A method to improve genetic analysis of lung cancer samples

Abstract

To the Editors: The Oncomine Dx Target Test (ODxTT) (Ion Torrent PGM Dx Sequencer; Thermo Fisher Scientific) is a nextgeneration sequencing panel, which detects 46 genes on DNA and RNA isolated from formalin-fixed and paraffinembedded (FFPE) specimens using the Ion PGMTM Dx System. This test enables comprehensive biomarker testing for non-small cell lung cancer (NSCLC), and was approved as a companion diagnostic for targeted therapies by the US Food and Drug Administration in June 2017, and the Ministry of Health, Labor and Welfare of Japan in February 2019. Although the quantity of tumour cells in surgical samples is greater than in small biopsy samples, the quality of nucleic acids, especially RNA, is prone to deterioration in surgical samples. Therefore, we experienced invalid RNA analysis results due to a failure to meet the RNA sample QC (quality control) metrics, especially in lobectomy samples. We believed the causes were the delay until the beginning of formalin fixation and insufficient formalin fixation. We retrospectively assessed the influence of a modified lobectomy sample preparation process on nucleic acid quality and the success rate of the ODxTT. This retrospective study was conducted at Matsusaka Municipal Hospital, Japan. We reviewed the electronic data from consecutive patients diagnosed with NSCLC whose FFPE surgical lung samples had been submitted for ODxTT between August 2019 and August 2020. Samples collected in other hospitals and archived samples were excluded. Clinical data assessments included surgical method, pathological findings, genetic test results and quantity and quality of nucleic acids. Figure 1 shows a flow chart of the FFPE sample preparation process for lung surgery. The limited resection samples, including lung segmentectomy and wedge resections, were immediately put in 10% neutral buffered formalin (NBF) after sampling for intraoperative rapid