通过基因型填充增加家系群体的样本量。

Genotype imputation to increase sample size in pedigreed populations.

作者信息

Hickey John M, Cleveland Matthew A, Maltecca Christian, Gorjanc Gregor, Gredler Birgit, Kranis Andreas

机构信息

School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia.

出版信息

Methods Mol Biol. 2013;1019:395-410. doi: 10.1007/978-1-62703-447-0_17.

DOI:10.1007/978-1-62703-447-0_17

PMID:23756901

Abstract

Genotype imputation is a cost-effective way to increase the power of genomic selection or genome-wide association studies. While several genotype imputation algorithms are available, this chapter focuses on a heuristic algorithm, as implemented in the AlphaImpute software. This algorithm combines long-range phasing, haplotype library imputation, and segregation analysis and it is specifically designed to work with pedigreed populations.The chapter is organized in different sections. First the challenges related to genotype imputation in pedigreed populations are described, along with the specifics of the imputation algorithm used in AlphaImpute. In the second section, factors affecting the accuracy of genotype imputation using this algorithm are discussed. The different parameters that control AlphaImpute are detailed and examples of how to apply AlphaImpute are given.

摘要

基因型填充是一种提高基因组选择或全基因组关联研究效能的经济有效的方法。虽然有几种基因型填充算法可供使用，但本章重点介绍一种启发式算法，该算法在AlphaImpute软件中实现。此算法结合了长程定相、单倍型库填充和分离分析，并且专门设计用于处理有系谱的群体。本章分为不同的章节。首先描述了与有系谱群体中基因型填充相关的挑战，以及AlphaImpute中使用的填充算法的细节。在第二节中，讨论了使用该算法影响基因型填充准确性的因素。详细介绍了控制AlphaImpute的不同参数，并给出了应用AlphaImpute的示例。