Abstract 4264: Clinical targeted sequencing from FFPE tumor tissue samples for early-phase clinical trials at the National Cancer Center of Japan
Authors: Hitoshi Ichikawa, Mamoru Kato, Kenji Tamura, Noboru Yamamoto, Yuko Tanabe, Takashi Kohno
Journal: Cancer Research (2015)

Abstract Next-generation sequencing is becoming an important tool in diagnosis for personalized cancer treatment because of its ability to examine a large number of genes in a single test and to detect mutations with high sensitivity. We developed a clinical sequencing system at the National Cancer Center of Japan that can identify actionable genetic alterations from FFPE tumor tissue samples, and started to use this system for patient entry into early-phase clinical trials of molecular target drugs. In the present version of this system, 90 potentially actionable genes were selected to construct an original panel (NCC oncopanel v2). All exons of these 90 genes and introns of 10 genes among them are captured and sequenced for detection of mutations/gene amplifications and gene fusions, respectively. Target capturing and sequencing are performed using an Agilent SureSelect system and an Illumina MiSeq sequencer. To ensure the stable operation on FFPE samples, we developed a method to qualify FFPE tissue-derived DNA using the content of PCR-amplifiable DNA as a quality value. This value is calculated as a ratio of DNA concentration determined by quantitative PCR to that measured using a fluorescent dye-binding method. By changing the DNA quantity used for sequencing depending on their quality values, approximately 90% of the archived FFPE samples were able to be successfully analyzed. In addition, we also developed a novel algorithm, cisCall, to accurately identify genetic alterations in FFPE samples. At present, our clinical sequencing system has enabled highly accurate mutation detection; accuracies of the base substitution and indel mutations were verified as being more than 99% and more than 90%, respectively, in a MassARRAY examination. To evaluate the feasibility and utility of our system in a clinical setting, we initiated a study to use our system for early-phase clinical trials, which we named TOPICS-1 (Trial of Onco-Panel for Introduction into Clinical Study-Phase 1). Up to the present, more than 100 patients with breast, gastric, ovarian, lung, and other cancers have been subjected to the study, and 1.9 mutations and 0.3 amplifications have been found in each patient on average. Among those mutations, 40% were COSMIC database-registered mutations and 25% were truncating mutations. Nearly half of the patients had at least 1 actionable alteration, which is informative for the entry into some clinical trials. Citation Format: Hitoshi Ichikawa, Mamoru Kato, Kenji Tamura, Noboru Yamamoto, Yuko Tanabe, Takashi Kohno. Clinical targeted sequencing from FFPE tumor tissue samples for early-phase clinical trials at the National Cancer Center of Japan. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4264. doi:10.1158/1538-7445.AM2015-4264