Effective testing of gene-disease associations

We propose a method for testing any hypothesized association between a candidate allele, for which there is a specific laboratory test, and a common chronic disease. Families in which this allele is segregating are identified through index individuals who are homozygous or heterozygous for the allele. The sample consists of the subset of identified families who also have at least one member with the common disease of interest. For each independent family in this subset, select one person with the disease and determine if he or she is heterozygous for the allele. The observed proportion of heterozygotes in this sample is compared to the proportion expected on the basis of each diseased relative's null probability of being heterozygous for the allele; this null probability depends only on the relative's relationship to the index individual and the population allele frequency. We provide these null probabilities, develop appropriate inference procedures, discuss sample size requirements, and compare this method to a standard case-control design. Results using this method are unlikely to be influenced by confounders, systematic bias, or genetic heterogeneity.