PRIMUS：利用线粒体和Y单倍型改进系谱重建
PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes.
作者信息
Staples Jeffrey, Ekunwe Lynette, Lange Ethan, Wilson James G, Nickerson Deborah A, Below Jennifer E
机构信息
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
College of Public Service, Jackson State University, Jackson Heart Study, Jackson, MS 39213, USA.
出版信息
Bioinformatics. 2016 Feb 15;32(4):596-8. doi: 10.1093/bioinformatics/btv618. Epub 2015 Oct 29.
UNLABELLED
PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data. However, when genetic data for individuals within a pedigree are missing, often multiple pedigrees can be reconstructed that fit the data. We report a major expansion of PRIMUS that uses mitochondrial (mtDNA) and non-recombining Y chromosome (NRY) haplotypes to eliminate many pedigree structures that are inconsistent with the genetic data. We demonstrate that discordances in mtDNA and NRY haplotypes substantially reduce the number of potential pedigrees, and often lead to the identification of the correct pedigree.
AVAILABILITY AND IMPLEMENTATION
We have implemented PRIMUS updates in PERL and it is available at primus.gs.washington.edu.
未加标注
PRIMUS是一种系谱重建算法，它利用全基因组同源性估计来重建与观察到的遗传数据一致的系谱。然而，当系谱中个体的遗传数据缺失时，通常可以重建出多个符合数据的系谱。我们报告了PRIMUS的一次重大扩展，它利用线粒体（mtDNA）和非重组Y染色体（NRY）单倍型来消除许多与遗传数据不一致的系谱结构。我们证明，mtDNA和NRY单倍型中的不一致性大幅减少了潜在系谱的数量，并常常能确定正确的系谱。
可用性与实现方式
我们已用PERL实现了PRIMUS的更新版本，可在primus.gs.washington.edu获取。
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