TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.
TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.
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DOI：
10.3389/fgene.2023.1227176
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发表时间：
2023
影响因子：
3.7
通讯作者：
Ge, Jianye
中科院分区：
文献类型：
--
作者：
Wang, Xuewen;Huang, Meng;Budowle, Bruce;Ge, Jianye
关键词：
从DNA序列中识别串联重复序列（TR）变异具有重要的理论和实际意义。已经开发了一些生物信息学工具用于检测或基因分型TR。然而，对来自长读段测序数据的TR等位基因进行基因分型的研究很少，并且对来自下一代测序数据的TR等位基因进行基因分型的准确性仍需要提高。在本文中，描述了一种新的算法来从序列比对中检索TR区域，并且已经开发了软件程序TRcaller并将其整合到门户网站中，以从短读段序列和长读段序列两者、从多个测序平台生成的全基因组和靶向序列两者中调用TR等位基因。所有TR等位基因都作为单倍型进行基因分型，并且将报告稳健的等位基因，甚至是DNA混合物中的多个等位基因。TRcaller可以在检测TR等位基因时提供实质上更高的准确性（在289个人类个体中>99%），其幅度更快（例如，300倍人类序列数据的200 s）比主流软件工具。该门户网站从法医学、家谱和疾病相关TR基因座中预选了119个TR基因座。TRcaller被验证在各种应用中具有可扩展性，例如DNA取证和疾病诊断，可以扩展到育种计划等其他领域。可用性：TRcaller可在https://www.trcaller.com/SignIn.aspx上获得。
Calling 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., ∼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.
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影响因子：
14.9
作者：
Highnam G;Franck C;Martin A;Stephens C;Puthige A;Mittelman D
通讯作者：
Mittelman D
分析下一代测序数据中法医STR标记的种群结构。
DOI：
10.1016/j.fsigen.2020.102364
发表时间：
2020-11
期刊：
Forensic science international. Genetics
影响因子：
--
作者：
Aalbers SE;Hipp MJ;Kennedy SR;Weir BS
通讯作者：
Weir BS
DOI：
10.1038/s41576-020-0236-x
发表时间：
2020-10
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Logsdon GA;Vollger MR;Eichler EE
通讯作者：
Eichler EE
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
3.1
作者：
Hoogenboom, Jerry;van der Gaag, Kristiaan J.;Laros, Jeroen F. J.
通讯作者：
Laros, Jeroen F. J.