B-249 Usefulness of Simultaneous Detection of Germline and Somatic Variants From Different Specimen Types by Next-generation Sequencing

Abstract

Abstract Background Genetic variants detection by next-generation sequencing (NGS) from tumor specimen only is considered limited in diagnosis due to difficulties in discriminating somatic variants from germline ones. It will be even more helpful in diagnosing patients with cancer if we perform NGS analysis from specimen of both tumor and blood. This study shows the usefulness of simultaneous detection of germline and somatic variants from different specimen types by NGS. Methods NGS panel assay designed for solid tumor composed of 80 genes was conducted for detection of both somatic and germline variants. DNA samples extracted from both buffy coat of whole blood and formalin-fixed paraffin-embedded (FFPE) specimen from 4 patients with renal cancer and 3 patients with ovarian cancer were used in assay. We compared results from both specimen and finalized somatic and germline variants detected. Results In 4 patients specimen with renal cell carcinoma, we were able to rule out germline variants from somatic variants by analysis of NGS assay from both specimen types. Genes ruled out for germline variants of uncertain significance (tier 3) or higher levels are ARID1B: c.1031C>T, p.A344V, ERBB2: c.3430G>C, p.D1144H, BRCA2: c.3220A>T, p.S1074C, POLE: c.2974G>A, p.A992T, EP300: c.1666A>G, p.M556V, EP300: c.2539C>T, p.P847S, ERBB3: c.1115C>G, p.P372R, BAP1: c.1124A>T, p.E375V. In 3 patients with ovarian cancer, genes ruled out are EGFR: c.739G>C, p.D247H, MET: c.4172A>T, p.D1391V, PBRM1: c.2678A>G, p.Y893C, SETD2: c.1208G>A, p.S403N, AKT1: c.1373T>C, p.M458T, FGFR3: c.160G>A, p.G54R, KMT2C: c.9530G>A, p.R3177H, SMARCB1: c.1116G>A, p.T372T. All variants confirmed are tier 3 level of clinical significance. Conclusion According to the results of this study, we were able to exclude germline variants form somatic ones in NGS assay reports for cancer patients. This study shows the usefulness of simultaneous detection of germline and somatic variants from different specimen types by NGS.