ArticleBioinformatics (Oxford, England)2014
Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 69 citations in OpenAlex.
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- Detection of repeat expansions in large next generation DNA and RNA sequencing data without alignment.Scientific reports · 2022Article
- Neurodegenerative diseases associated with non-coding CGG tandem repeat expansions.Nature reviews. Neurology · 2022Review
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- Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences.Genome research · 2022Review
- Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study.Brain : a journal of neurology · 2021Article
- GC-rich repeat expansions: associated disorders and mechanisms.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2021Article
- 30 years of repeat expansion disorders: What have we learned and what are the remaining challenges?American journal of human genetics · 2021Review
- Finding long tandem repeats in long noisy reads.Bioinformatics (Oxford, England) · 2021Article
- Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data.BMC bioinformatics · 2021Article
- Article
- Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3.Nature communications · 2019Article
- Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease.Nature genetics · 2019Article
- Polyglutamine Repeats in Viruses.Molecular neurobiology · 2019Review
- Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development.G3 (Bethesda, Md.) · 2019Article
- Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases.Journal of human genetics · 2019Article
- Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools.Turkish journal of biology = Turk biyoloji dergisi · 2019Article
Corrections and comments
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationLong expansions of short tandem repeats (STRs), i.e. DNA repeats of 2-6 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads.
resultsWe propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRT(TM) sequencing (Pacific Biosciences), determined 2.3-3.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads. AVAILABILITY AND IMPLEMENTATION: Our TRhist software is available at http://trhist.gi.k.u-tokyo.ac.jp/. CONTACT: moris@cb.k.u-tokyo.ac.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.