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Two cases and nine controls were identified for excess or insufficient heterozygosity at sex chromosomes and were removed. Finally SNPs with MAF http://www.selleckchem.com/PD-1-PD-L1.html This filter is used to detect where genotyping error rates differ across studies, and is a critical QC step when multiple genotyping experiments are combined into a single data set for analysis. A 4 degree of freedom (df) Fisher's exact test with 10,000 permutations was used at all SNPs to test frequency differences for genotypes generated from the three genotyping chips in the study. SNPs were removed if the p-value for this test was less than 0.001 (546 SNPs). After all QC procedures, 604 cases and 619 controls with 491,376 SNPs were available for association analysis in the HIHG GWAS http://www.selleckchem.com/products/Adriamycin.html dataset. The sex and age distributions for these samples are described in Table 1. Data were downloaded from dbGAP (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap) for the CIDR (Pankratz et al., 2009) and NINDS (Fung et al., 2006a) PD GWAS. Imputation of SNP genotypes from these and the HIHG data was performed independently using the software package Impute (Marchini et al., 2007). Samples were removed from these GWAS for genotyping efficiency http://www.selleck.cn/products/MK-1775.html disease status p