Next generation sequencing for the formalin-fixed paraffin-embedded samples of ovarian cancer in Vietnam

Abstract

Ovarian cancer is one of the most popular causes of mortality among women, and the prevalence of ovarian cancer is increased. Early diagnosis of this disease via genetic variant testing is one potential strategy for enhancing treatment and disease outcome. In this study, we used the formalin-fixed, paraffin-embedded (FFPE) samples of ovarian tumor tissues from Vietnamese patients to detect pathogenic variants in BRCA1/BRCA2 via next-generation sequencing. DNA was extracted using QIAamp DNA FFPE Tissue Kit, and then its quality was assessed using BioDrop and Qubit. The BRCAaccuTestTM PLUS kit and Illumina MiSeqDx instrument were used for both library preparation and sequencing. All samples had passed the A260/280 ratio cut-off for DNA purity and the requirement of DNA concentration. Excepted for the 1st time, the percentage of ≥ Q30 was more than 80%, while the density was approximately 1,200 K/mm2, while the phasing and prephasing (%) metrics were satisfied to be less than 0.1%. 5 pathogenic variants in BRCA1/BRCA2, including both single nucleotide polymorphisms and indels were successfully detected using NgeneAnalySysTM software.