Application of targeted nanopore sequencing for the screening and determination of structural variants in patients with Lynch syndrome

• Published in: Journal of human genetics Vol. 66; no. 11; pp. 1053 - 1060
• Main Authors: Yamaguchi, Kiyoshi, Kasajima, Rika, Takane, Kiyoko, Hatakeyama, Seira, Shimizu, Eigo, Yamaguchi, Rui, Katayama, Kotoe, Arai, Masami, Ishioka, Chikashi, Iwama, Takeo, Kaneko, Satoshi, Matsubara, Nagahide, Moriya, Yoshihiro, Nomizu, Tadashi, Sugano, Kokichi, Tamura, Kazuo, Tomita, Naohiro, Yoshida, Teruhiko, Sugihara, Kenichi, Nakamura, Yusuke, Miyano, Satoru, Imoto, Seiya, Furukawa, Yoichi, Ikenoue, Tsuneo
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 01-11-2021
• Subjects: Breakpoints; Colorectal cancer; Colorectal carcinoma; Colorectal Neoplasms - complications; Colorectal Neoplasms - genetics; Colorectal Neoplasms - pathology; Colorectal Neoplasms, Hereditary Nonpolyposis - complications; Colorectal Neoplasms, Hereditary Nonpolyposis - genetics; Colorectal Neoplasms, Hereditary Nonpolyposis - pathology; DNA damage; DNA Mismatch Repair - genetics; DNA probes; Female; Genes; Genetic disorders; Genetic Predisposition to Disease; Genetic testing; Genetic Testing - standards; Genetics; Genomes; Germ-Line Mutation - genetics; Hereditary diseases; Humans; Hybridization; Male; Mass Screening; Medical research; Mismatch repair; MLH1 protein; MSH2 protein; MutL Protein Homolog 1 - genetics; MutL Protein Homolog 1 - ultrastructure; MutS Homolog 2 Protein - genetics; MutS Homolog 2 Protein - ultrastructure; Nanopore Sequencing; Polymorphism, Single Nucleotide - genetics; Precision medicine; Protein Conformation; Rectum; Research centers
• ISSN: 1434-5161; 1435-232X
• DOI: 10.1038/s10038-021-00927-9

Lynch syndrome is a hereditary disease characterized by an increased risk of colorectal and other cancers. Germline variants in the mismatch repair (MMR) genes are responsible for this disease. Previously, we screened the MMR genes in colorectal cancer patients who fulfilled modified Amsterdam II criteria, and multiplex ligation-dependent probe amplification (MPLA) identified 11 structural variants (SVs) of MLH1 and MSH2 in 17 patients. In this study, we have tested the efficacy of long read-sequencing coupled with target enrichment for the determination of SVs and their breakpoints. DNA was captured by array probes designed to hybridize with target regions including four MMR genes and then sequenced using MinION, a nanopore sequencing platform. Approximately, 1000-fold coverage was obtained in the target regions compared with other regions. Application of this system to four test cases among the 17 patients correctly mapped the breakpoints. In addition, we newly found a deletion across an 84 kb region of MSH2 in a case without the pathogenic single nucleotide variants. These data suggest that long read-sequencing combined with hybridization-based enrichment is an efficient method to identify both SVs and their breakpoints. This strategy might replace MLPA for the screening of SVs in hereditary diseases.