Table 2 Detectable somatic mutations in circulating cell-free DNA (ccfDNA) from blood plasma compared to genomic DNA (gDNA) derived from the surgical tumour specimens utilising next-generation sequencing with a panel of 12 genes including BRAF, DDR2, ERBB2, HRAS, KEAP1, KRAS, NFE2L2, NRAS, PIK3CA, PTEN, RHOA and TP53 as well as digital droplet PCR. Measured allele frequencies are shown in %.
Case | estimated tumour cell content | mutational analysis gDNA | mutational analysis ccfDNA | ||
|---|---|---|---|---|---|
NGS | ddPCR | NGS | ddPCR | ||
1 | 40% | wildtype | not analysed | wildtype | not analysed |
2 | 80% | TP53: c.818G > A p.R273H 37% | TP53: c.818G > A p.R273H 39% | wildtype | wildtype |
3 | 10% | TP53: c.742C > T p.R248W 9% | TP53: c.742C > T p.R248W 10% | wildtype | wildtype |
4 | 90% | TP53: c.401T > C p.F134S 58% | TP53: c.401T > C p.F134S 55% | wildtype | wildtype |
5 | 70% | TP53: c.434delT p.L145Rfs*25 29% | TP53: c.434delT p.L145Rfs*25 48% | TP53: c.434delT p.L145Rfs*25 1% | TP53: c.434delT p.L145Rfs*25 1.1% |
6 | 90% | RHOA: c.205C > G p.L69V 33%; | RHOA: not analysed; | wildtype | wildtype |
PIK3CA: c.1633G > A p.E545K 42% | PIK3CA: c.1633G> Ap.E545K 42% | ||||
7 | 10% | wildtype | not analysed | wildtype | not analysed |
8 | 10% | wildtype | not analysed | wildtype | not analysed |
9 | 10% | TP53: c.733G > A p.G245S 17% | TP53: c.733G > A p.G245S 17% | wildtype | wildtype |
10 | 2% | not analysed (low tumour content) | wildtype | not analysed | |
11 | 90% | TP53: c.734G > C p.G245A 72% | TP53: c.734G > C p.G245A 73% | TP53: c.734G > C p.G245A 1% | TP53: c.734G > C p.G245A 0.22% |
12 | 80% | TP53: c.376–3C > G 71% | TP53: c.376–3C > G 72% | wildtype | TP53: c.376–3C > G 1.4% |
13 | 80% | TP53: c.559 + 1G > A 49% | TP53: c.559 + 1G > A 75% | wildtype | wildtype |
14 | 60% | TP53: c.818G > A p.R273H 14% | TP53: c.818G > A p.R273H 14% | wildtype | TP53: c.818G > A p.R273H 1.4% |
15 | 2% | not analysed (low tumour content) | wildtype | not analysed | |
16 | 20% | TP53: c.818G > A p.R273H 16%; TP53: c.733G > A p.G245S 9% | TP53: c.818G > A p.R273H 16%; TP53: c.733G > A p.G245S 10% | wildtype | wildtype |
17 | 90% | TP53: c.844C > T p.R282W 45% | TP53: c.844C > T p.R282W 47% | wildtype | TP53: c.844C > T p.R282W 0.25% |
18 | 70% | wildtype | not analysed | wildtype | not analysed |
19 | 30% | TP53: c.833C > T p.P278L 30% | TP53: c.833C > T p.P278L 31% | wildtype | wildtype |
20 | 80% | TP53: c.844C > T p.R282W 63% | TP53: c.844C > T p.R282W 41% | wildtype | wildtype |
21 | 90% | PIK3CA: c.1637A > C p.Q546P 30% | PIK3CA: c.1637A > C p.Q546P 31% | wildtype | PIK3CA: c.1637A > C p.Q546P 0.5% |
22 | 40% | BRAF: c.1781A > G p.D594G 31%; TP53: c.614 A > T p.Y205F 35% | BRAF: c.1781A > G p.D594G 31%; TP53: not analysed | wildtype | wildtype |
23 | 50% | KRAS: c.35G > C p.G12A 25%; KRAS: c.347A > G p.N116S 25%; PTEN: c.79 T > A p.Y27N 36% | KRAS: c.35G > C p.G12A 25%; KRAS: c.347A > G not analysed; PTEN: not analysed | wildtype | wildtype |
24 | 70% | TP53: c.614A > C p.Y205S 36%; TP53: c.880G > T p.E294* 25% | TP53: c.614A > C p.Y205S 35%; TP53: c.880G > T not analysed | wildtype | wildtype |
25 | 80% | ERBB2: c.2327G > T p.G776V 30% | ERBB2: c.2327G > T p.G776V 34% | wildtype | ERBB2: c.2327G > T p.G776V 0.2% |
26 | 60% | TP53: c.743G > A p.R248Q 9% | TP53: c.743G > A p.R248Q 7% | wildtype | wildtype |
27 | 80% | TP53: c.844C > T p.R282W 53% | TP53: c.844C > T p.R282W 52% | TP53: c.844C > T p.R282W 2.4% | TP53: c.844C > T p.R282W 3.5% |
Positive Control: | |||||
M1 | 10% (in 2014) | PIK3CA: c.1624G > A p.E542K 5% | PIK3CA: c.1624G > A p.E542K 20% | PIK3CA: c.1624G > A p.E542K 14% | PIK3CA: c.1624G > A p.E542K 6% |
