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Retrieving y chromosomal haplogroup trees using GWAS data

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收录情况： ◇ SCIE

作者：
Peng, M.-S[a,b,c] ; He, J.-D[a,b,d] ; Fan, L[b,e] ; Liu, J[a,f] ; Adeola, A.C[a,f] ; Wu, S.-F[a,b] ; Murphy, R.W[a,g] ; Yao, Y.-G[b,h] ; Zhang, Y.-P[a,b,i] ;
机构： [a]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China [b]KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [c]Youth Innovation Promotion Association, Chinese Academy of Sciences, Beijing, China [d]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 [e]School of Life Sciences, Chinese University of Hong Kong, Hong Kong Special Administrative Region, Shatin, Hong Kong [f]Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China [g]Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada [h]Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [i]Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
出处：
DOI： 10.1038/ejhg.2013.272
ISSN：

关键词： GWAS haplogroup Myanmar phylogeny Y chromosome Y-SNPs

摘要：
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. © 2014 Macmillan Publishers Limited All rights reserved.

基金：
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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外文
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中科院(CAS)分区：
出版当年[2015]版：
大类 | 2 区 生物
小类 | 3 区 生化与分子生物学 3 区 遗传学
最新[2023]版：
大类 | 2 区 生物学
小类 | 2 区 生化与分子生物学 2 区 遗传学
JCR分区：
出版当年[2014]版：
Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Q1 GENETICS & HEREDITY
最新[2023]版：
Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Q2 GENETICS & HEREDITY

影响因子： 最新[2023版] 最新五年平均 出版当年[2014版] 出版当年五年平均 出版前一年[2013版] 出版后一年[2015版]

第一作者：
第一作者机构： [a]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China [b]KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China [c]Youth Innovation Promotion Association, Chinese Academy of Sciences, Beijing, China
通讯作者：
推荐引用方式(GB/T 7714)：
Peng M.-S,He J.-D,Fan L,et al.Retrieving y chromosomal haplogroup trees using GWAS data[J].EUROPEAN JOURNAL OF HUMAN GENETICS.2014,22(8):doi:10.1038/ejhg.2013.272.
APA：
Peng, M.-S,He, J.-D,Fan, L,Liu, J,Adeola, A.C...&Zhang, Y.-P.(2014).Retrieving y chromosomal haplogroup trees using GWAS data.EUROPEAN JOURNAL OF HUMAN GENETICS,22,(8)
MLA：
Peng, M.-S,et al."Retrieving y chromosomal haplogroup trees using GWAS data".EUROPEAN JOURNAL OF HUMAN GENETICS 22..8(2014)

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