Long-read sequencing across the DM2 repeat expansion reveals unique insight of repeat expansion structure

2022 Fiscal Year Annual Research Report

• Project/Area Number: 20K07740
• Research Institution: Jichi Medical University
• Principal Investigator: 松浦 徹 自治医科大学, 医学部, 教授 (90402560)
• Project Period (FY): 2020-04-01 – 2023-03-31
• Keywords: DM2 / CCTG repeat expansion / ancestral origin / repeat structure

Outline of Annual Research Achievements

Myotonic dystrophy type 2 (DM2) is a subtype of myotonic dystrophy caused by the expansion of a tetranucleotide CCTG repeat in intron 1 of the cellular nucleic acid-binding protein (CNBP) gene1. The aim of this study is to characterize the origin and features of expanded repeats in Japanese DM2 patients. We identified 7 DM2 patients from 5 unrelated families over the last 15 years in Japan. We used Nanopore long-read sequencing (LRS) to investigate the following measures: (1) Repeat length of the expanded repeat, (2) sequence of the repeat tract, (3) adjacent DNA modifications, and (4) the phase of SNPs flanking the repeat. LRS revealed that Japanese DM2 patients share a common haplotype, different from European DM2. Simultaneous detection of CNBP repeat region revealed that each read has different number of repeats, suggesting the somatic mosaicism of the expanded repeat allele. The sequence inside the repeat showed the interruptions of the CAGA repeat as recently reported in European DM2. We also detected the CpG modifications of the native DNA molecules, which were not substantially altered as previously reported. Japanese DM2 patients have a unique founder haplotype. Regardless of origin, the similar clinical features found in DM2 patients from Japan and other parts of the world are likely attributed to the pathogenic effects of the repeat expansion. The study demonstrates the usefulness of LRS to analyze expanded repeats in a single sequencing experiment.