STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci

Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for "novel" STRs, which include new motifs at known loci or ST...

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Published inGenome Biology Vol. 23; no. 1; pp. 257 - 20
Main Authors Dashnow, Harriet, Pedersen, Brent S, Hiatt, Laurel, Brown, Joe, Beecroft, Sarah J, Ravenscroft, Gianina, LaCroix, Amy J, Lamont, Phillipa, Roxburgh, Richard H, Rodrigues, Miriam J, Davis, Mark, Mefford, Heather C, Laing, Nigel G, Quinlan, Aaron R
Format Journal Article
LanguageEnglish
Published England BioMed Central 14.12.2022
BMC
Subjects
Ataxia
Disease
DNA methylation
DNA sequencing
Genomes
High-Throughput Nucleotide Sequencing
Method
Microsatellite Repeats
Patients
Sequence Analysis, DNA
Short tandem repeats
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Summary:Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for "novel" STRs, which include new motifs at known loci or STRs absent from the reference genome. We developed STRling to efficiently count k-mers to recover informative reads and call expansions at known and novel STR loci. STRling is sensitive to known STR disease loci, has a low false discovery rate, and resolves novel STR expansions to base-pair position accuracy. It is fast, scalable, open-source, and available at: github.com/quinlan-lab/STRling .
Bibliography:ObjectType-Article-1
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content type line 23
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02826-4