Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan.
Institute of Forensic Medicine, Ministry of Justice, New Taipei City, 23016, Taiwan.
J Hum Genet. 2022 Aug;67(8):487-493. doi: 10.1038/s10038-022-01033-0. Epub 2022 Mar 28.
The application of massively parallel sequencing (MPS) data from whole genomes has allowed very many more Y-SNP loci to be genotyped simultaneously than previously possible. Although this greatly increases the resolution of Y-SNP haplogroups to link common ancestors, it remains a great challenge to provide a phylogenetic tree to clearly display the relationship of varying haplogroups. Y-SNP Haplogroup Hierarchy Finder is a web tool to generate hierarchical haplogroups based on Y-SNP data with the derived allele at the terminal of a haplogroup tree. The input data can include that from whole-genome sequencing. Confidence in assignment using Y-SNP Haplogroup Hierarchy Finder was demonstrated using Y-SNP genotypes of 1233 samples, sourced from the 1000 genomes project phase 3, used to generate the expected haplogroups. The outcome includes 2 reports: a 'Haplogroup Report' lists mutation types from the submitted Y-SNPs and their corresponding haplogroups, and a 'Haplogroup Hierarchy Report' lists all possible hierarchical haplogroups and ranks the three most supported haplogroups. Each layer of the descending haplogroups from one step to the next is shown and the supporting numbers of Y-SNPs are also included in these reports. All haplogroups that exhibited a clear relationship between the ancestral through to the derived SNPs can be clustered into a hierarchy of haplogroups. The assigned 1233 haplogroups were compared with 2 other software programs designed to assemble haplogroups, which resulted in one where there were many differences and the other one where there was only minor difference. The advantage of this web-based tool is that it provides an easy way to assign Y-SNP haplogroup based on the visualized hierarchical pattern.
大规模并行测序（MPS）全基因组数据的应用使得同时进行的 Y-SNP 基因座数量比以往任何时候都多。虽然这大大提高了 Y-SNP 单倍型群体的分辨率，以便将共同祖先联系起来，但提供一个清晰显示不同单倍型群体关系的系统发育树仍然是一个巨大的挑战。Y-SNP 单倍型群体层次结构查找器是一个网络工具，用于根据 Y-SNP 数据生成层次结构单倍型群体，其中衍生等位基因位于单倍型群体树的末端。输入数据可以包括全基因组测序的数据。使用来自 1000 基因组项目第 3 阶段的 1233 个样本的 Y-SNP 基因型，通过生成预期的单倍型群体来证明使用 Y-SNP 单倍型群体层次结构查找器进行分配的置信度。结果包括 2 份报告：一份“单倍型报告”列出了提交的 Y-SNPs 及其对应的单倍型的突变类型，一份“单倍型层次结构报告”列出了所有可能的层次结构单倍型，并对三个最支持的单倍型进行排名。从一步到下一步的下降单倍型的每一层都显示出来，并且这些报告还包括支持的 Y-SNP 数量。所有显示从祖先到衍生 SNP 之间存在明显关系的单倍型都可以聚类为单倍型层次结构。将分配的 1233 个单倍型与另外 2 个设计用于组装单倍型的软件程序进行比较，其中一个有很多差异，另一个只有微小差异。这个基于网络的工具的优势在于，它提供了一种根据可视化的层次结构模式轻松分配 Y-SNP 单倍型的方法。
