Human genome-wide screen of haplotype-like blocks of reduced diversity.
An important proportion of the human genome is organized in regions of high linkage disequilibrium (LD) and low haplotype diversity, referred to as haplotype blocks. Here, we perform a genome-wide screen of haplotype-like blocks presenting just two main haplotypes at a frequency higher than 1%, based on single-nucleotide polymorphism (SNP) frequencies from two populations: African-Americans and Caucasians, using data from the Celera SNP database. These haplotype-like blocks of reduced diversity are more abundant and of longer size in Caucasians, in agreement with population history. Several of the discovered blocks are good candidates for targets of natural selection, such as those blocks containing a cluster of bitter taste receptors or the apolipoprotein L1. In addition, several genes putatively involved in susceptibility to common diseases are included in these haplotype-like blocks of reduced diversity. This fact may present important implications in association studies, leading to a reduction of genotyping efforts.
Costas
Javier
J
Centro Nacional de Genotipado, Fundación Pública Galega de Medicina Xenómica, Hospital Clínico Universitario, Universidade de Santiago de Compostela, E15706, Santiago de Compostela, Spain. bfcostas@usc.es
Salas
Antonio
A
Phillips
Christopher
C
Carracedo
Angel
A
D044383:Black People; D002874:Chromosome Mapping; D030541:Databases, Genetic; D005787:Gene Frequency; D040961:Genetic Drift; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D044465:White People; D001741:Black or African American