Retrieving Y chromosomal haplogroup trees using GWAS data
Nature Publishing Group, 2013
Online
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Zugriff:
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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Retrieving Y chromosomal haplogroup trees using GWAS data
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Autor/in / Beteiligte Person: | Fan, Long ; He, Jun-Dong ; Yao, Yong-Gang ; Adeola, Adeniyi C. ; Zhang, Ya-Ping ; Peng, Min-Sheng ; Murphy, Robert W. ; Liu, Jie ; Wu, Shi-Fang |
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Veröffentlichung: | Nature Publishing Group, 2013 |
Medientyp: | unknown |
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