Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases View Full Text


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Article Info

DATE

2018-12-17

AUTHORS

Takeshi Mizuguchi, Tomoko Toyota, Hiroaki Adachi, Noriko Miyake, Naomichi Matsumoto, Satoko Miyatake

ABSTRACT

Long-read sequencing technology is now capable of reading single-molecule DNA with an average read length of more than 10 kb, fully enabling the coverage of large structural variations (SVs). This advantage may pave the way for the detection of unprecedented SVs as well as repeat expansions. Pathogenic SVs of only known genes used to be selectively analyzed based on prior knowledge of target DNA sequence. The unbiased application of long-read whole-genome sequencing (WGS) for the detection of pathogenic SVs has just begun. Here, we apply PacBio SMRT sequencing in a Japanese family with benign adult familial myoclonus epilepsy (BAFME). Our SV selection of low-coverage WGS data (7×) narrowed down the candidates to only six SVs in a 7.16-Mb region of the BAFME1 locus and correctly determined an approximately 4.6-kb SAMD12 intronic repeat insertion, which is causal of BAFME1. These results indicate that long-read WGS is potentially useful for evaluating all of the known SVs in a genome and identifying new disease-causing SVs in combination with other genetic methods to resolve the genetic causes of currently unexplained diseases. More... »

PAGES

191-197

References to SciGraph publications

  • 2018-08-21. STRetch: detecting and discovering pathogenic short tandem repeat expansions in GENOME BIOLOGY
  • 2018-05-23. NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data in BMC BIOINFORMATICS
  • 2018-03-05. Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy in NATURE GENETICS
  • 2016-10-05. De novo assembly and phasing of a Korean human genome in NATURE
  • 2017-09-05. Parkinson’s disease associated with pure ATXN10 repeat expansion in NPJ PARKINSON'S DISEASE
  • 2011-08-18. Remapping and mutation analysis of benign adult familial myoclonic epilepsy in a Japanese pedigree in JOURNAL OF HUMAN GENETICS
  • 2017-06-22. Long-read genome sequencing identifies causal structural variation in a Mendelian disease in GENETICS IN MEDICINE
  • 2018-04-30. Accurate detection of complex structural variations using single molecule sequencing in NATURE METHODS
  • 2018-02-05. Tandem repeats mediating genetic plasticity in health and disease in NATURE REVIEWS GENETICS
  • 2015-01-22. Detecting copy-number variations in whole-exome sequencing data using the eXome Hidden Markov Model: an ‘exome-first’ approach in JOURNAL OF HUMAN GENETICS
  • 2018-01-22. Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet–Biedl Syndrome 9 (BBS9) deletion in NPJ GENOMIC MEDICINE
  • 2014-06-10. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping in BMC BIOINFORMATICS
  • 2016-02-29. Mechanisms underlying structural variant formation in genomic disorders in NATURE REVIEWS GENETICS
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    http://scigraph.springernature.com/pub.10.1038/s10038-018-0551-7

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    http://dx.doi.org/10.1038/s10038-018-0551-7

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30559482


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