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

English, Adam C.; Dolzhenko, Egor; Ziaei Jam, Helyaneh; McKenzie, Sean K.; Olson, Nathan D.; De Coster, Wouter; Park, Jonghun; Gu, Bida; Wagner, Justin; Eberle, Michael A.; Gymrek, Melissa; Chaisson, Mark J. P.; Zook, Justin M.; Sedlazeck, Fritz J.

doi:10.1038/s41587-024-02225-z

Cited by 10 publications

(2 citation statements)

References 75 publications

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“…We ran LongTR to genotype repeats in a reference set of 937,122 human TRs from Project Adotto [ 9 ] using 30× PacBio HiFi reads from HG002 (Data Availability). To evaluate the accuracy of genotype calls, we extracted alleles for genotyped TRs from the haplotype-resolved genome assembly of HG002 [ 10 ], which was generated using multiple technologies and orthogonal computational methods and is thus treated as a ground truth here.…”

Section: Resultsmentioning

confidence: 99%

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

Ziaei Jam,

Zook,

Javadzadeh

et al. 2024

Genome Biol

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Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analysis, especially for long or complex repeats. Here, we introduce LongTR, which accurately genotypes tandem repeats from high-fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr and https://zenodo.org/doi/10.5281/zenodo.11403979.

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Section: Resultsmentioning

confidence: 99%

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

Ziaei Jam,

Zook,

Javadzadeh

et al. 2024

Genome Biol

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“…Tandem repeats (TRs), including simple sequence repeats or short tandem repeats (STRs) with 1 to 6 base pair (bp) repeat motifs 1 and variable number tandem repeats (VNTRs) with >7 bp repeat motifs 2 , constitute about 7 to 8% of the human genome 3 , 4 . Many TR loci are highly polymorphic and exhibit marked divergence in length and sequence composition (i.e., the number and types of repeat motifs they harbor) 2 , 5 , 6 .…”

Section: Introductionmentioning

confidence: 99%

A comprehensive tandem repeat catalog of the human genome

Chiu,

Rajan Babu,

Friedman

et al. 2024

Preprint

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With the increasing availability of long-read sequencing data, high-quality human genome assemblies, and software for fully characterizing tandem repeats, genome-wide genotyping of tandem repeat loci on a population scale becomes more feasible. Such efforts not only expand our knowledge of the tandem repeat landscape in the human genome but also enhance our ability to differentiate pathogenic tandem repeat mutations from benign polymorphisms. To this end, we analyzed 272 genomes assembled using datasets from three public initiatives that employed different long-read sequencing technologies. Here, we report a catalog of over 18 million tandem repeat loci, many of which were previously unannotated. Some of these loci are highly polymorphic, and many of them reside within coding sequences.

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Advancements and future perspectives of human tandem repeats

Ye,

Li,

et al. 2024

Science Bulletin

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

Cited by 10 publications

References 75 publications

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

A comprehensive tandem repeat catalog of the human genome

Advancements and future perspectives of human tandem repeats

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