Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions
文献类型：期刊论文
| 作者 | Zhou, Y.1,2; Yuan, K.1,2; Xu, S.1,2; Yu, Y.3; Xie, P.3; Xing, E. P.3; Ni, X.4; Xu, S.5,6; , |
| 刊名 | HEREDITY
 |
| 出版日期 | 2017 |
| 卷号 | 118期号:5页码:503-510 |
| 关键词 | Brachydactyly type A1 Indian hedgehog Gli1 E95K |
| ISSN号 | 0018-067X |
| DOI | 10.1038/hdy.2017.5 |
| 文献子类 | Article |
| 英文摘要 | To infer the histories of population admixture, one important challenge with methods based on the admixture linkage disequilibrium (ALD) is to remove the effect of source LD (SLD), which is directly inherited from source populations. In previous methods, only the decay curve of weighted LD between pairs of sites whose genetic distance were larger than a certain starting distance was fitted by single or multiple exponential functions, for the inference of recent single-or multiple-wave admixture. However, the effect of SLD has not been well defined and no tool has been developed to estimate the effect of SLD on weighted LD decay. In this study, we defined the SLD in the formularized weighted LD statistic under the two-way admixture model and proposed a polynomial spectrum (p-spectrum) to study the weighted SLD and weighted LD. We also found that reference populations could be used to reduce the SLD in weighted LD statistics. We further developed a method, iMAAPs, to infer multiple-wave admixture by fitting ALD using a p-spectrum. We evaluated the performance of iMAAPs under various admixture models in simulated data and applied iMAAPs to the analysis of genome-wide single nucleotide polymorphism data from the Human Genome Diversity Project and the HapMap Project. We showed that iMAAPs is a considerable improvement over other current methods and further facilitates the inference of histories of complex population admixtures. |
| 学科主题 | Environmental Sciences & Ecology ; Evolutionary Biology ; Genetics & Heredity |
| WOS关键词 | DYNAMICS ; GENES |
| 语种 | 英语 |
| WOS记录号 | WOS:000399328400010 |
| 出版者 | NATURE PUBLISHING GROUP |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1177]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Chinese Acad Sci, Max Planck Independent Res Grp Populat Genom, CAS MPG Partner Inst Computat Biol, Key Lab Computat Biol,Shanghai Inst Biol Sci, 320 Yueyang Rd, Shanghai 200031, Peoples R China; 2.Univ Chinese Acad Sci, Beijing, Peoples R China; 3.Carnegie Mellon Univ, Machine Learning Dept, Pittsburgh, PA 15213 USA; 4.Beijing Jiaotong Univ, Sch Sci, Dept Math, Beijing, Peoples R China; 5.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China; 6.Collaborat Innovat Ctr Genet & Dev, Shanghai, Peoples R China, |
| 推荐引用方式 GB/T 7714 | Zhou, Y.,Yuan, K.,Xu, S.,et al. Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions[J]. HEREDITY,2017,118(5):503-510. |
| APA | Zhou, Y..,Yuan, K..,Xu, S..,Yu, Y..,Xie, P..,...&,.(2017).Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions.HEREDITY,118(5),503-510. |
| MLA | Zhou, Y.,et al."Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions".HEREDITY 118.5(2017):503-510. |
入库方式： OAI收割
来源：上海营养与健康研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。