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

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 cr...

Full description

Saved in:
Bibliographic Details
Published in:Journal of human genetics 2021-11, Vol.66 (11), p.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: Article
Language:English
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
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1434-5161
1435-232X
DOI:10.1038/s10038-021-00927-9