Abstract
BackgroundGenome wide association (GWA) studies provide the opportunity to develop new kinds of analysis. Analysing pairs of markers from separate regions might lead to the detection of allelic association which might indicate an interaction between nearby genes.Methods396,591 markers typed in 541 subjects were studied. 7.8*1010 pairs of markers were screened and those showing initial evidence for allelic association were subjected to more thorough investigation along with 10 flanking markers on either side.ResultsNo evidence was detected for interaction. However 6 markers appeared to have an incorrect map position according to NCBI Build 35. One of these was corrected in Build 36 and 2 were dropped. The remaining 3 were left with map positions inconsistent with their allelic association relationships.DiscussionAlthough no interaction effects were detected the method was successful in identifying markers with probably incorrect map positions.ConclusionThe study of allelic association can supplement other methods for assigning markers to particular map positions. Analyses of this type may usefully be applied to data from future GWA studies.
Highlights
Genome wide association (GWA) studies provide the opportunity to develop new kinds of analysis
The study of allelic association can supplement other methods for assigning markers to particular map positions. Analyses of this type may usefully be applied to data from future GWA studies
Pairs of markers genotyped in the course of a GWA were identified as showing allelic association with each other in spite of being separated by a very large genetic distance
Summary
Genome wide association (GWA) studies provide the opportunity to develop new kinds of analysis. If two genes carry out a similar function but only one copy of either is needed for survival a population might sustain relatively common loss-offunction mutations If these occurred in both copies of both genes would an organism not be viable. Were the genotypes of markers close to both loci to be considered jointly it might become apparent that there was a very marked reduction in the number of subjects being homozygous at both loci for alleles associated with the mutations. Effects such as this could be detectable through finding allelic association between pairs of markers far apart on the genome. Such an investigation would (page number not for citation purposes)
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