Article

European Journal of Human Genetics (2014) 22, 1046–1050; doi:10.1038/ejhg.2013.272; published online 27 November 2013

Retrieving Y chromosomal haplogroup trees using GWAS data

Min-Sheng Peng1,2,3,10, Jun-Dong He1,2,4,10, Long Fan2,5,10, Jie Liu1,6, Adeniyi C Adeola1,6, Shi-Fang Wu1,2, Robert W Murphy1,7, Yong-Gang Yao2,8 and Ya-Ping Zhang1,2,9

  1. 1State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
  2. 2KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
  3. 3Youth Innovation Promotion Association, Chinese Academy of Sciences, Beijing, China
  4. 4Institute of Clinical and Basic Medical Sciences, First People’s Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, China
  5. 5School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
  6. 6Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
  7. 7Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
  8. 8Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
  9. 9Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China

Correspondence: Professor Y-P Zhang, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. Tel: +86 871 6519 9030; Fax: +86 871 6519 5430; E-mail: zhangyp@mail.kiz.ac.cn

10These authors contributed equally to this work.

Received 29 May 2013; Revised 6 October 2013; Accepted 25 October 2013
Advance online publication 27 November 2013

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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.

Keywords:

Y chromosome; Y-SNPs; haplogroup; phylogeny; GWAS; Myanmar