Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads
Abstract Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from careful alignments of long but error-prone (PacBio and nanopore) reads to a reference...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-03-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-019-1667-6 |
| _version_ | 1819083167834832896 |
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| author | Satomi Mitsuhashi Martin C. Frith Takeshi Mizuguchi Satoko Miyatake Tomoko Toyota Hiroaki Adachi Yoko Oma Yoshihiro Kino Hiroaki Mitsuhashi Naomichi Matsumoto |
| author_facet | Satomi Mitsuhashi Martin C. Frith Takeshi Mizuguchi Satoko Miyatake Tomoko Toyota Hiroaki Adachi Yoko Oma Yoshihiro Kino Hiroaki Mitsuhashi Naomichi Matsumoto |
| author_sort | Satomi Mitsuhashi |
| collection | DOAJ |
| description | Abstract Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from careful alignments of long but error-prone (PacBio and nanopore) reads to a reference genome. Our method is robust to systematic sequencing errors, inexact repeats with fuzzy boundaries, and low sequencing coverage. By comparing to healthy controls, we prioritize pathogenic expansions within the top 10 out of 700,000 tandem repeats in whole genome sequencing data. This may help to elucidate the many genetic diseases whose causes remain unknown. |
| first_indexed | 2024-12-21T20:28:16Z |
| format | Article |
| id | doaj.art-375652e5b6a34ae1afdfc702a64030a5 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-21T20:28:16Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-375652e5b6a34ae1afdfc702a64030a52022-12-21T18:51:19ZengBMCGenome Biology1474-760X2019-03-0120111710.1186/s13059-019-1667-6Tandem-genotypes: robust detection of tandem repeat expansions from long DNA readsSatomi Mitsuhashi0Martin C. Frith1Takeshi Mizuguchi2Satoko Miyatake3Tomoko Toyota4Hiroaki Adachi5Yoko Oma6Yoshihiro Kino7Hiroaki Mitsuhashi8Naomichi Matsumoto9Department of Human Genetics, Yokohama City University Graduate School of MedicineArtificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST)Department of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Human Genetics, Yokohama City University Graduate School of MedicineDepartment of Neurology, University of Occupational and Environmental Health School of MedicineDepartment of Neurology, University of Occupational and Environmental Health School of MedicineDepartment of Liberal Arts, Faculty of Medicine, Saitama Medical UniversityDepartment of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical UniversityDepartment of Applied Biochemistry, School of Engineering, Tokai UniversityDepartment of Human Genetics, Yokohama City University Graduate School of MedicineAbstract Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from careful alignments of long but error-prone (PacBio and nanopore) reads to a reference genome. Our method is robust to systematic sequencing errors, inexact repeats with fuzzy boundaries, and low sequencing coverage. By comparing to healthy controls, we prioritize pathogenic expansions within the top 10 out of 700,000 tandem repeats in whole genome sequencing data. This may help to elucidate the many genetic diseases whose causes remain unknown.http://link.springer.com/article/10.1186/s13059-019-1667-6Tandem repeatRepeat diseasesLong-read sequencingNanoporePacBio |
| spellingShingle | Satomi Mitsuhashi Martin C. Frith Takeshi Mizuguchi Satoko Miyatake Tomoko Toyota Hiroaki Adachi Yoko Oma Yoshihiro Kino Hiroaki Mitsuhashi Naomichi Matsumoto Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads Genome Biology Tandem repeat Repeat diseases Long-read sequencing Nanopore PacBio |
| title | Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads |
| title_full | Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads |
| title_fullStr | Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads |
| title_full_unstemmed | Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads |
| title_short | Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads |
| title_sort | tandem genotypes robust detection of tandem repeat expansions from long dna reads |
| topic | Tandem repeat Repeat diseases Long-read sequencing Nanopore PacBio |
| url | http://link.springer.com/article/10.1186/s13059-019-1667-6 |
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