Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls.
Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls.
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从无阶段的本地血统调用中同时推断亲本混合比例和混合时间。
DOI：
10.1016/j.ajhg.2022.06.016
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发表时间：
2022
影响因子：
9.8
通讯作者：
Williams,AmyL
中科院分区：
文献类型：
--
作者：
Avadhanam,Siddharth;Williams,AmyL
对当地祖先区域的群体遗传分析通常假设祖先的混合过程对于个体的双亲是相同的，当考虑最近的混合时，这种假设可能是无效的。在这里，我们提出了父母混合比例推断（PAPI），贝叶斯工具推断的混合比例和混合时间为每一个单一的混合个体的父母。PAPI分析非定相的本地祖先道，并有两个组成部分：一个二项式模型，利用全基因组的祖先分数来推断父母的混合比例和隐马尔可夫模型（HMM），推断混合时间从道长度。至关重要的是，隐马尔可夫模型占未观察到的内祖先重组近似的谱系交叉动力学，使父母的混合时间的推断。在模拟中，我们发现PAPI的混合比例估计值平均偏离真实值0.047，分别优于ANCESTOR和PedMix 46.0%和57.6%。此外，PAPI的混合时间估计值与真实值（）密切相关，但平均向下偏差为1.01代，部分原因是当地祖先推断的不准确。为了说明其效用，我们对PAGE研究中的非裔美国人基因型（N = 5，786）进行了PAPI，并发现了祖先比例的间接交配的强有力证据：夫妇的祖先比例高度相关（R= 0.87），并且比随机交配下的预期更接近彼此（p < 10−6）。我们预计，PAPI将是有用的研究人口动态的混合物，也将有兴趣的个人寻求了解他们的个人家谱。
Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inference of parental admixture times. In simulations, we find that PAPI's admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI's admixture time estimates were strongly correlated with the truth () but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (R= 0.87) and are closer to each other than expected under random mating (p < 10−6). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.
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DOI：
--
发表时间：
1984
期刊：
Cleft Palate Journal
影响因子：
--
作者：
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通讯作者：
J. Blank
DOI：
--
发表时间：
1961
期刊：
Journal of Speech and Hearing Research
影响因子：
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DOI：
--
发表时间：
1987
期刊：
The Cleft palate journal
影响因子：
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作者：
Hairfield,WM;Warren,DW;Hinton,VA;Seaton,DL
通讯作者：
Seaton,DL
影响因子：
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不同出血和咬合条件下的口腔内气压和口腔气流。
DOI：
--
发表时间：
1986
期刊：
Journal of Speech and Hearing Research
影响因子：
--
作者：
A. H. Putnam;R. Shelton;C. Kastner
通讯作者：
C. Kastner