Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing
Abstract 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 sof...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2022-10-01
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| Series: | npj Genomic Medicine |
| Online Access: | https://doi.org/10.1038/s41525-022-00331-y |
| _version_ | 1811335002348060672 |
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| author | Satoko Miyatake Eriko Koshimizu Atsushi Fujita Hiroshi Doi Masaki Okubo Taishi Wada Kohei Hamanaka Naohisa Ueda Hitaru Kishida Gaku Minase Atsuhiro Matsuno Minori Kodaira Katsuhisa Ogata Rumiko Kato Atsuhiko Sugiyama Ayako Sasaki Takabumi Miyama Mai Satoh Yuri Uchiyama Naomi Tsuchida Haruka Hamanoue Kazuharu Misawa Kiyoshi Hayasaka Yoshiki Sekijima Hiroaki Adachi Kunihiro Yoshida Fumiaki Tanaka Takeshi Mizuguchi Naomichi Matsumoto |
| author_facet | Satoko Miyatake Eriko Koshimizu Atsushi Fujita Hiroshi Doi Masaki Okubo Taishi Wada Kohei Hamanaka Naohisa Ueda Hitaru Kishida Gaku Minase Atsuhiro Matsuno Minori Kodaira Katsuhisa Ogata Rumiko Kato Atsuhiko Sugiyama Ayako Sasaki Takabumi Miyama Mai Satoh Yuri Uchiyama Naomi Tsuchida Haruka Hamanoue Kazuharu Misawa Kiyoshi Hayasaka Yoshiki Sekijima Hiroaki Adachi Kunihiro Yoshida Fumiaki Tanaka Takeshi Mizuguchi Naomichi Matsumoto |
| author_sort | Satoko Miyatake |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-13T17:17:31Z |
| format | Article |
| id | doaj.art-5c4b0d3d0ea14f9fa7378606182803e5 |
| institution | Directory Open Access Journal |
| issn | 2056-7944 |
| language | English |
| last_indexed | 2024-04-13T17:17:31Z |
| publishDate | 2022-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Genomic Medicine |
| spelling | doaj.art-5c4b0d3d0ea14f9fa7378606182803e52022-12-22T02:38:06ZengNature Portfolionpj Genomic Medicine2056-79442022-10-017111510.1038/s41525-022-00331-yRapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencingSatoko Miyatake0Eriko Koshimizu1Atsushi Fujita2Hiroshi Doi3Masaki Okubo4Taishi Wada5Kohei Hamanaka6Naohisa Ueda7Hitaru Kishida8Gaku Minase9Atsuhiro Matsuno10Minori Kodaira11Katsuhisa Ogata12Rumiko Kato13Atsuhiko Sugiyama14Ayako Sasaki15Takabumi Miyama16Mai Satoh17Yuri Uchiyama18Naomi Tsuchida19Haruka Hamanoue20Kazuharu Misawa21Kiyoshi Hayasaka22Yoshiki Sekijima23Hiroaki Adachi24Kunihiro Yoshida25Fumiaki Tanaka26Takeshi Mizuguchi27Naomichi Matsumoto28Department of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Neurology and Stroke Medicine, Yokohama City University Graduate School of MedicineDepartment of Neurology and Stroke Medicine, Yokohama City University Graduate School of MedicineDepartment of Neurology and Stroke Medicine, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Neurology, Yokohama City University Medical CenterDepartment of Neurology, Yokohama City University Medical CenterDepartment of Obstetrics and Gynecology, Asahikawa Medical UniversityDepartment of Medicine (Neurology and Rheumatology), Shinshu University School of MedicineDepartment of Medicine (Neurology and Rheumatology), Shinshu University School of MedicineDepartment of Neurology, National Hospital Organization Higashisaitama National HospitalDepartment of Pediatrics, National Hospital Organization Higashisaitama National HospitalDepartment of Neurology, Graduate School of Medicine, Chiba UniversityDepartment of Pediatrics, Yamagata University School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Clinical Genetics, Yokohama City University HospitalDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Pediatrics, Yamagata University School of MedicineDepartment of Medicine (Neurology and Rheumatology), Shinshu University School of MedicineDepartment of Neurology, University of Occupational and Environmental Health School of MedicineDepartment of Neurology, JA Nagano Kouseiren, Kakeyu-Misayama Rehabilitation Center, Kakeyu HospitalDepartment of Neurology and Stroke Medicine, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineAbstract 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.https://doi.org/10.1038/s41525-022-00331-y |
| spellingShingle | Satoko Miyatake Eriko Koshimizu Atsushi Fujita Hiroshi Doi Masaki Okubo Taishi Wada Kohei Hamanaka Naohisa Ueda Hitaru Kishida Gaku Minase Atsuhiro Matsuno Minori Kodaira Katsuhisa Ogata Rumiko Kato Atsuhiko Sugiyama Ayako Sasaki Takabumi Miyama Mai Satoh Yuri Uchiyama Naomi Tsuchida Haruka Hamanoue Kazuharu Misawa Kiyoshi Hayasaka Yoshiki Sekijima Hiroaki Adachi Kunihiro Yoshida Fumiaki Tanaka Takeshi Mizuguchi Naomichi Matsumoto Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing npj Genomic Medicine |
| title | Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing |
| title_full | Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing |
| title_fullStr | Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing |
| title_full_unstemmed | Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing |
| title_short | Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing |
| title_sort | rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing |
| url | https://doi.org/10.1038/s41525-022-00331-y |
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