Abstract
Recent technological improvements in the field of genetic data extraction give rise to the possibility of reconstructing the historical pedigrees of entire populations from the genotypes of individuals living today. Current methods are still not practical for real data scenarios as they have limited accuracy and assume unrealistic assumptions of monogamy and synchronized generations. In order to address these issues, we develop a new method for pedigree reconstruction, , which is based on formulations of the pedigree reconstruction problem as variants of graph coloring. The new formulation allows us to consider features that were overlooked by previous methods, resulting in a reconstruction of up to 5 generations back in time, with an order of magnitude improvement of false-negatives rates over the state of the art, while keeping a lower level of false positive rates. We demonstrate the accuracy of compared to previous approaches using simulation studies over a range of population sizes, including inbred and outbred populations, monogamous and polygamous mating patterns, as well as synchronous and asynchronous mating.
Highlights
Pedigree reconstruction is an important problem in the field of computational genetics, with many potential applications such as genealogy inference, heritability estimation, and victim identification [1,2,3,4]
It has the potential to improve the accuracy of current state-of-the-art relationship inference methods as it uses family structure in a broader sense than just using pairwise genetic similarity information. [5,6]
A wide variety of statistical methods for genetic analysis assume the relationships between individuals are known, and can manifest relatedness information to improve inference
Summary
Pedigree reconstruction is an important problem in the field of computational genetics, with many potential applications such as genealogy inference, heritability estimation, and victim identification [1,2,3,4]. In this paper we consider a more difficult variation of the problem, where we are given the genotypes of the currently living population only, and try to reconstruct the historical pedigree of unobserved ancestors. This variant suits well the scenario of reconstructing the pedigrees of living human populations. This variant of pedigree reconstruction was previously studied in several theoretical works [12,13] These papers focus on presenting theoretical bounds on the length of sequence required for reconstructing pedigrees under various combinatorial and stochastic heritability models, but in contrast to our work, do not aim to provide practical solutions for the problem
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