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.
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Acknowledgements
We are grateful to all volunteers and samplers. We thank Zhong-Yin Zhou, Wen-Zhi Wang, and Ni-Ni Shi for technical assistance. This study was supported by grants from National Natural Science Foundation of China and Bureau of Science and Technology of Yunnan Province. The Youth Innovation Promotion Association, Chinese Academy of Sciences provided support to M-SP. This work was also supported, in part, by a Visiting Professorship for Senior International Scientists from the Chinese Academy of Sciences, and manuscript preparation by a Natural Sciences and Engineering Research Council of Canada Discovery Grant A3148 to RWM.
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Peng, MS., He, JD., Fan, L. et al. Retrieving Y chromosomal haplogroup trees using GWAS data. Eur J Hum Genet 22, 1046–1050 (2014). https://doi.org/10.1038/ejhg.2013.272
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DOI: https://doi.org/10.1038/ejhg.2013.272
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