title: Retrieving Y chromosomal haplogroup trees using GWAS data.
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.
authors.affiliation: 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [3] Youth Innovation Promotion Association, Chinese Academy of Sciences, Beijing, China.
authors.forename: Min-Sheng
authors.initials: MS
authors.lastname: Peng
authors.affiliation: 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [3] Institute of Clinical and Basic Medical Sciences, First People's Hospital of Yunnan Province (Affiliated Hospital of Kunming University of Science and Technology), Kunming, China.
authors.forename: Jun-Dong
authors.initials: JD
authors.lastname: He
authors.affiliation: 1] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
authors.forename: Long
authors.initials: L
authors.lastname: Fan
authors.affiliation: 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
authors.forename: Adeniyi C
authors.initials: AC
authors.lastname: Adeola
authors.affiliation: 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors.forename: Shi-Fang
authors.initials: SF
authors.lastname: Wu
authors.affiliation: 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Murphy
authors.affiliation: 1] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
authors.forename: Yong-Gang
authors.initials: YG
authors.lastname: Yao
authors.affiliation: 1] State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [2] KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [3] Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D041322:Chromosomes, Human, Y; D019295:Computational Biology / Q000379:methods; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D020407:Internet; D008297:Male; D002052:Myanmar; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012984:Software