Rapid genomic profiling of circulating tumor DNA in non-small cell lung cancer using Oncomine Precision Assay with Genexus™ integrated sequencer

Siew-Kee Low; Ryo Ariyasu; Ken Uchibori; Rie Hayashi; Hiu Ting Chan; Yoon Ming Chin; Takahiro Akita; Yuhei Harutani; Ayu Kiritani; Ryosuke Tsugitomi; Ryo Manabe; Shinsuke Ogusu; Yoshiaki Amino; Satoru Kitazono; Noriko Yanagitani; Yusuke Nakamura; Makoto Nishio

doi:10.21037/tlcr-21-981

Rapid genomic profiling of circulating tumor DNA in non-small cell lung cancer using Oncomine Precision Assay with Genexus™ integrated sequencer

Transl Lung Cancer Res. 2022 May;11(5):711-721. doi: 10.21037/tlcr-21-981.

Authors

Siew-Kee Low^#¹, Ryo Ariyasu^#², Ken Uchibori², Rie Hayashi¹, Hiu Ting Chan¹, Yoon Ming Chin¹, Takahiro Akita², Yuhei Harutani², Ayu Kiritani², Ryosuke Tsugitomi², Ryo Manabe², Shinsuke Ogusu², Yoshiaki Amino², Satoru Kitazono², Noriko Yanagitani², Yusuke Nakamura¹, Makoto Nishio²

Affiliations

¹ Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
² Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.

^# Contributed equally.

Abstract

Background: Genomic profiling of tumors from cancer patients facilitates molecular-guided therapy. The turnaround time is one of important issues to deliver results timely for clinical decisions. The Ion Torrent™ Genexus™ Integrated Sequencer automates all next generation sequencing (NGS) workflows and delivers results within a day.

Methods: In this study, we conducted a feasibility study to evaluate the detection rate of genomic alterations from cell-free total nucleic acid (cfTNA, containing cfDNA and cfRNA) of 119 non-small cell lung cancer using Oncomine Precision Assay on Genexus™ Integrated Sequencer. Oncomine Precision Assay (OPA) covers actionable mutations, copy number variations and fusion genes and that are applicable for the selection of targeted therapy. cfTNA isolated from plasma (derived from 14 ml of blood) were subjected to the Genexus system for library construction, templating, sequencing, and data analyses.

Results: The sequencing resulted in median overall depth of 35,773× and median molecular coverage of 2,192× with cfTNA input ranged from 11 to 36 ng. Among the 119 samples evaluated, we detected at least one genomic alteration in plasma cfTNA of 79 cases (66%). When comparing to standard-of-care testing, the sensitivity and specificity of mutation detection in non-small cell lung cancer related genes using liquid biopsy with Genexus-OPA ranged between 49-67% and 93-100%, respectively. 59% of actionable mutations, which were present in tumor tissues, were detected by the Genexus- Oncomine Precision Assay using plasma cfTNA. Among the 5 mutations detected from liquid biopsy only, three mutations are of level 1 evidence according to OncoKB database, highlighting the clinical utilities of liquid biopsy in addressing tumor heterogeneity. Extrathoracic metastasis and levels of lactate dehydrogenase (LDH), C-reactive protein (CRP) and Carcinoembryonic Antigen (CEA) are found to be associated with increased circulating tumor DNA detection.

Conclusions: The Genexus™ Integrated Sequencer system is an automated, accurate NGS system with short turnaround time (TAT) that could assist clinicians to make more timely decision.

Keywords: Non-small cell lung cancer (NSCLC); actionable mutation; circulating tumor DNA; liquid biopsy; next generation sequencing (NGS).