A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

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Every individual carries two copies of each chromosome (haplotypes), one from each of their parents, that consist of a long sequence of alleles. Modern genotyping technologies do not measure haplotypes directly, but the combined sum (or genotype) of alleles at each site. Statistical methods are needed to infer (or phase) the haplotypes from the observed genotypes. Haplotype estimation is a key first step of many disease and population genetic studies. Much recent work in this area has focused on phasing in cohorts of nominally unrelated individuals. So called ‘long range phasing’ is a relatively recent concept for phasing individuals with intermediate levels of relatedness, such as cohorts taken from population isolates. Methods also exist for phasing genotypes for individuals within explicit pedigrees. Whilst high quality phasing techniques are available for each of these demographic scenarios, to date, no single method is applicable to all three. In this paper, we present a general approach for phasing cohorts that contain any level of relatedness between the study individuals. We demonstrate high levels of accuracy in all demographic scenarios, as well as the ability to detect (Mendelian consistent) genotyping error and recombination events in duos and trios, the first method with such a capability.

Vyšlo v časopise: A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness. PLoS Genet 10(4): e32767. doi:10.1371/journal.pgen.1004234
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004234

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