Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin‐fixed paraffin‐embedded specimens

Shinji Kohsaka, Kenji Tatsuno(The University of Tokyo), Toshihide Ueno, Masaaki Nagano(The University of Tokyo), Aya Shinozaki‐Ushiku(The University of Tokyo), Tetsuo Ushiku(The University of Tokyo), Daiya Takai(University of Tokyo Hospital), Masachika Ikegami(University of Tokyo Hospital), Hiroshi Kobayashi(University of Tokyo Hospital), Hidenori Kage(University of Tokyo Hospital), Mizuo Ando(University of Tokyo Hospital), Keisuke Hata(The University of Tokyo), Hiroki Ueda(Tokyo University of Science), Shogo Yamamoto(The University of Tokyo), Shinya Kojima, Kumiko Oseto(University of Tokyo Hospital), Keisuke Akaike(Juntendo University), Yoshiyuki Suehara(Juntendo University), Takuo Hayashi(Juntendo University), Tsuyoshi Saito(Juntendo University), Fumiyuki Takahashi(Juntendo University), Kazuhisa Takahashi(Juntendo University), Kazuya Takamochi(Juntendo University), Kenji Suzuki(Juntendo University), Satoshi Nagayama(Japanese Foundation For Cancer Research), Yoshinao Oda(Kyushu University), Koshi Mimori(Kyushu University Beppu Hospital), Soichiro Ishihara(The University of Tokyo), Yutaka Yatomi(University of Tokyo Hospital), Takahide Nagase(University of Tokyo Hospital), Jun Nakajima(The University of Tokyo), Sakae Tanaka(University of Tokyo Hospital), Masashi Fukayama(The University of Tokyo), Katsutoshi Oda(The University of Tokyo), Masaomi Nangaku(University of Tokyo Hospital), Kohei Miyazono(The University of Tokyo), Kiyoshi Miyagawa(University of Tokyo Hospital), Hiroyuki Aburatani(The University of Tokyo), Hiroyuki Mano
Cancer Science
February 9, 2019
10.1111/cas.13968
Cited by 69Open Access
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Abstract

Tumor molecular profiling is becoming a standard of care for patients with cancer, but the optimal platform for cancer sequencing remains undetermined. We established a comprehensive assay, the Todai OncoPanel (TOP), which consists of DNA and RNA hybridization capture-based next-generation sequencing panels. A novel method for target enrichment, named the junction capture method, was developed for the RNA panel to accurately and cost-effectively detect 365 fusion genes as well as aberrantly spliced transcripts. The TOP RNA panel can also measure the expression profiles of an additional 109 genes. The TOP DNA panel was developed to detect single nucleotide variants and insertions/deletions for 464 genes, to calculate tumor mutation burden and microsatellite instability status, and to infer chromosomal copy number. Clinically relevant somatic mutations were identified in 32.2% (59/183) of patients by prospective TOP testing, signifying the clinical utility of TOP for providing personalized medicine to cancer patients.

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