Analytical performance evaluation of a commercial next generation sequencing liquid biopsy platform using plasma ctDNA, reference standards, and synthetic serial dilution samples derived from normal plasma

Table 1 Synthetic serial dilution variants

Sr#	Gene Name	chr	Position	dbSNP ID	Coding change	Amino acid change	AF (%)
1	NTRK1	chr1	156876441	rs6334	c.1674G > A	p.Gln558Gln	43.7
2	FGFR2	chr10	121551357	rs755793	c.557 T > C	p.Met186Thr	48.6
3	BRCA2	chr13	32332343	rs766173	c.865A > C	p.Asn289His	43.7
4	BRCA2	chr13	32332843	rs1801439	c.1365A > G	p.Ser455Ser	41
5	BRCA2	chr13	32336584	rs1801499	c.2229 T > C	p.His743His	50.3
6	BRCA2	chr13	32337326	rs1799944	c.2971A > G	p.Asn991Asp	46.5
7	BRCA2	chr13	32355095	rs1799955	c.7242A > G	p.Ser2414Ser	46.1
8	BRCA2	chr13	32379413	rs11571769	c.8851G > A	p.Ala2951Thr	48.1
9	BRCA1	chr17	43071077	rs1799966;rs730880287	c.4900A > G	p.Ser1634Gly	46.7
10	BRCA1	chr17	43082453	rs1060915;rs397509161	c.4308 T > C	p.Ser1436Ser	47.9
11	BRCA1	chr17	43091983	rs16942	c.3548A > G	p.Lys1183Arg	46.3
12	BRCA1	chr17	43092418	rs16941	c.3113A > G	p.Glu1038Gly	49.3
13	BRCA1	chr17	43093220	rs16940	c.2311 T > C	p.Leu771Leu	47.8
14	BRCA1	chr17	43093449	rs1799949	c.2082C > T	p.Ser694Ser	45.7
15	ALK	chr2	29320870	rs35093491	c.1427 T > C	p.Val476Ala	48.4
16	FGFR3	chr4	1799815	rs3135868	c.445 + 3A > G	N/A	43.7
17	FGFR3	chr4	1801524	rs2305181	c.603 T > C	p.Ile201Ile	49.5
18	PDGFRA	chr4	54263911	rs2229307	c.612 T > C	p.Asn204Asn	46.3
19	PDGFRA	chr4	54267559	rs4358459	c.939 T > G	p.Gly313Gly	51.2
20	CSF1R	chr5	150080792	rs41287102	c.282C > T	p.Ser94Ser	46.1
21	PMS2	chr7	5982995	rs140788589	c.2007-4G > A	N/A	45.7
22	PTCH1	chr9	95476097	rs1805155	c.1665 T > C	p.Asn555Asn	47.1

Variant calls were generated by AVENIO Oncology Analysis Server (OAS). Twenty-two mutations were identified at ~ 50% allele frequency in one of the normal plasma sample. This sample was designated as mutant sample. The sample was serially diluted in the background of pooled cfDNA generated from normal plasma samples lacking these mutations, to generate plasma cfDNA samples mutations ranging from 5 to 0.1% AF

ISSN: 1471-2407