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Dashnow H, Pedersen BS, Hiatt L, Brown J, Beecroft SJ, Ravenscroft G, LaCroix AJ, Lamont P, Roxburgh RH, Rodrigues MJ, Davis M, Mefford HC, Laing NG, Quinlan AR. STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci. Genome Biol 2022; 23:257. [PMID: 36517892 PMCID: PMC9753380 DOI: 10.1186/s13059-022-02826-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
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 .
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Affiliation(s)
- Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Utrecht University Medical Center, Utrecht, The Netherlands
| | - Laurel Hiatt
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Joe Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Sarah J Beecroft
- Pawsey Supercomputing Research Centre, Kensington, WA, Australia
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Amy J LaCroix
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Phillipa Lamont
- Neurogenetic Unit, Royal Perth Hospital, Perth, WA, Australia
| | | | - Miriam J Rodrigues
- Neurology, Auckland City Hospital, Auckland, New Zealand
- Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Mark Davis
- Neurogenetics Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, Western Australian Department of Health, Nedlands, Australia
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA, Australia
- Neurogenetics Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, Western Australian Department of Health, Nedlands, Australia
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
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