Analysis and benchmarking of small and large genomic variants across tandem repeats

ABSTRACT 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. Access through your institution Buy or subscribe This is a preview of

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* Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS DISCOVERY AND QUALITY ANALYSIS OF A COMPREHENSIVE SET OF

STRUCTURAL VARIANTS AND SHORT TANDEM REPEATS Article Open access 10 June 2020 A DEEP POPULATION REFERENCE PANEL OF TANDEM REPEAT VARIATION Article Open access 23 October 2023 VARIANT CALLING

AND BENCHMARKING IN AN ERA OF COMPLETE HUMAN GENOME SEQUENCES Article 14 April 2023 DATA AVAILABILITY The TR catalog (version 1.2) can be found at https://zenodo.org/records/8387564 (ref.

74). Supplementary Table 4 holds the paths to the input assemblies used to create the pVCF. The pVCF can be found at https://zenodo.org/records/6975244 (ref. 76). The TandemRepeat benchmark

is hosted at https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/TandemRepeats_v1.0 (ref. 83). Comparison VCFs from TR callers HipSTR, GangSTR,

Medaka and TRGT and whole-genome VCFs from DeepVariant, BioGraph and Sniffles are available at https://zenodo.org/records/10724503 (ref. 84). CODE AVAILABILITY All code created for this

project is available under an open-source license. Analysis scripts for this project are hosted at https://github.com/ACEnglish/adotto/ (ref. 85). Truvari can be found at

https://github.com/ACEnglish/truvari/ (ref. 86). Laytr can be found at https://github.com/ACEnglish/laytr/ (ref. 87). A lightweight version of the TR catalog creation process is available as

a snakemake pipeline at https://github.com/nate-d-olson/adotto-smk (ref. 88). The overlap permutation tool regioners can be downloaded from https://github.com/ACEnglish/regioners (ref. 89).

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(2023). Download references ACKNOWLEDGEMENTS We would like to thank the GIAB community for constant support. We thank J. McDaniel for very helpful comments on the paper, M. Wykes and S. Nurk

for assistance in processing Medaka results and V. Bafna for contributions to the TR catalog. A.C.E. and F.J.S. were supported by HHSN268201800002I, U01AG058589, 1U01HG011758-01 and

1UG3NS132105-01. H.Z.J. was supported by NIH/NHGRI R01HG010149. M.J.P.C. and B.G. were supported by R01HG011649 and 5U24HG007497, respectively. J.P. was supported in part by HG010149.

Certain commercial equipment, instruments or materials are identified to adequately specify the experimental conditions or reported results. Such identification does not imply recommendation

or endorsement by the National Institute of Standards and Technology, nor does it imply that the equipment, instruments or materials identified are necessarily the best available for the

purpose. AUTHOR INFORMATION Author notes * These authors contributed equally: Justin M. Zook, Fritz J. Sedlazeck. AUTHORS AND AFFILIATIONS * Human Genome Sequencing Center, Baylor College of

Medicine, Houston, TX, USA Adam C. English & Fritz J. Sedlazeck * Pacific Biosciences of California, Menlo Park, CA, USA Egor Dolzhenko & Michael A. Eberle * Department of Computer

Science and Engineering, University of California, San Diego, La Jolla, CA, USA Helyaneh Ziaei Jam, Jonghun Park & Melissa Gymrek * Oxford Nanopore Technologies, Inc., New York, NY, USA

Sean K. McKenzie * Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA Nathan D. Olson, Justin Wagner & Justin M. Zook * Applied and

Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium Wouter De Coster * Applied and Translational Neurogenomics Group, Department of Biomedical

Sciences, University of Antwerp, Antwerp, Belgium Wouter De Coster * Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA Bida Gu 

& Mark J. P. Chaisson * Department of Medicine, University of California, San Diego, La Jolla, CA, USA Melissa Gymrek * Department of Molecular and Human Genetics, Baylor College of

Medicine, Houston, TX, USA Fritz J. Sedlazeck * Department of Computer Science, Rice University, Houston, TX, USA Fritz J. Sedlazeck Authors * Adam C. English View author publications You

can also search for this author inPubMed Google Scholar * Egor Dolzhenko View author publications You can also search for this author inPubMed Google Scholar * Helyaneh Ziaei Jam View author

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Olson View author publications You can also search for this author inPubMed Google Scholar * Wouter De Coster View author publications You can also search for this author inPubMed Google

Scholar * Jonghun Park View author publications You can also search for this author inPubMed Google Scholar * Bida Gu View author publications You can also search for this author inPubMed 

Google Scholar * Justin Wagner View author publications You can also search for this author inPubMed Google Scholar * Michael A. Eberle View author publications You can also search for this

author inPubMed Google Scholar * Melissa Gymrek View author publications You can also search for this author inPubMed Google Scholar * Mark J. P. Chaisson View author publications You can

also search for this author inPubMed Google Scholar * Justin M. Zook View author publications You can also search for this author inPubMed Google Scholar * Fritz J. Sedlazeck View author

publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS A.C.E. performed data analysis and software development. E.D., H.Z.J., N.D.O., S.K.M., J.P., B.G.,

J.W., M.G. and M.J.P.C. contributed to testing and data processing. A.C.E., J.M.Z. and F.J.S. designed the study. A.C.E., E.D., H.Z.J., N.D.O., S.K.M., J.P., W.D.C., M.A.E., B.G., J.W.,

M.G., M.J.P.C., J.M.Z. and F.J.S. reviewed and edited the paper. CORRESPONDING AUTHORS Correspondence to Adam C. English or Fritz J. Sedlazeck. ETHICS DECLARATIONS COMPETING INTERESTS F.J.S.

receives research support from Illumina, Genentech, PacBio and ONT. E.D. and M.A.E. are employees and shareholders of PacBio. S.K.M. is an employee and shareholder of ONT. W.D.C. has

received free consumables from ONT. The other authors declare no competing interests. PEER REVIEW PEER REVIEW INFORMATION _Nature Biotechnology_ thanks the anonymous reviewer(s) for their

contribution to the peer review of this work. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional

affiliations. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Figs. 1–7, Methods and Tables 1–3, 6 and 8–13. REPORTING SUMMARY SUPPLEMENTARY TABLES Supplementary Tables 4

(assembly sources), 5 (assembly statistics), 7 (replicate tiers) and 14 (pathogenic and phenotypic TRs). SUPPLEMENTARY MATERIAL 1 Laytr HTML report for TRGT. SUPPLEMENTARY MATERIAL 2 Laytr

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law. Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE English, A.C., Dolzhenko, E., Ziaei Jam, H. _et al._ Analysis and benchmarking of small and large genomic variants across

tandem repeats. _Nat Biotechnol_ 43, 431–442 (2025). https://doi.org/10.1038/s41587-024-02225-z Download citation * Received: 30 October 2023 * Accepted: 28 March 2024 * Published: 26 April

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