Power of direct vs. indirect haplotyping in association studies

S. Thomas, D. Porteous, P. M. Visscher

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Haplotype analysis is essential to studies of the genetic factors underlying human disease, but requires a large sample size of phase-known data. Recently, directly haplotyping individuals was suggested as a means of maximizing the phase-known data from a sample. Haplotyping, however, is much more labor-intensive than indirectly inferring haplotypes from genotypes (genotyping). This study uses simulations to compare the power of each methodology to detect associations between a haplotype and a trait or disease locus under conditions of varying linkage disequilibrium. The relative power of haplotyping over genotyping in association studies increases with decreasing sample size, decreasing linkage disequilibrium, increasing [corrected] numbers of marker loci, and decreasing numbers of different haplotypes. In addition, the frequency of the haplotype of interest and the magnitude of its association with the disease affect the power. From a cost-benefit standpoint, genotyping would be favored with large multiplicative risks (relative risk of haplotype >2.5). If case numbers are limiting rather than cost, haplotyping would maximize the information obtained. At small haplotype frequencies (e.g.,
Original languageEnglish
Pages (from-to)116-124
Number of pages9
JournalGenetic Epidemiology
Issue number2
Publication statusPublished - 2004

Keywords / Materials (for Non-textual outputs)

  • Algorithms Gene Frequency/genetics Genetic Markers/genetics *Genotype Haplotypes/*genetics Humans Linkage Disequilibrium/*genetics Locus Control Region/genetics *Models, Genetic *Models, Statistical Phenotype Probability Reproducibility of Results


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