MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples

Masachika Ikegami; Shinji Kohsaka; Takeshi Hirose; Toshihide Ueno; Satoshi Inoue; Naoki Kanomata; Hideko Yamauchi; Taisuke Mori; Shigeki Sekine; Yoshihiro Inamoto; Yasushi Yatabe; Hiroshi Kobayashi; Sakae Tanaka; Hiroyuki Mano

doi:10.1038/s42003-021-02930-4

Communications Biology (Dec 2021)

MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples

Masachika Ikegami,
Shinji Kohsaka,
Takeshi Hirose,
Toshihide Ueno,
Satoshi Inoue,
Naoki Kanomata,
Hideko Yamauchi,
Taisuke Mori,
Shigeki Sekine,
Yoshihiro Inamoto,
Yasushi Yatabe,
Hiroshi Kobayashi,
Sakae Tanaka,
Hiroyuki Mano

Affiliations

Masachika Ikegami: Division of Cellular Signaling, National Cancer Center Research Institute
Shinji Kohsaka: Division of Cellular Signaling, National Cancer Center Research Institute
Takeshi Hirose: Division of Cellular Signaling, National Cancer Center Research Institute
Toshihide Ueno: Division of Cellular Signaling, National Cancer Center Research Institute
Satoshi Inoue: Division of Cellular Signaling, National Cancer Center Research Institute
Naoki Kanomata: Department of Pathology, St Luke’s International Hospital
Hideko Yamauchi: Department of Breast Surgical Oncology, St Luke’s International Hospital
Taisuke Mori: Division of Molecular Pathology, National Cancer Center Research Institute
Shigeki Sekine: Division of Molecular Pathology, National Cancer Center Research Institute
Yoshihiro Inamoto: Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital
Yasushi Yatabe: Division of Molecular Pathology, National Cancer Center Research Institute
Hiroshi Kobayashi: Department of Orthopaedic Surgery, Faculty of Medicine, The University of Tokyo
Sakae Tanaka: Department of Orthopaedic Surgery, Faculty of Medicine, The University of Tokyo
Hiroyuki Mano: Division of Cellular Signaling, National Cancer Center Research Institute

DOI: https://doi.org/10.1038/s42003-021-02930-4
Journal volume & issue: Vol. 4, no. 1
pp. 1 – 13

Abstract

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Masachika Ikegami and Shinji Kohsaka et al. develop MicroSEC, a computational pipeline to filter sequencing artifacts from archival formalin-fixed and paraffin-embedded samples. Given that archival FFPE tissue is of great interest for genomic analysis, but difficult to reliably analyze, this tool may improve the ability of researchers to probe sequencing data from these samples.

Published in Communications Biology

ISSN: 2399-3642 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General)
Website: https://www.nature.com/commsbio/

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