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Linkage disequilibrium (LD) is an important measure used in the analysis of single-nucleotide polymorphism (SNP) data. We used the Genetic Analysis Workshop 16 (GAW16) Framingham Heart Study 500 k SNP data to explore the effect of sampling methods on estimating of LD for SNP data.We found 332 trios in the GAW16 Framingham SNP data. Repeated random samples without replacement, of different sizes of trios and independent individuals, are drawn from these 332 trios. For each sample, the LD is calculated using the Haploview program for the chromosome 1 SNP data. Percents of D' > 0.8 and r2 > 0.8 are calculated for different distance bins based on the Haploview output. The results are summarized by sample size and sampling methods to give us an overall view of the effect of sample size and sampling methods on the LD estimation.Trios design gave stable estimates. A sample of 30 to 40 trios gave estimates of percent of LD > 0.8 very close to those from 332 trios. When independent individuals are used, the estimates are less stable and are different from those obtained from the 332 trios for both D' and r2, with larger differences for D'.Our results suggest that trio design gives a stable estimate of LD. Therefore it may be more suitable for LD analysis than using independent individuals. We must be cautious when comparing the LD estimates from trios, and those from independent individuals.

Linkage disequilibrium of single-nucleotide polymorphism data: how sampling methods affect estimates of linkage disequilibrium