Analysis of Tandem Repeat Expansions Using Long DNA Reads

Satomi Mitsuhashi; Martin C Frith

doi:10.1007/978-1-0716-2996-3_11

Analysis of Tandem Repeat Expansions Using Long DNA Reads

Methods Mol Biol. 2023:2632:147-159. doi: 10.1007/978-1-0716-2996-3_11.

Authors

Satomi Mitsuhashi^{1

2}, Martin C Frith^{3

4

5}

Affiliations

¹ Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Tokyo, Japan. [email protected].
² Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan. [email protected].
³ Artificial Intelligence Research Center, AIST, Tokyo, Japan.
⁴ Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.
⁵ Computational Bio Big-Data Open Innovation Laboratory, AIST, Tokyo, Japan.

PMID: 36781727
DOI: 10.1007/978-1-0716-2996-3_11

Abstract

Abnormal expansion or shortening of tandem repeats can cause a variety of genetic diseases. The use of long DNA reads has facilitated the analysis of disease-causing repeats in the human genome. Long read sequencers enable us to directly analyze repeat length and sequence content by covering whole repeats; they are therefore considered suitable for the analysis of long tandem repeats. Here, we describe an expanded repeat analysis using target sequencing data produced by the Oxford Nanopore Technologies (hereafter referred to as ONT) nanopore sequencer.

Keywords: Long read sequencer; Nanopore sequencer; Repeat expansion diseases; Tandem repeat.

MeSH terms

DNA / genetics
High-Throughput Nucleotide Sequencing*
Humans
Nanopores*
Sequence Analysis, DNA
Tandem Repeat Sequences / genetics

Substances

DNA