Kirkpatrick Bonnie, Li Shuai Cheng, Karp Richard M, Halperin Eran
Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA.
J Comput Biol. 2011 Nov;18(11):1481-93. doi: 10.1089/cmb.2011.0156. Epub 2011 Oct 28.
Can we find the family trees, or pedigrees, that relate the haplotypes of a group of individuals? Collecting the genealogical information for how individuals are related is a very time-consuming and expensive process. Methods for automating the construction of pedigrees could stream-line this process. While constructing single-generation families is relatively easy given whole genome data, reconstructing multi-generational, possibly inbred, pedigrees is much more challenging. This article addresses the important question of reconstructing monogamous, regular pedigrees, where pedigrees are regular when individuals mate only with other individuals at the same generation. This article introduces two multi-generational pedigree reconstruction methods: one for inbreeding relationships and one for outbreeding relationships. In contrast to previous methods that focused on the independent estimation of relationship distances between every pair of typed individuals, here we present methods that aim at the reconstruction of the entire pedigree. We show that both our methods out-perform the state-of-the-art and that the outbreeding method is capable of reconstructing pedigrees at least six generations back in time with high accuracy. The two programs are available at http://cop.icsi.berkeley.edu/cop/.
我们能否找到将一组个体的单倍型联系起来的家族谱系，即系谱呢？收集个体之间亲属关系的系谱信息是一个非常耗时且昂贵的过程。自动化构建系谱的方法可以简化这个过程。虽然给定全基因组数据构建单代家族相对容易，但重建多代、可能存在近亲繁殖的系谱则更具挑战性。本文探讨了重建一夫一妻制、规则系谱这一重要问题，当个体仅与同一代的其他个体交配时，系谱就是规则的。本文介绍了两种多代系谱重建方法：一种用于近亲繁殖关系，另一种用于远亲繁殖关系。与以往专注于独立估计每对分型个体之间关系距离的方法不同，这里我们提出的方法旨在重建整个系谱。我们表明，我们的两种方法都优于现有技术，并且远亲繁殖方法能够高精度地重建至少追溯到六代以前的系谱。这两个程序可在http://cop.icsi.berkeley.edu/cop/获取。
