600k methods used for these samples revealed r = 0.95 correlations between pooled and individual genotyping in extensive validation studies [12] (see below). Much of this variation (1–2%) can be attributed to variations in pipetting and DNA quantification required for pool construction (TD and DW, unpublished observations, 2002–2006). The remainder of the variance is reduced for arrays used at the end of a study, in comparison to validating experiments that use data from some of the first arrays of this type that were studied within this laboratory. The r = 0.95 correlation is thus likely to reflect an upper limit of the variance noted in actual disease vs control comparisons. 1M SNP assays can reveal even higher correlations between individual genotyping and pooled genotyping datasets (Liu et al, in preparation).
