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NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Authors
  • De Roeck, Arne1, 2
  • De Coster, Wouter1, 2
  • Bossaerts, Liene1, 2
  • Cacace, Rita1, 2
  • De Pooter, Tim3
  • Van Dongen, Jasper1, 2
  • D’Hert, Svenn3
  • De Rijk, Peter3
  • Strazisar, Mojca3
  • Van Broeckhoven, Christine1, 2
  • Sleegers, Kristel1, 2
  • 1 University of Antwerp-CDE, Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Universiteitsplein 1, Antwerp, B-2610, Belgium , Antwerp (Belgium)
  • 2 University of Antwerp, Biomedical Sciences, Antwerp, Belgium , Antwerp (Belgium)
  • 3 VIB - University of Antwerp, Neuromics Support Facility, Center for Molecular Neurology, Antwerp, Belgium , Antwerp (Belgium)
Type
Published Article
Publication Date
Nov 14, 2019
Volume
20
Issue
1
Identifiers
DOI: 10.1186/s13059-019-1856-3
Source
Springer Nature
Keywords
License
Green

Abstract

Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer’s disease-associated ABCA7 VNTR. The Guppy “flip-flop” base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.

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