TY - JOUR AU - Kato, Mamoru AU - Nakamura, Hiromi AU - Nagai, Momoko AU - Kubo, Takashi AU - Elzawahry, Asmaa AU - Totoki, Yasushi AU - Tanabe, Yuko AU - Furukawa, Eisaku AU - Miyamoto, Joe AU - Sakamoto, Hiromi AU - Matsumoto, Shingo AU - Sunami, Kuniko AU - Arai, Yasuhito AU - Suzuki, Yutaka AU - Yoshida, Teruhiko AU - Tsuchihara, Katsuya AU - Tamura, Kenji AU - Yamamoto, Noboru AU - Ichikawa, Hitoshi AU - Kohno, Takashi AU - Shibata, Tatsuhiro PY - 2018 DA - 2018/06/07 TI - A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing JO - Genome Medicine SP - 44 VL - 10 IS - 1 AB - 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. SN - 1756-994X UR - https://doi.org/10.1186/s13073-018-0547-0 DO - 10.1186/s13073-018-0547-0 ID - Kato2018 ER -