Simulating linkage disequilibrium structures in a human population for SNP association studies

Biochem Genet. 2011 Jun;49(5-6):395-409. doi: 10.1007/s10528-011-9416-x. Epub 2011 Jan 14.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Case-Control Studies
  • Computer Simulation*
  • Gene Frequency
  • Genetic Association Studies
  • Genetic Markers
  • Genetic Phenomena
  • Genotype
  • Humans
  • Linkage Disequilibrium*
  • Models, Genetic
  • Online Systems
  • Polymorphism, Single Nucleotide*
  • Software

Substances

  • Genetic Markers