false-negative findings in our first analysis. 4a) Many of the results of individually-genotyped studies represented in dbGAP are analyzed based on the assumption that the detailed haplotype structures identified in data from CEPH and Yoruban individuals will provide accurate representations of the haplotypes identified in European-American and African-American samples identified far from Utah. 4b) The approach that we use here is based on distances between SNP genomic markers, rather than assumptions about the extent to which the exact haplotype structure of these reference populations will be maintained in the samples that we have studied. 5a) Dense individual genotypes provide the opportunity for unequivocal matching with DNA databases; 5b) Pooled genotypes provide a much stronger barrier for matching with DNA databases, which is an enhanced consideration in studies of illegal behaviors. 6a) “Template” analyses focus on strength of association for individual SNPs; 6b) The current analyses assume that most bona fide associations that are based on phenotypic differences will be present at multiple nearby SNPs. In any single sample, many of the clusters of positive findings at nearby SNPs could be due to stochastic differences in haplotype frequencies between cases and controls that are not related to phenotype. As the same
