Fast and accurate inference of local ancestry in Latino populations
Fast and accurate inference of local ancestry in Latino populations
复制标题
DOI：
10.1093/bioinformatics/bts144
复制
发表时间：
2012-05-15
期刊：
影响因子：
5.8
通讯作者：
Halperin, Eran
中科院分区：
文献类型：
--
作者：
Baran, Yael;Pasaniuc, Bogdan;Halperin, Eran
结果：为了解决这些挑战，我们引入了利用祖先群体中连锁不平衡结构（LAMP-LD）的本地祖先推断方法，并在推断核心家族三组（LAMP-HAP）的本地祖先时纳入孟德尔隔离约束。我们的算法独特地将单倍型多样性的隐马尔可夫模型（hmm）结合在一个新颖的基于窗口的框架内，与已发表的方法相比，实现了更高的准确性。此外，与以前的方法不同，我们的HMM结构不依赖于参考单倍型的数量，而是依赖于一个固定的常数，因此它能够利用大型数据集，同时保持高效和对过拟合的鲁棒性。通过模拟和分析来自美国大陆、波多黎各和墨西哥的489个核心三重奏家庭的真实数据，我们证明了我们的方法与已发表的拉丁美洲人本地血统推断方法相比具有更高的准确性。
Results: To address these challenges we introduce here methods for local ancestry inference which leverage the structure of linkage disequilibrium in the ancestral population (LAMP-LD), and incorporate the constraint of Mendelian segregation when inferring local ancestry in nuclear family trios (LAMP-HAP). Our algorithms uniquely combine hidden Markov models (HMMs) of haplotype diversity within a novel window-based framework to achieve superior accuracy as compared with published methods. Further, unlike previous methods, the structure of our HMM does not depend on the number of reference haplotypes but on a fixed constant, and it is thereby capable of utilizing large datasets while remaining highly efficient and robust to over-fitting. Through simulations and analysis of real data from 489 nuclear trio families from the mainland US, Puerto Rico and Mexico, we demonstrate that our methods achieve superior accuracy compared with published methods for local ancestry inference in Latinos.