Article abstract
Nature Genetics 40, 1068 - 1075 (2008)
Published online: 17 August 2008 | doi:10.1038/ng.216
Detection of sharing by descent, long-range phasing and haplotype imputation
Augustine Kong1, Gisli Masson1, Michael L Frigge1, Arnaldur Gylfason1, Pasha Zusmanovich1, Gudmar Thorleifsson1, Pall I Olason1, Andres Ingason1, Stacy Steinberg1, Thorunn Rafnar1, Patrick Sulem1, Magali Mouy1, Frosti Jonsson1, Unnur Thorsteinsdottir1, Daniel F Gudbjartsson1, Hreinn Stefansson1 & Kari Stefansson1
Abstract
Uncertainty about the phase of strings of SNPs creates complications in genetic analysis, although methods have been developed for phasing population-based samples. However, these methods can only phase a small number of SNPs effectively and become unreliable when applied to SNPs spanning many linkage disequilibrium (LD) blocks. Here we show how to phase more than 1,000 SNPs simultaneously for a large fraction of the 35,528 Icelanders genotyped by Illumina chips. Moreover, haplotypes that are identical by descent (IBD) between close and distant relatives, for example, those separated by ten meioses or more, can often be reliably detected. This method is particularly powerful in studies of the inheritance of recurrent mutations and fine-scale recombinations in large sample sets. A further extension of the method allows us to impute long haplotypes for individuals who are not genotyped.
- deCODE genetics, Sturlugata 8, 101 Reykjavík, Iceland.
Correspondence to: Augustine Kong1 e-mail: kong@decode.is
Correspondence to: Kari Stefansson1 e-mail: kari.stefansson@decode.is
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