Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing

• Published in: Npj genomic medicine Vol. 7; no. 1; p. 62
• Main Authors: Miyatake, Satoko, Koshimizu, Eriko, Fujita, Atsushi, Doi, Hiroshi, Okubo, Masaki, Wada, Taishi, Hamanaka, Kohei, Ueda, Naohisa, Kishida, Hitaru, Minase, Gaku, Matsuno, Atsuhiro, Kodaira, Minori, Ogata, Katsuhisa, Kato, Rumiko, Sugiyama, Atsuhiko, Sasaki, Ayako, Miyama, Takabumi, Satoh, Mai, Uchiyama, Yuri, Tsuchida, Naomi, Hamanoue, Haruka, Misawa, Kazuharu, Hayasaka, Kiyoshi, Sekijima, Yoshiki, Adachi, Hiroaki, Yoshida, Kunihiro, Tanaka, Fumiaki, Mizuguchi, Takeshi, Matsumoto, Naomichi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26.10.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208/2489/1512; 692/308/2056; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Cerebellar ataxia; Cerebellum; Disease; Gene Function; Gene Therapy; Genetic screening; Genomes; Hospitals; Human Genetics; Internal Medicine; Medicine; Methods; Neurology; Neuromuscular diseases; Patients; Pediatrics; Software
• ISSN: 2056-7944; 2056-7944
• DOI: 10.1038/s41525-022-00331-y

We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.