |
| KIT (NM_000222.2) c.2447A>T; p.D816V | 9 | 15.79 |
| KRAS (NM_004985.3) c.35G>A; p.G12D | 5.50 | 11.81 |
| KRAS (NM_004985.3) c.38G>A; p.G13D | 16 | 16.79 |
| NRAS (NM_002524.4) c.181C>A; p.Q61K | 10 | 8.84 |
| PIK3CA (NM_006218.2) c.1633G>A; p.E545K | 7.60 | 4.32 |
| PIK3CA (NM_006218.2) c.3140A>G; p.H1047R | 20 | 25 |