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 Saito; Fumiyuki 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

doi:10.1111/cas.13968

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

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36 Citations (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 language	English
Pages (from-to)	1464-1479
Number of pages	16
Journal	Cancer Science
Volume	110
Issue number	4
DOIs	https://doi.org/10.1111/cas.13968
Publication status	Published - Apr 2019

All Science Journal Classification (ASJC) codes

Oncology
Cancer Research

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1111/cas.13968

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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., ... 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

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

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

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.",

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

note = "Funding Information: The authors would like to thank F. Tanabe, A. Maruyama and H. Tomita for technical assistance. We thank our collaborating company, Xcoo (Tokyo, Japan), which made contributions to the knowledge database and reporting for the TOP. This study was financially supported in part through grants from the Program for Integrated Database of Clinical and Genomic Information under grant number 17kk0205003h0002, the Leading Advanced Projects for Medical Innovation (LEAP) under grant number JP17am0001001, the Practical Research for Innovative Cancer Control under grant number JP17ck0106252, and the Project for Cancer Research And Therapeutic Evolution (P-CREATE) under grant number JP17cm0106502 from the Japan Agency for Medical Research and Development, AMED. Sequencing analysis of the clinical specimens was funded in part by the Sysmex. This work was supported in-part by a grant from Eisai. Publisher Copyright: {\textcopyright} 2019 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.",

year = "2019",

month = apr,

doi = "10.1111/cas.13968",

language = "English",

volume = "110",

pages = "1464--1479",

journal = "Cancer Science",

issn = "1347-9032",

publisher = "Wiley-Blackwell",

number = "4",

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TY - JOUR

T1 - Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens

AU - Kohsaka, Shinji

AU - Tatsuno, Kenji

AU - Ueno, Toshihide

AU - Nagano, Masaaki

AU - Shinozaki-Ushiku, Aya

AU - Ushiku, Tetsuo

AU - Takai, Daiya

AU - Ikegami, Masachika

AU - Kobayashi, Hiroshi

AU - Kage, Hidenori

AU - Ando, Mizuo

AU - Hata, Keisuke

AU - Ueda, Hiroki

AU - Yamamoto, Shogo

AU - Kojima, Shinya

AU - Oseto, Kumiko

AU - Akaike, Keisuke

AU - Suehara, Yoshiyuki

AU - Hayashi, Takuo

AU - Saito, Tsuyoshi

AU - Takahashi, Fumiyuki

AU - Takahashi, Kazuhisa

AU - Takamochi, Kazuya

AU - Suzuki, Kenji

AU - Nagayama, Satoshi

AU - Oda, Yoshinao

AU - Mimori, Koshi

AU - Ishihara, Soichiro

AU - Yatomi, Yutaka

AU - Nagase, Takahide

AU - Nakajima, Jun

AU - Tanaka, Sakae

AU - Fukayama, Masashi

AU - Oda, Katsutoshi

AU - Nangaku, Masaomi

AU - Miyazono, Kohei

AU - Miyagawa, Kiyoshi

AU - Aburatani, Hiroyuki

AU - Mano, Hiroyuki

N1 - Funding Information: The authors would like to thank F. Tanabe, A. Maruyama and H. Tomita for technical assistance. We thank our collaborating company, Xcoo (Tokyo, Japan), which made contributions to the knowledge database and reporting for the TOP. This study was financially supported in part through grants from the Program for Integrated Database of Clinical and Genomic Information under grant number 17kk0205003h0002, the Leading Advanced Projects for Medical Innovation (LEAP) under grant number JP17am0001001, the Practical Research for Innovative Cancer Control under grant number JP17ck0106252, and the Project for Cancer Research And Therapeutic Evolution (P-CREATE) under grant number JP17cm0106502 from the Japan Agency for Medical Research and Development, AMED. Sequencing analysis of the clinical specimens was funded in part by the Sysmex. This work was supported in-part by a grant from Eisai. Publisher Copyright: © 2019 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

PY - 2019/4

Y1 - 2019/4

N2 - 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.

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

Abstract

All Science Journal Classification (ASJC) codes

UN SDGs

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