The Center for Inherited Disease Research (CIDR) at Johns Hopkins University genotyped all samples on the Illumina Human 1M array. An extensive data cleaning effort had been made to ensure data quality. These procedures included, but not limited to, using HapMap controls, detection of gender mis-annotation and chromosomal anomalies, cryptic relatedness, population structure, batch effects, Mendelian error detection, and duplication error detection. A detailed description of data cleaning effort is described elsewhere (Bierut et al., 2010; Laurie et al.).
