Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology

Author:

Otsuki AkihitoORCID,Okamura YasunobuORCID,Ishida Noriko,Tadaka ShuORCID,Takayama Jun,Kumada Kazuki,Kawashima Junko,Taguchi KeikoORCID,Minegishi Naoko,Kuriyama Shinichi,Tamiya Gen,Kinoshita Kengo,Katsuoka FumikiORCID,Yamamoto MasayukiORCID

Abstract

AbstractLong-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T lymphocytes, which can be established efficiently in a biobank to stably supply high-grade genomic DNA sufficiently. We conducted nanopore sequencing of 333 individuals constituting 111 trios with high-coverage long-read sequencing data (depth 22.2x, N50 of 25.8 kb) and identified 74,201 SVs. Our trio-based analysis revealed that more than 95% of the SVs were concordant with Mendelian inheritance. We also identified SVs associated with clinical phenotypes, all of which appear to be stably transmitted from parents to offspring. Our data provide a catalog of SVs in the general Japanese population, and the applied approach using the activated T-lymphocyte resource will contribute to biobank-based human genetic studies focusing on SVs at the population scale.

Funder

MEXT | Japan Society for the Promotion of Science

Japan Agency for Medical Research and Development

Publisher

Springer Science and Business Media LLC

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Medicine (miscellaneous)

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