| Literature DB >> 24281365 |
Min-Sheng Peng1, Jun-Dong He2, Long Fan3, Jie Liu4, Adeniyi C Adeola4, Shi-Fang Wu5, Robert W Murphy6, Yong-Gang Yao7, Ya-Ping Zhang8.
Abstract
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.Mesh：
Year: 2013 PMID： 24281365 PMCID： PMC4350590 DOI： 10.1038/ejhg.2013.272
Source DB: PubMed Journal: Eur J Hum Genet ISSN： 1018-4813 Impact factor: 4.246