The Illumina 1M –Duo array has a total of 1,072,820 probes, of which 23,812 are “intensity-only,” leaving 1,049,008 probes as SNP assays. These SNP assays demonstrate excellent data quality—95% of SNPs have a missing call rate< 1.4% and the median of the missing call rate is 0.05%. A thorough data cleaning procedure was applied to ensure the highest possible data quality, including the use of HapMap controls, detection of gender and chromosomal anomalies, hidden relatedness, population structure, missing call rates, batch effects, Mendelian error detection, duplication error detection, and Hardy-Weinberg equilibrium(23). Of the 1,049,008 SNPs, 948,658 SNPs passed data cleaning procedures. Further details are provided in the comprehensive data cleaning report posted on the GENEVA website http://www.genevastudy.org/docs/GENEVA_Alcohol_QC_report_8Oct2008.pdf).
