Retrieving Y chromosomal haplogroup trees using GWAS data
Retrieving Y chromosomal haplogroup trees using GWAS data
复制标题
DOI：
10.1038/ejhg.2013.272
复制
发表时间：
2013-11
影响因子：
5.2
通讯作者：
Min-Sheng Peng;Jun-dong He;Long Fan;Jie Liu;A. Adeola;Shi‐Fang Wu;R. Murphy;Yong-Gang Yao;
中科院分区：
文献类型：
--
作者：
Min-Sheng Peng;Jun-dong He;Long Fan;Jie Liu;A. Adeola;Shi‐Fang Wu;R. Murphy;Yong-Gang Yao;
系统发育信息的Y染色体单核苷酸多态性（Y-SNPs）整合在DNA芯片中还没有得到充分的探索，在大多数全基因组关联研究（GWAS）。在这里，我们介绍了一个管道来检索Y-SNP数据。介绍了YTool软件（http：//mitotool. org/ytool/）来处理数据的转换、过滤和注释。来自缅甸人群的全基因组SNP数据用于构建基于369个高置信度Y-SNP的117条Y染色体的单倍型群树。平行基因分型和发表的Y染色体重测序数据证实了我们的管道的有效性。我们将这一策略应用于CEU HapMap数据集，并构建了一个单倍群树，其中包含来自39个个体的107个Y-SNP。检索到的Y-SNPs可以识别群体的亲本遗传结构。鉴于GWAS的大量数据，这种方法有利于未来Y染色体多样性的研究。
Phylogenetically informative Y chromosomal single-nucleotide polymorphisms (Y-SNPs) integrated in DNA chips have not been sufficiently explored in most genome-wide association studies (GWAS). Herein, we introduce a pipeline to retrieve Y-SNP data. We introduce the software YTool (http://mitotool. org/ytool/) to handle conversion, filtering, and annotation of the data. Genome-wide SNP data from populations in Myanmar are used to construct a haplogroup tree for 117 Y chromosomes based on 369 high-confidence Y-SNPs. Parallel genotyping and published resequencing data of Y chromosomes confirm the validity of our pipeline. We apply this strategy to the CEU HapMap data set and construct a haplogroup tree with 107 Y-SNPs from 39 individuals. The retrieved Y-SNPs can discern the parental genetic structure of populations. Given the massive quantity of data from GWAS, this method facilitates future investigations of Y chromosome diversity.