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Open Access Methodology article

Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling

Fei Ji1, Stephen J Finch2, Chad Haynes1, Nancy R Mendell2 and Derek Gordon3*

Author Affiliations

1 Lab of Statistical Genetics, Rockefeller University, New York, NY, USA

2 Department of Applied Math and Statistics, Stony Brook University, Stony Brook, NY, USA

3 Department of Genetics, Rutgers University, Piscataway, NJ, USA

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BMC Genomics 2007, 8:238  doi:10.1186/1471-2164-8-238

Published: 16 July 2007

Abstract

Background

Studies of association methods using DNA pooling of single nucleotide polymorphisms (SNPs) have focused primarily on the effects of "machine-error", number of replicates, and the size of the pool. We use the non-centrality parameter (NCP) for the analysis of variance test to compute the approximate power for genetic association tests with DNA pooling data on cases and controls. We incorporate genetic model parameters into the computation of the NCP. Parameters involved in the power calculation are disease allele frequency, frequency of the marker SNP allele in coupling with the disease locus, disease prevalence, genotype relative risk, sample size, genetic model, number of pools, number of replicates of each pool, and the proportion of variance of the pooled frequency estimate due to machine variability. We compute power for different settings of number of replicates and total number of genotypings when the genetic model parameters are fixed. Several significance levels are considered, including stringent significance levels (due to the increasing popularity of 100 K and 500 K SNP "chip" data). We use a factorial design with two to four settings of each parameter and multiple regression analysis to assess which parameters most significantly affect power.

Results

The power can increase substantially as the genotyping number increases. For a fixed number of genotypings, the power is a function of the number of replicates of each pool such that there is a setting with maximum power. The four most significant parameters affecting power for association are: (1) genotype relative risk, (2) genetic model, (3) sample size, and (4) the interaction term between disease and SNP marker allele probabilities.

Conclusion

For a fixed number of genotypings, there is an optimal number of replicates of each pool that increases as the number of genotypings increases. Power is not substantially reduced when the number of replicates is close to but not equal to the optimal setting.