Genome medicine · 2018
A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing.
СтатьяПоддержка исследования: вне правительства СШАНазвание и аннотация: Перевод в очереди
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Kato Mamoru, Nakamura Hiromi, Nagai Momoko, Kubo Takashi, Elzawahry Asmaa, Totoki Yasushi, Tanabe Yuko, Furukawa Eisaku, Miyamoto Joe, Sakamoto Hiromi, Matsumoto Shingo, Sunami Kuniko, Arai Yasuhito, Suzuki Yutaka, Yoshida Teruhiko, Tsuchihara Katsuya, Tamura Kenji, Yamamoto Noboru, Ichikawa Hitoshi, Kohno Takashi, Shibata Tatsuhiro
Аннотация
Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used in hospitals. Here, we developed a computational tool tailored to the detection of single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples. Elaborated multilayer noise filters reduced the inherent noise while maintaining high sensitivity, as evaluated in tumor-unmatched normal samples using orthogonal technologies. This tool, cisCall, should facilitate clinical sequencing in everyday diagnostics. It is available at https://www.ciscall.org .