Inferring parental genomic ancestries using pooled semi-Markov processes.
Inferring parental genomic ancestries using pooled semi-Markov processes.
复制标题
使用混合半马尔可夫过程推断亲代基因组祖先。
DOI：
10.1093/bioinformatics/btv239
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发表时间：
2015
期刊：
影响因子：
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通讯作者：
Sankararaman,Sriram
中科院分区：
文献类型：
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作者：
Zou,JamesY;Halperin,Eran;Burchard,Esteban;Sankararaman,Sriram
动机：公众和科学界广泛关注的一个基本问题是利用个体的DNA来推断父母的基因组祖先。特别是，我们通常对来自特定祖先（例如欧洲人，非洲人，美洲原住民等）的每个父母的基因组的部分感兴趣。这有许多应用程序，从了解遗传的祖先相关的风险和特征，以量化人类的交配模式。结果：我们的模型作为一个汇集半马尔可夫过程的问题，父母的基因组血统推断。我们开发了一个通用的数学框架池半马尔可夫过程，并为这些模型构建有效的推理算法。将我们的推理算法应用于231个墨西哥三重奏和258个波多黎各三重奏的基因型数据，我们拥有每个父母的真实基因组祖先，我们证明了我们的方法准确地推断了半马尔可夫过程和父母的基因组祖先的参数。我们还验证了模拟的方法。我们的混合半马尔可夫过程模型和推理算法可能在基因组学和机器学习的其他设置中具有独立的兴趣。联系方式：jazo@microsoft.com
Motivation:A basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent’s genome that comes from specific ancestries (e.g. European, African, Native American, etc). This has many applications ranging from understanding the inheritance of ancestry-related risks and traits to quantifying human assortative mating patterns.Results:We model the problem of parental genomic ancestry inference as a pooled semi-Markov process. We develop a general mathematical framework for pooled semi-Markov processes and construct efficient inference algorithms for these models. Applying our inference algorithm to genotype data from 231 Mexican trios and 258 Puerto Rican trios where we have the true genomic ancestry of each parent, we demonstrate that our method accurately infers parameters of the semi-Markov processes and parents’ genomic ancestries. We additionally validated the method on simulations. Our model of pooled semi-Markov process and inference algorithms may be of independent interest in other settings in genomics and machine learning.Contact:jazo@microsoft.com