To enhance power for GWA tests, two additional data sets were combined with the AGP data. We analyzed the AGRE data using family-based analyses and the AGRE and AGP data combined using mega-analyses. All primary analyses were performed with both data sets. We limited exploratory analyses to these nine: broad diagnostic group; verbal and nonverbal status by the diagnostic groups and by ancestry. For the primary analyses, we also analyzed two other sets of combined samples: AGP trios together with AGRE families; AGP trios together with unrelated SAGE controls; and all three data sets. The method to analyze control and family-based data (49) builds on two related ideas: matched case–control analysis using conditional logistic regression (e.g. 52) and the natural connection between family-based analysis and conditional logistic regression of alleles found in probands (the transmitted alleles) and matched pseudo-controls (formed from transmitted and un-transmitted alleles) (49). Unrelated SAGE controls were matched by genetic ancestry to probands and combined with the ‘pseudo-controls’ produced by the family-based analysis: first, by spectral analysis, we estimated the genetic ancestry of probands and unrelated controls
