Genome-wide profiling of heritable and de novo STR variations
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Abstract
Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool.github.io/HipSTR.
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Software solutions like GeneMapper ID-X, STRait Razor, and HipSTR include peak-height ratios, heterozygosity thresholds, and ladder alignment checks to minimize false calls.
“While software solutions like GeneMapper® ID-X [41], STRait Razor [42], and the open-source Haplotype inference and phasing for STRs (HipSTR) [43] include peak-height ratios, heterozygosity thresholds, and ladder alignment checks to minimize false calls, expert review remains crucial [44].”
From Genetic Insights into the Economic Toll of Cell Line Misidentification: A Comprehensive Review (2026) · cites this paper as [43]
The Main Text identifies HipSTR as an STR-calling tool, supporting the citation’s identification of it. Online Methods (The HipSTR algorithm; Experiments) describe stutter modeling and a spanning-read support ratio used to filter de novo mutation calls, but do not establish that HipSTR includes peak-height ratios, heterozygosity thresholds, or ladder alignment checks. No page numbers are available in our copy. (LLM, conf=0.86)
Experimental — accuracy not yet measuredHealthy individuals have tens of thousands of relatively short STR tracts distributed throughout their genomes.
“Healthy individuals have tens of thousands of relatively short STR tracts distributed throughout their genomes (Gymrek and Erlich, 2013; Gymrek et al., 2016; Willems et al., 2017).”
From Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries (2018) · cites this paper as Willems et al., 2017
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- Authors
- Willems, T., Zielinski, D., Yuan, J., Gordon, A., Gymrek, M., & Erlich, Y.
- Affiliations
- New York Genome Center (US)
- Broad Institute (US)
- Corresponding author
- Willems, Thomas
- Erlich, Yaniv
- Venue
- Nature Methods
- Published
- 2017-04-24
- Volume
- 14
- Issue
- 6
- Pages
- 590-592
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC5482724
- OpenAlex
- W2609153336
- Cited by
- 329
- References
- 31
- Citations by year
- 2026: 37 · 2025: 40 · 2024: 52 · 2023: 36 · 2022: 55 · 2021: 39 · 2020: 18 · 2019: 21 · 2018: 20 · 2017: 10 · 2012: 1
- FWCI
- 13.04
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Burroughs Wellcome Fund
- National Human Genome Research Institute (UM1HG008901)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- microsatellite markers, STR genotyping, haplotype phasing, next-generation sequencing, genetic disorders, population genetics, forensic genetics
- MeSH terms
- Algorithms, Chromosome Mapping, Humans, Software, Genetic Variation, Genome, Human, DNA Fingerprinting, Sequence Alignment, Sequence Analysis, DNA, Microsatellite Repeats, Genetic Predisposition to Disease, High-Throughput Nucleotide Sequencing
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