Newman et al. (2001) have assesed the importance of genealogy in determining genetic associations with complex traits in Hutterites. In my opinion the key parts of their note is:
"In general, the significance of association with a given marker was considerably inflated when pedigree structure was not included, although in some cases the reverse was true."
"In addition, many more loci showed evidence of association when the pedigree structure was not included (see fig. 2). In fact, 10%–22% of all markers appeared to have a strong association (P<.01) with the phenotype, when pedigree structure was not included." "In an association study in which it is not possible to take into account all familial relationships, as we have done with the Hutterites, another option is to use genomic controls (Devlin and Roeder 1999). Otherwise, naïve approaches to genetic-association analysis could result in an enormous amount of time and of money spent in following up artifactual associations."
The same conclusions (more or less) were obtained by Kennedy et al. in year 1992!. The paper is "Estimation of effects of single genes on quantitative traits".