Feasibility study of cancer genome alterations identified by next generation sequencing: ABC study

• Published in: Japanese journal of clinical oncology 2018-06, Vol.48 (6), p.559-564
• Main Authors: Naito, Yoichi, Takahashi, Hideaki, Shitara, Kohei, Okamoto, Wataru, Bando, Hideaki, Kuwata, Takeshi, Kuboki, Yasutoshi, Matsumoto, Shingo, Miki, Izumi, Yamanaka, Takeharu, Watanabe, Atsushi, Kojima, Motohiro
• Format: Article
• Language: English
• Subjects: Adult; Aged, 80 and over; Biopsy; Feasibility Studies; Female; Genome, Human; High-Throughput Nucleotide Sequencing - methods; Humans; INDEL Mutation - genetics; Male; Middle Aged; Mutation - genetics; Neoplasms - genetics; Original article; Prospective Studies; Young Adult
• ISSN: 1465-3621; 0368-2811; 1465-3621
• DOI: 10.1093/jjco/hyy052

We confirmed the feasibility of NGS-based amplicon sequencing using biopsy samples, making the basis for nationwide genome screening for cancer patients using biopsy samples. Abstract Background To confirm the feasibility and explore the clinical applicability of amplicon sequencing by next generation sequencing (NGS) of biopsy samples from patients with advanced solid tumors, we conducted a prospective study. Methods Patients with unresectable, advanced, or recurrent solid tumors were included. Key eligibility criteria were as follows: 20 years or older, any planned systemic therapy, adequate lesion for biopsy, and written informed consent. Samples were fixed in 10% buffered formalin and embedded in paraffin. Cancer-derived DNA was extracted, and amplicon sequencing was performed using Ion AmpliseqTM Cancer Hotspot Panel version 1.0 or version 2.0 by central vendor. We evaluated the success rate of sequencing, and the proportion of the patients with actionable mutations. We organized an expert panel to share the results of targeted sequence, make annotations and reports, and discuss concomitant ethical/legal/social issues. Results A total of 232 patients were included, and 208 were successfully analyzed (success rate of 89.7%). The biopsy procedures were safe, with only one case of Grade 3 vasovagal reaction. The proportion of actionable/druggable mutations was 38.9% (81/208), which was not significantly different between the cancer panel version 1.0 and version 2.0 (P = 0.476). Expert panel could discuss the findings and make sufficient reports. Conclusions We confirmed the feasibility of NGS-based amplicon sequencing using biopsy samples, making the basis for nationwide genome screening for cancer patients using biopsy samples. Our results suggest that focused panel may be sufficient to detect major mutations.