RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci.

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2024-01-31 DOI:10.1186/s13059-024-03171-4
Sarah Fazal, Matt C Danzi, Isaac Xu, Shilpa Nadimpalli Kobren, Shamil Sunyaev, Chloe Reuter, Shruti Marwaha, Matthew Wheeler, Egor Dolzhenko, Francesca Lucas, Stefan Wuchty, Mustafa Tekin, Stephan Züchner, Vanessa Aguiar-Pulido
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Abstract

Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are being identified, and interpreting them is a challenge. We present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), a machine learning tool for distinguishing pathogenic from benign TR expansions. Our results demonstrate that an ensemble approach classifies TRs with an average precision of 93% and recall of 83%. RExPRT's high precision will be valuable in large-scale discovery studies, which require prioritization of candidate loci for follow-up studies.

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REXPRT:预测串联重复位点致病性的机器学习工具。
串联重复序列(TRs)的扩展导致了大约 60 种单基因疾病。我们预计,更多致病性重复序列扩展的发现将缩小许多疾病的诊断差距。越来越多的串联重复序列扩展被发现,而解释这些扩展是一项挑战。我们介绍了 RExPRT(Repeat EXpansion Pathogenicity pRediction Tool,重复扩展致病性预测工具),这是一种用于区分致病性和良性 TR 扩展的机器学习工具。我们的研究结果表明,采用集合方法对 TR 进行分类的平均精确度为 93%,召回率为 83%。RExPRT 的高精确度将在大规模发现研究中发挥重要作用,因为大规模发现研究需要为后续研究确定候选位点的优先顺序。
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来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
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