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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >INFERRING HAPLOTYPES FROM GENOTYPES ON A PEDIGREE WITH MUTATIONS, GENOTYPING ERRORS AND MISSING ALLELES
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INFERRING HAPLOTYPES FROM GENOTYPES ON A PEDIGREE WITH MUTATIONS, GENOTYPING ERRORS AND MISSING ALLELES

机译：从具有突变，基因分型错误和等位基因缺失的花序上的基因型推断单倍型

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摘要

Inferring the haplotypes of the members of a pedigree from their genotypes has been extensively studied. However, most studies do not consider genotyping errors and de novo mutations. In this paper, we study how to infer haplotypes from genotype data that may contain genotyping errors, de novo mutations, and missing alleles. We assume that there are no recombinants in the genotype data, which is usually true for tightly linked markers. We introduce a combinatorial optimization problem, called haplotype configuration with mutations and errors (HCME), which calls for haplotype configurations consistent with the given genotypes that incur no recombinants and require the minimum number of mutations and errors. HCME is NP-hard. To solve the problem, we propose a heuristic algorithm, the core of which is an integer linear program (ILP) using the system of linear equations over Galois field GF(2). Our algorithm can detect and locate genotyping errors that cannot be detected bysimply checking the Mendelian law of inheritance. The algorithm also offers error correction in genotypes/haplotypes rather than just detecting inconsistencies and deleting the involved loci. Our experimental results show that the algorithm can infer haplotypes with a very high accuracy and recover 65%–94% of genotyping errors depending on the pedigree topology.
机译：从基因型推断谱系成员的单倍型已被广泛研究。但是，大多数研究没有考虑基因分型错误和从头突变。在本文中，我们研究了如何从可能包含基因分型错误，从头突变和缺失等位基因的基因型数据推断单倍型。我们假设基因型数据中没有重组体，通常对于紧密连接的标记而言是正确的。我们引入了一个组合优化问题，称为带有突变和错误的单倍型构型（HCME），该问题要求与不产生重组体且需要最少数量的突变和错误的给定基因型一致的单倍型构型。 HCME是NP硬的。为了解决该问题，我们提出了一种启发式算法，其核心是在Galois场GF（2）上使用线性方程组的整数线性程序（ILP）。我们的算法可以通过简单地检查孟德尔遗传定律来检测和定位无法检测到的基因分型错误。该算法还提供了基因型/单倍型的错误校正，而不仅仅是检测不一致并删除相关基因座。我们的实验结果表明，该算法可以非常准确地推断出单倍型，并且可以根据谱系拓扑恢复65％至94％的基因分型错误。

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