Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin‐fixed paraffin‐embedded specimens. Issue 4 (5th March 2019)

• Record Type: Journal Article
• Authors: 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;
• Is Part Of: Cancer science. Volume 110:Issue 4(2019)
• Page Start: 1464
• Page End: 1479
• Publication Date: 2019-03-05
• Subjects: clinical sequencing -- junction capture method -- molecular profiling -- personalized medicine -- Todai OncoPanel; Cancer -- Periodicals; Neoplasms -- Periodicals; Research -- Periodicals; Electronic journals; 616.994005
• DOI: 10.1111/cas.13968
• Languages: English
• ISSNs: 1347-9032

Abstract

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. Abstract : The original TOP RNA panel achieved the accurate and cost‐effective detection of fusion genes and exon skipping. Gene expression clustering using the RNA panel data may predict the primary organs of cancers. The twin DNA and RNA panel system broadens cancer treatment options by precisely and sensitively detecting a wide variety of genomic alterations in cancer.