Analysis and benchmarking of small and large genomic variants across tandem repeats
Open accessAbstract
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits and are linked to over 60 disease phenotypes. However, they are often excluded from at-scale studies because of challenges with variant calling and representation, as well as a lack of a genome-wide standard. Here, to promote the development of TR methods, we created a catalog of TR regions and explored TR properties across 86 haplotype-resolved long-read human assemblies. We curated variants from the Genome in a Bottle (GIAB) HG002 individual to create a TR dataset to benchmark existing and future TR analysis methods. We also present an improved variant comparison method that handles variants greater than 4 bp in length and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ~24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 ‘truth-set’ TR benchmark. We demonstrate the utility of this pipeline across short-read and long-read technologies. A truth-set catalog of human tandem repeats allows benchmarking of variant analysis tools.
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STR expansions are associated with a wide range of severe neurological disorders, such as amyotrophic lateral sclerosis, Friedreich ataxia and Huntington's disease.
“Furthermore, STR expansions are associated with a wide range of severe neurological disorders, such as amyotrophic lateral sclerosis, Friedreich ataxia and Huntington’s disease50,72.”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [50]
The Abstract states that tandem-repeat alleles are associated with many neurological or neurodegenerative diseases, and reference 8 identifies a repeat expansion linked to ALS. Our copy does not identify Friedreich ataxia, and its Huntington-related reference concerns Huntington disease-like 2 rather than Huntington’s disease itself. (LLM, conf=0.84)
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Comprehensive genome analysis and variant detection at scale using DRAGEN
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“52 Although several tools have been developed to discover VNTRs in genomes, 53,54 our understanding of the cause, prevalence, and function of VNTRs remains limited.”
- Authors
- English, A. C., Dolzhenko, E., Ziaei Jam, H., McKenzie, S. K., Olson, N. D., De Coster, W., Park, J., Gu, B., Wagner, J., Eberle, M. A., Gymrek, M., Chaisson, M. J. P., Zook, J. M., & Sedlazeck, F. J.
- Affiliations
- Baylor College of Medicine (US)
- Pacific Biosciences (United States) (US)
- National Institute of Standards and Technology (US)
- University of California San Diego (US)
- University of Southern California (US)
- Corresponding author
- English, Adam C.
- Sedlazeck, Fritz J.
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2024-04-26
- Volume
- 43
- Issue
- 3
- Pages
- 431-442
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC11952744
- OpenAlex
- W4395667653
- Semantic Scholar
- bb8b3679ae28b7144d02e83dcdb21a9b036ce41d
- Cited by
- 68
- References
- 81
- Citations by year
- 2026: 23 · 2025: 29 · 2024: 15 · 2023: 1
- FWCI
- 9.09
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Commons-TMC (Texas Medical Center) (submittedVersion)
- Funders
- National Institutes of Health (1ug3ns132105-01)
- National Institute of Standards and Technology
- National Institute on Aging (U01AG058589, P30AG066546)
- National Human Genome Research Institute (HG010149, U24HG007497, R01HG011649, R01HG010149, U01HG011758)
- National Institute of Neurological Disorders and Stroke (UG3 NS132105)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- tandem repeats, genetic variants, variant calling, long-read assembly, haplotype-resolved genome assembly, Genome in a Bottle, HG002
- MeSH terms
- Haplotypes, Humans, Genetic Variation, Genome, Human, Benchmarking, Tandem Repeat Sequences, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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