title: Detection of sharing by descent, long-range phasing and haplotype imputation.
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.
authors.affiliation: deCODE genetics, Reykjavik, Iceland. kong@decode.is
authors.forename: Augustine
authors.initials: A
authors.lastname: Kong
authors.forename: Gisli
authors.initials: G
authors.lastname: Masson
authors.forename: Michael L
authors.initials: ML
authors.lastname: Frigge
authors.forename: Arnaldur
authors.initials: A
authors.lastname: Gylfason
authors.forename: Pasha
authors.initials: P
authors.lastname: Zusmanovich
authors.forename: Gudmar
authors.initials: G
authors.lastname: Thorleifsson
authors.forename: Pall I
authors.initials: PI
authors.lastname: Olason
authors.forename: Andres
authors.initials: A
authors.lastname: Ingason
authors.forename: Stacy
authors.initials: S
authors.lastname: Steinberg
authors.forename: Thorunn
authors.initials: T
authors.lastname: Rafnar
authors.forename: Patrick
authors.initials: P
authors.lastname: Sulem
authors.forename: Magali
authors.initials: M
authors.lastname: Mouy
authors.forename: Frosti
authors.initials: F
authors.lastname: Jonsson
authors.forename: Unnur
authors.initials: U
authors.lastname: Thorsteinsdottir
authors.forename: Daniel F
authors.initials: DF
authors.lastname: Gudbjartsson
authors.forename: Hreinn
authors.initials: H
authors.lastname: Stefansson
authors.forename: Kari
authors.initials: K
authors.lastname: Stefansson
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D005260:Female; D017353:Gene Deletion; D005819:Genetic Markers; D005828:Genetics, Population; D006239:Haplotypes; D006801:Humans; D007055:Iceland; D040582:Inheritance Patterns; D008285:Major Histocompatibility Complex; D008297:Male; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers