title: Simulating linkage disequilibrium structures in a human population for SNP association studies.
abstract: Existing simulation methods usually simulate linkage disequilibrium (LD) structures starting with an initial population that is randomly generated according to specified allele frequencies. These at random based methods might be unstable because the LD level of the initial population is generally extremely low. This study presents a new algorithm, SIMLD, to simulate genome populations with real LD structures. SIMLD begins from an initial population with possibly the highest LD level, and then the LD decays to fit the desired level through processes of mating and recombination over generations. SIMLD can produce case-control samples according to various disease models. Using empirical SNP marker information from three populations of HapMap data, we implement the proposed algorithm and demonstrate a set of experimental results.
authors.affiliation: School of Computer Science and Technology, Xidian University, Xi'an, China. xgyuan@vt.edu
authors.forename: Xiguo
authors.initials: X
authors.lastname: Yuan
authors.forename: Junying
authors.initials: J
authors.lastname: Zhang
authors.forename: Yue
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D016022:Case-Control Studies; D003198:Computer Simulation; D005787:Gene Frequency; D056726:Genetic Association Studies; D005819:Genetic Markers; D055614:Genetic Phenomena; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D009862:Online Systems; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D005819:Genetic Markers