TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads

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dc.creatorWang, Xuewen
dc.creatorHuang, Meng
dc.creatorBudowle, Bruce
dc.creatorGe, Jianye
dc.creator.orcid0000-0001-8724-075X (Ge, Jianye)
dc.date.accessioned2023-08-07T21:42:55Z
dc.date.available2023-08-07T21:42:55Z
dc.date.issued2023-08-03
dc.description.abstractCalling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., approximately 2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.
dc.description.sponsorshipThis work was supported in part by award 15PNIJ-21-GG04159-RESS, awarded by the National Institute of Justice, Office of Justice Programs, United States Department of Justice and by internal funds from the Center for Human Identification. The opinions, findings, and conclusions or recommendations expressed are those of the authors and do not necessarily reflect those of the United States Department of Justice.
dc.identifier.citationWang, X., Huang, M., Budowle, B., & Ge, J. (2023). TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads. Frontiers in genetics, 14, 1227176. https://doi.org/10.3389/fgene.2023.1227176
dc.identifier.issn1664-8021
dc.identifier.urihttps://hdl.handle.net/20.500.12503/32383
dc.identifier.volume14
dc.publisherFrontiers Media S.A.
dc.relation.urihttps://doi.org/10.3389/fgene.2023.1227176
dc.rights.holder© 2023 Wang, Huang, Budowle and Ge.
dc.rights.licenseAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourceFrontiers in Genetics
dc.subjectdisease TR genotyping
dc.subjectforensics STR identification
dc.subjecthigh throughput sequencing
dc.subjecttandem repeat
dc.subjectvariant caller
dc.titleTRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads
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dc.type.materialArticle

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