Detection of sharing by descent, long-range phasing and haplotype imputation.
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.
Kong
Augustine
A
deCODE genetics, Reykjavik, Iceland. kong@decode.is
Masson
Gisli
G
Frigge
Michael L
ML
Gylfason
Arnaldur
A
Zusmanovich
Pasha
P
Thorleifsson
Gudmar
G
Olason
Pall I
PI
Ingason
Andres
A
Steinberg
Stacy
S
Rafnar
Thorunn
T
Sulem
Patrick
P
Mouy
Magali
M
Jonsson
Frosti
F
Thorsteinsdottir
Unnur
U
Gudbjartsson
Daniel F
DF
Stefansson
Hreinn
H
Stefansson
Kari
K
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
D005819:Genetic Markers