Simple method to analyze SNP‐based association studies using DNA pools

Abstract

Association studies using DNA pools are in principle powerful and efficient to detect association between a marker allele and disease status, e.g., in a case-control design. A common observation with the use of DNA pools is that the two alleles at a polymorphic SNP locus are not amplified in equal amounts in heterozygous individuals. In addition, there are poolspecific experimental errors so that there is variation in the estimates of allele frequencies from different pools that are from the same individuals. As a result of these additional sources of variation, the outcome of an experiment is an estimated count of alleles rather than the usual outcome in terms of observed counts. In this study, we show analytically and by computer simulation that unequal amplification should be taken into account when testing for differences in allele frequencies between pools, and suggest a simple modification of the standard w 2 test to control the type I error rate in the presence of experimental error variation. The impact of experimental errors on the power of association studies is shown.

A Comparison of DNA Pools Constructed Following Whole Genome Amplification for Two-Stage SNP Genotyping Designs

“…The mean absolute difference between frequency estimates from individual genotypes and pooled samples was .034 similar to values of .033 to .04 reported previously using the Sequenom MassARRAY (Bansal et al, 2002;Le Hellard et al, 2002;Mohlke et al, 2002;Visscher & Le Hellard, 2003). We found allele frequency estimates must be corrected for unequal amplification of alleles, but there was no significant difference when using data from two or eight heterozygous individuals.…”

“…A pooling strategy reduces genotyping costs and the time required to complete large genotyping projects (Bansal et al, 2002;Hoogendoorn et al, 2000;Le Hellard et al, 2002;Mohlke et al, 2002;Sham et al, 2002;Visscher & Le Hellard, 2003). However pooling results in a loss of information because of increased errors in the experimental procedure and the loss of haplotype information.…”

Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease

“…To account for variance due to DNA pooling, an estimate of pooling error was calculated according to Visscher and Le Hellard (48). The resulting error factor of 0.014 was then used to adjust the c 2 test statistic.…”

A genetic analysis of serotonergic biosynthetic and metabolic enzymes in migraine using a DNA pooling approach

“…Depending upon the magnitude of experimental error produced in the estimation of pooled allele frequencies, a classical v 2 -test statistic or an adjusted v 2 -test statistic (v adj 2 ) was used to assess the null hypothesis (Le Hellard et al 2002;Visscher and Le Hellard 2003).…”