Comprehensive Assay for the Molecular Profiling of Cancer by Target Enrichment from Formalin-fixed Paraffin-embedded Specimens

Overview

Journal Cancer Sci

Specialty Oncology

Date 2019 Feb 10

PMID 30737998

Citations 33

Authors

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

Affiliations

Soon will be listed here.

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.

Citing Articles

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PMID: 39493594 PMC: 11528640. DOI: 10.1177/11782234241288671.

Cancer risk assessment of premalignant breast tissues from patients with BRCA mutations by genome profiling.

Hirose T, Ikegami M, Kida K, Ueno T, Kitada R, Wang L NPJ Breast Cancer. 2024; 10(1):87.

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Analysis of quality metrics in comprehensive cancer genomic profiling using a dual DNA-RNA panel.

Watanabe K, Kohsaka S, Tatsuno K, Shinozaki-Ushiku A, Isago H, Kage H Pract Lab Med. 2024; 39:e00368.

PMID: 38404525 PMC: 10883814. DOI: 10.1016/j.plabm.2024.e00368.

The development of a custom RNA-sequencing panel for the identification of predictive and diagnostic biomarkers in glioma.

Shirai Y, Ueno T, Kojima S, Ikeuchi H, Kitada R, Koyama T J Neurooncol. 2024; 167(1):75-88.

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LMNA::NTRK1 Fusion-positive Leiomyosarcoma: Discrepancy between DNA-based Comprehensive Genomic Profiling and RNA Sequencing.

Suzuki N, Idogawa M, Emori M, Murase K, Arihara Y, Nakamura H Intern Med. 2023; 63(15):2215-2219.

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