Association analyses are the methods most commonly employed in gene identification efforts today, and the methodology that has been widely incorporated into developmental research. Association analyses are straightforward to understand; they basically test whether a particular genetic variant is more likely to be found in affected individuals than in unaffected individuals (in a case–control design; Figure 1), or more likely to be transmitted to affected children (in family-based designs; though these are increasingly less common since population stratification concerns have been alleviated by genome-wide data, as described below). Association relies on genotyping genetic markers, in the same way that linkage analyses did. The major difference between linkage and association methods is that linkage is a within-family statistic, whereas association is a between-family statistic. In linkage, this meant that the same marker had to be shared across affected members within a family, but it could be a different marker from one family to the next. Association analyses, on the other hand, require that it is the same marker that is shared across all affected individuals in the sample. Linkage analyses only
