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Genes 2014, 5(3), 561-575; doi:10.3390/genes5030561

An Efficient Estimator of the Mutation Parameter and Analysis of Polymorphism from the 1000 Genomes Project

1
Division of Biostatistics and Human Genetics Center, The University of Texas Health Science Centerat Houston, 1200 Herman Pressler, Houston, TX 77025, USA
2
Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University,Kunming 650091, China 
Received: 27 March 2014 / Revised: 20 June 2014 / Accepted: 24 June 2014 / Published: 22 July 2014
(This article belongs to the Special Issue Grand Celebration: 10th Anniversary of the Human Genome Project)
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Abstract

The mutation parameter θ is fundamental and ubiquitous in the analysis of population samples of DNA sequences. This paper presents a new highly efficient estimator of θ by utilizing the phylogenetic information among distinct alleles in a sample of DNA sequences. The new estimator, called Allelic BLUE, is derived from a generalized linear model about the mutations in the allelic genealogy. This estimator is not only highly accurate, but also computational efficient, which makes it particularly useful for estimating θ for large samples, as well as for a large number of cases, such as the situation of analyzing sequence data from a large genome project, such as the 1000 Genomes Project. Simulation shows that Allelic BLUE is nearly unbiased, with variance nearly as small as the minimum achievable variance, and in many situations, it can be hundreds- or thousands-fold more efficient than a previous method, which was already quite efficient compared to other approaches. One useful feature of the new estimator is its applicability to collections of distinct alleles without detailed frequencies. The utility of the new estimator is demonstrated by analyzing the pattern of θ in the data from the 1000 Genomes Project. View Full-Text
Keywords: mutation parameter; coalescent; allelic genealogy; 1000 Genomes Project mutation parameter; coalescent; allelic genealogy; 1000 Genomes Project
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Fu, Y. An Efficient Estimator of the Mutation Parameter and Analysis of Polymorphism from the 1000 Genomes Project. Genes 2014, 5, 561-575.

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