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

Shinji Kohsaka, Kenji Tatsuno, Toshihide Ueno, Masaaki Nagano, Aya Shinozaki-Ushiku, Tetsuo Ushiku, Daiya Takai, Masachika Ikegami, Hiroshi Kobayashi, Hidenori Kage, Mizuo Ando, Keisuke Hata, Hiroki Ueda, Shogo Yamamoto, Shinya Kojima, Kumiko Oseto, Keisuke Akaike, Yoshiyuki Suehara, Takuo Hayashi, Tsuyoshi SaitoFumiyuki Takahashi, Kazuhisa Takahashi, Kazuya Takamochi, Kenji Suzuki, Satoshi Nagayama, Yoshinao Oda, Koshi Mimori, Soichiro Ishihara, Yutaka Yatomi, Takahide Nagase, Jun Nakajima, Sakae Tanaka, Masashi Fukayama, Katsutoshi Oda, Masaomi Nangaku, Kohei Miyazono, Kiyoshi Miyagawa, Hiroyuki Aburatani, Hiroyuki Mano

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish
Pages (from-to)1464-1479
Number of pages16
JournalCancer Science
Volume110
Issue number4
DOIs
Publication statusPublished - Apr 1 2019

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Paraffin
Formaldehyde
RNA
Neoplasms
Microsatellite Instability
Precision Medicine
Mutation
Gene Fusion
DNA
Gene Deletion
Standard of Care
Tumor Burden
Nucleotides
Costs and Cost Analysis
Genes

All Science Journal Classification (ASJC) codes

  • Oncology
  • Cancer Research

Cite this

Kohsaka, S., Tatsuno, K., Ueno, T., Nagano, M., Shinozaki-Ushiku, A., Ushiku, T., ... Mano, H. (2019). Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens. Cancer Science, 110(4), 1464-1479. https://doi.org/10.1111/cas.13968

Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens. / Kohsaka, Shinji; Tatsuno, Kenji; Ueno, Toshihide; Nagano, Masaaki; Shinozaki-Ushiku, Aya; Ushiku, Tetsuo; Takai, Daiya; Ikegami, Masachika; Kobayashi, Hiroshi; Kage, Hidenori; Ando, Mizuo; Hata, Keisuke; Ueda, Hiroki; Yamamoto, Shogo; Kojima, Shinya; Oseto, Kumiko; Akaike, Keisuke; Suehara, Yoshiyuki; Hayashi, Takuo; Saito, Tsuyoshi; Takahashi, Fumiyuki; Takahashi, Kazuhisa; Takamochi, Kazuya; Suzuki, Kenji; Nagayama, Satoshi; Oda, Yoshinao; Mimori, Koshi; Ishihara, Soichiro; Yatomi, Yutaka; Nagase, Takahide; Nakajima, Jun; Tanaka, Sakae; Fukayama, Masashi; Oda, Katsutoshi; Nangaku, Masaomi; Miyazono, Kohei; Miyagawa, Kiyoshi; Aburatani, Hiroyuki; Mano, Hiroyuki.

In: Cancer Science, Vol. 110, No. 4, 01.04.2019, p. 1464-1479.

Research output: Contribution to journalArticle

Kohsaka, S, Tatsuno, K, Ueno, T, Nagano, M, Shinozaki-Ushiku, A, Ushiku, T, Takai, D, Ikegami, M, Kobayashi, H, Kage, H, Ando, M, Hata, K, Ueda, H, Yamamoto, S, Kojima, S, Oseto, K, Akaike, K, Suehara, Y, Hayashi, T, Saito, T, Takahashi, F, Takahashi, K, Takamochi, K, Suzuki, K, Nagayama, S, Oda, Y, Mimori, K, Ishihara, S, Yatomi, Y, Nagase, T, Nakajima, J, Tanaka, S, Fukayama, M, Oda, K, Nangaku, M, Miyazono, K, Miyagawa, K, Aburatani, H & Mano, H 2019, 'Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens', Cancer Science, vol. 110, no. 4, pp. 1464-1479. https://doi.org/10.1111/cas.13968
Kohsaka, Shinji ; Tatsuno, Kenji ; Ueno, Toshihide ; Nagano, Masaaki ; Shinozaki-Ushiku, Aya ; Ushiku, Tetsuo ; Takai, Daiya ; Ikegami, Masachika ; Kobayashi, Hiroshi ; Kage, Hidenori ; Ando, Mizuo ; Hata, Keisuke ; Ueda, Hiroki ; Yamamoto, Shogo ; Kojima, Shinya ; Oseto, Kumiko ; Akaike, Keisuke ; Suehara, Yoshiyuki ; Hayashi, Takuo ; Saito, Tsuyoshi ; Takahashi, Fumiyuki ; Takahashi, Kazuhisa ; Takamochi, Kazuya ; Suzuki, Kenji ; Nagayama, Satoshi ; Oda, Yoshinao ; Mimori, Koshi ; Ishihara, Soichiro ; Yatomi, Yutaka ; Nagase, Takahide ; Nakajima, Jun ; Tanaka, Sakae ; Fukayama, Masashi ; Oda, Katsutoshi ; Nangaku, Masaomi ; Miyazono, Kohei ; Miyagawa, Kiyoshi ; Aburatani, Hiroyuki ; Mano, Hiroyuki. / Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens. In: Cancer Science. 2019 ; Vol. 110, No. 4. pp. 1464-1479.
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AU - Ueno, Toshihide

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AU - Shinozaki-Ushiku, Aya

AU - Ushiku, Tetsuo

AU - Takai, Daiya

AU - Ikegami, Masachika

AU - Kobayashi, Hiroshi

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AU - Hata, Keisuke

AU - Ueda, Hiroki

AU - Yamamoto, Shogo

AU - Kojima, Shinya

AU - Oseto, Kumiko

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AU - Takahashi, Kazuhisa

AU - Takamochi, Kazuya

AU - Suzuki, Kenji

AU - Nagayama, Satoshi

AU - Oda, Yoshinao

AU - Mimori, Koshi

AU - Ishihara, Soichiro

AU - Yatomi, Yutaka

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AU - Nakajima, Jun

AU - Tanaka, Sakae

AU - Fukayama, Masashi

AU - Oda, Katsutoshi

AU - Nangaku, Masaomi

AU - Miyazono, Kohei

AU - Miyagawa, Kiyoshi

AU - Aburatani, Hiroyuki

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