Abstract B29: Feasibility of amplicon sequencing using a pan-cancer gene panel with pre-treatment biopsy samples of (Japanese) patients with advanced solid tumors: Analyses of Biopsy Samples for Cancer Genomics (ABC) study

• Published in: Molecular cancer therapeutics 2013-11, Vol.12 (11_Supplement), p.B29-B29
• Main Authors: Takahashi, Hideaki, Shitara, Kohei, Kuwata, Takeshi, Naito, Yoichi, Matsumoto, Shingo, Okamoto, Wataru, Niho, Seiji, Bando, Hideaki, Kuboki, Yasutoshi, Yamada, Yoko, Miki, Izumi, Yamanaka, Takeharu, Watanabe, Atsushi, Kojima, Motohiro, Ishii, Genichiro, Fujii, Satoshi, Umemura, Shigeki, Ikeda, Masafumi, Kohno, Takashi, Sato, Akihiro, Ohtsu, Atsushi, Esumi, Hiroyasu, Ochiai, Atsushi, Yoshino, Takayuki, Tsuchihara, Katsuya
• Format: Article
• Language: English
• ISSN: 1535-7163; 1538-8514
• DOI: 10.1158/1535-7163.TARG-13-B29

Background: Next-generation sequencing (NGS) is a powerful tool to individualize cancer treatment by detecting alterations in target genes. Safe, robust, and feasible diagnostic systems are urgently required. Methods: Recruited patients had advanced solid tumors and were planning to receive anticancer drugs at National Cancer Center Hospital East. Genomic DNA was extracted from pretreatment FFPE biopsy samples, and 10 ng of double strand (ds) DNA was applied to the amplicon sequence using Ion AmpliSeq™ Cancer Panel ver1.0, targeting 739 COSMIC-registered mutations of 46 oncogenes and tumor suppressor genes. A multidisciplinary institutional cancer board (“Expert panel”) was organized to review the safety of the biopsy and quality of the sequencing. The panel also gave qualified reports to clinicians. Results are presented for the prespecified feasibility evaluation with over 100 full analysis sets. Results: From July 2012 to February 2013, 105 patients were enrolled. Primary tumor sites were stomach (n=28), colorectal (n=20), lung (n=12), breast (n=11), liver (n=9), and others (n=25). Most patients were enrolled before receiving first-line chemotherapy (74.3%). No serious adverse events were observed with biopsy procedures. Adequate biopsy samples for DNA extraction were obtained from 92 patients, and successful sequencing was performed in 90 patients using only 10 ng dsDNA, for a sequence success rate for all enrolled patients and for DNA extracted samples of 85.7% (90/105), and 97.8% (90/92), respectively. Mutation analyses were performed in 93 patients, which included archival tissue or re-biopsied samples from three patients. The median amount of extracted dsDNA was 3334 ng; more than 100 ng dsDNA was retrieved from 92 of 93 samples (99%), which provided enough material for the Cancer Panel and for other additional analyses. The mean number of mutations detected was 1.6 per patient. Potentially targetable mutations were detected in 44% of the patients; these included PIK3CA (15%), KRAS (15%), CTNNB1 (7.5%), EGFR (3.2%), GNAS (3.2%), BRAF (2.1%), ERBB2 (2.1%), KIT (1.1%), and NRAS (1.1%). Proportions of patient with these mutations in major types of malignancies were as follows: breast (77%), colorectal (66%), liver (63%), lung (45%), and stomach (29%). These mutation profiles resulted in treatment of one colon cancer patient with an ERBB2 mutation and amplification with trastuzumab, while other colon cancer patients with KRAS mutations (p.Q61P or p.A14