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

Ovarian cancer is one of the most common causes of mortality among women, and the prevalence of ovarian cancer increases. Early diagnosis of this disease via genetic variant testing is one potential strategy for enhancing treatment and disease outcome. Our aim was to establish a standard procedure of next generation sequencing (NGS) for the formalin-fixed paraffin-embedded (FFPE) forms of ovarian tumor tissue to detect genetic mutation in our laboratory. Here, we used the FFPE samples of ovarian tumor tissues from Vietnamese patients to detect pathogenic variants in BRCA1/BRCA2 via the NGS. DNA was extracted using the QIAamp DNA FFPE Tissue Kit, and then its quality was assessed by the 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%. Five pathogenic variants in BRCA1/BRCA2, including both single nucleotide polymorphisms and indels were successfully detected using NgeneAnalySysTM software. In conclusion, DNA extraction from the FFPE sample was qualified for sequencing and the sequencing results met all the required metrics for variant analysis.