Introduction

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.

Publications

  1. Retrieving Y chromosomal haplogroup trees using GWAS data.
    Cite this
    Peng MS, He JD, Fan L, Liu J, Adeola AC, Wu SF, Murphy RW, Yao YG, Zhang YP, 2014-08-01 - European journal of human genetics : EJHG

Credits

  1. Min-Sheng Peng
    Developer

    1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, China

  2. Jun-Dong He
    Developer

    1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, China

  3. Long Fan
    Developer

    1] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, China

  4. Jie Liu
    Developer

    1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, China

  5. Adeniyi C Adeola
    Developer

    1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, China

  6. Shi-Fang Wu
    Developer

    1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, China

  7. Robert W Murphy
    Developer

    1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, China

  8. Yong-Gang Yao
    Developer

    1] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, China

  9. Ya-Ping Zhang
    Investigator

    1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, China

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Summary
AccessionBT002424
Tool TypeApplication
Category
PlatformsWindows
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByYa-Ping Zhang