Mengyuan Song , Yuxiang Zhou , Chenxi Zhao , Feng Song , Yiping Hou
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引用次数: 0
摘要
人类 Y 染色体反映了男性的进化过程。通过 Y 染色体追踪男性世系在进化、法医和人类学研究中具有重要作用。根据 Y 单倍群的具体分布情况确定男性世系可缩小调查范围,这已被用于法医研究。然而,现有软件在利用 Y-STR(Y 染色体短串联重复序列)预测 Y-SNP(Y 染色体单核苷酸多态性)单倍群进行家族搜索时,往往缺乏分辨率。在这项研究中,我们开发了 YHP(Y Haplogroup Predictor),这是一款无需大量 Y-SNP 测序就能提供高分辨率单倍群推断的新型软件。利用现有数据集(219 个单倍群,共 4064 个样本),YHP 采用随机森林算法,在最高单倍群分辨率下预测单倍群的准确率为 0.923。YHP 可在 Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-) 上下载,它有助于高分辨率单倍群预测、单倍型错配分析和单倍型相似性比较。值得注意的是,它在东亚人群中显示出功效,从八个不同的东亚种族人群的训练数据中获益匪浅。此外,它还能无缝集成更多的训练集,将其用途扩展到不同的人群。
YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs
Human Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope, which has been used in forensic scenarios. However, existing software aids in familial searching using Y-STRs (Y-chromosome short tandem repeats) to predict Y-SNP (Y-chromosome single nucleotide polymorphism) haplogroups, they often lack resolution. In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. Leveraging existing datasets (219 haplogroups, 4064 samples in total), YHP predicts haplogroups with 0.923 accuracy under the highest haplogroup resolution, employing a random forest algorithm. YHP, available on Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-), facilitates high-resolution haplogroup prediction, haplotype mismatch analysis, and haplotype similarity comparison. Notably, it demonstrates efficacy in East Asian populations, benefiting from training data from eight distinct East Asian ethnic populations. Moreover, it enables seamless integration of additional training sets, extending its utility to diverse populations.
期刊介绍:
Forensic Science International is the flagship journal in the prestigious Forensic Science International family, publishing the most innovative, cutting-edge, and influential contributions across the forensic sciences. Fields include: forensic pathology and histochemistry, chemistry, biochemistry and toxicology, biology, serology, odontology, psychiatry, anthropology, digital forensics, the physical sciences, firearms, and document examination, as well as investigations of value to public health in its broadest sense, and the important marginal area where science and medicine interact with the law.
The journal publishes:
Case Reports
Commentaries
Letters to the Editor
Original Research Papers (Regular Papers)
Rapid Communications
Review Articles
Technical Notes.