A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration
文献类型：期刊论文
| 作者 | Ni, Xumin1; Guo, Wei2; Yuan, Kai3; Yang, Xiong3; Ma, Zhiming2 ; Xu, Shuhua3,4,5; Zhang, Shihua2
|
| 刊名 | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
 |
| 出版日期 | 2016-03-01 |
| 卷号 | 13期号:2页码:281-290 |
| 关键词 | Population genetics identity by descent probabilistic method Markov process |
| ISSN号 | 1545-5963 |
| DOI | 10.1109/TCBB.2015.2480074 |
| 英文摘要 | The inference of demographic history of populations is an important undertaking in population genetics. A few recent studies have developed identity-by-descent (IBD) based methods to reveal the signature of the relatively recent historical events. Notably, Pe'er and his colleagues have introduced a novel method (named PIBD here) by employing IBD sharing to infer effective population size and migration rate. However, under island model, PIBD neglects the coalescent information before the time to the most recent common ancestor (tMRCA) which leads to apparent deviations in certain situations. In this paper, we propose a new method, MIBD, by adopting a Markov process to describe the island model and develop a new formula for estimating IBD sharing. The new formula considers the coalescent information before tMRCA and the joint effect of the coalescent and migration events. We apply both MIBD and PIBD to the genome-wide data of two human populations (Palestinian and Bedouin) obtained from the HGDP-CEPH database, and demonstrate that MIBD is competitive to PIBD. Our simulation analyses also show that the results of MIBD are more accurate than those of PIBD especially in the case of small effective population size. |
| 资助项目 | National Natural Science Foundation of China (NSFC)[11426237] ; National Natural Science Foundation of China (NSFC)[91331204] ; National Natural Science Foundation of China (NSFC)[31171218] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040100] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; 973 Project[2011CB808000] ; Fundamental Research Funds for the Central Universities[2011JBZ019] ; National Excellent Doctoral Dissertation Foundation of PR China (FANEDD)[201312] ; Key Laboratory of Random Complex Structures and Data Science, CAS[2008DP173182] ; National Program for Top-notch Young Innovative Talents of The "Wanren Jihua" Project ; Outstanding Young Scientist Program of CAS, National Center for Mathematics and Interdisciplinary Sciences of CAS |
| WOS研究方向 | Biochemistry & Molecular Biology ; Computer Science ; Mathematics |
| 语种 | 英语 |
| WOS记录号 | WOS:000374305300009 |
| 出版者 | IEEE COMPUTER SOC |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/22525]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Ni, Xumin; Guo, Wei; Yuan, Kai; Yang, Xiong; Ma, Zhiming; Xu, Shuhua; Zhang, Shihua |
| 作者单位 | 1.Beijing Jiaotong Univ, Dept Math, Sch Sci, Beijing 100044, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Max Planck Independent Res Grp Populat Genom, CAS MPG Partner Inst Computat Biol, Shanghai 200031, Peoples R China 4.ShanghaiTec Univ, Sch Life Sci & Technol, Shanghai 200031, Peoples R China 5.Collaborat Innovat Ctr Genet & Dev, Shanghai 200438, Peoples R China |
| 推荐引用方式 GB/T 7714 | Ni, Xumin,Guo, Wei,Yuan, Kai,et al. A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2016,13(2):281-290. |
| APA | Ni, Xumin.,Guo, Wei.,Yuan, Kai.,Yang, Xiong.,Ma, Zhiming.,...&Zhang, Shihua.(2016).A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,13(2),281-290. |
| MLA | Ni, Xumin,et al."A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 13.2(2016):281-290. |
入库方式： OAI收割
来源：数学与系统科学研究院
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。