Retrieving Y chromosomal haplogroup trees using GWAS data

Peng, Min-Sheng; He, Jun-Dong; Fan, Long; Liu, Jie; Adeola, Adeniyi C; Wu, Shi-Fang; Murphy, Robert W; Yao, Yong-Gang; Zhang, Ya-Ping
August 2014
European Journal of Human Genetics;Aug2014, Vol. 22 Issue 8, p1046
Academic Journal
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.


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