title: Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection.
abstract: The hemoglobin E variant (HbE; ( beta )26Glu-->Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non-HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240-4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection.
authors.affiliation: Department of Human Genetics, The University of Tokyo, Tokyo, Japan. juno-tky@umin.ac.jp
authors.forename: Jun
authors.initials: J
authors.lastname: Ohashi
authors.forename: Izumi
authors.initials: I
authors.lastname: Naka
authors.forename: Jintana
authors.initials: J
authors.lastname: Patarapotikul
authors.forename: Hathairad
authors.initials: H
authors.lastname: Hananantachai
authors.forename: Gary
authors.initials: G
authors.lastname: Brittenham
authors.forename: Sornchai
authors.initials: S
authors.lastname: Looareesuwan
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Clark
authors.forename: Katsushi
authors.initials: K
authors.lastname: Tokunaga
mesh_terms: D000818:Animals; D005075:Biological Evolution; D003198:Computer Simulation; D019143:Evolution, Molecular; D005787:Gene Frequency; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D006239:Haplotypes; D006441:Hemoglobin A / Q000235:genetics; D006446:Hemoglobin E / Q000235:genetics*; D006579:Heterozygote; D006720:Homozygote; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D016778:Malaria, Falciparum / Q000235:genetics* / Q000517:prevention & control; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D013785:Thailand
chemical_list: D005819:Genetic Markers; D006441:Hemoglobin A; D006446:Hemoglobin E