title: Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift.
abstract: There is considerable interest in identifying and characterizing block-like patterns of linkage disequilibrium (LD; haplotype blocks) in the human genome as these may facilitate the identification of complex disease genes via genome-wide association studies. Although recombination hot-spots have been suggested as the primary mechanism to explain the block-like pattern of LD, other forces, such as genetic drift, may also be important. To this end, we have studied the effect of various recombination models on patterns of LD by using extensive simulations. As expected, haplotype blocks were observed under a model allowing recombination hot-spots. However, we also observed similar block-like patterns in the models where recombination crossovers are randomly and uniformly distributed, and we demonstrate that these blocks are generated by genetic drift. We caution that genetic drift may be an alternative mechanism (in addition to recombination hot-spots) that can lead to block-like patterns of LD. Our findings highlight the necessity of characterizing haplotype blocks in world-wide populations.
authors.affiliation: Center for Genome Information, 130 Kettering, Department of Environmental Health, University of Cincinnati, OH 45215, Cincinnati, USA.
authors.forename: Kun
authors.initials: K
authors.lastname: Zhang
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Akey
authors.forename: Ning
authors.initials: N
authors.lastname: Wang
authors.forename: Momiao
authors.initials: M
authors.lastname: Xiong
authors.forename: Ranajit
authors.initials: R
authors.lastname: Chakraborty
authors.forename: Li
authors.initials: L
authors.lastname: Jin
mesh_terms: D003198:Computer Simulation; D003434:Crossing Over, Genetic; D019143:Evolution, Molecular; D040961:Genetic Drift; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D010363:Pattern Recognition, Automated; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic