Linked-read sequencing for detecting short tandem repeat expansions.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
07 06 2022
07 06 2022
Historique:
received:
09
11
2021
accepted:
19
05
2022
entrez:
7
6
2022
pubmed:
8
6
2022
medline:
10
6
2022
Statut:
epublish
Résumé
Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences. In this study, we explored how the long-range sequence information of barcode linked-read sequencing (BLRS) can be leveraged to improve repeat-read detection. We also devised a novel algorithm using BLRS barcodes for distance estimation and evaluated its application for STR genotyping. Both approaches were designed for genotyping large expansions (> 1 kb) that cannot be sized accurately by existing methods. Using simulated and experimental data of genomes with STR expansions from multiple BLRS platforms, we validated the utility of barcode and phasing information in attaining better STR genotypes compared to standard short-read sequencing. Although the coverage bias of extremely GC-rich STRs is an important limitation of BLRS, BLRS is an effective strategy for genotyping many other STR loci.
Identifiants
pubmed: 35672336
doi: 10.1038/s41598-022-13024-4
pii: 10.1038/s41598-022-13024-4
pmc: PMC9174224
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
9352Subventions
Organisme : CIHR
ID : 153452
Pays : Canada
Informations de copyright
© 2022. The Author(s).
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