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| Genome-Wide genotyping data has been produced with the Affymetrix 6.0 platform and with the Birdseed calling algorithm. This analysis includes only the subset of subjects with African American ancestry. Data was filtered using criteria: 1) removal of sample heterozygosity outliers; 2) sample call rate greater than 97%; 3) SNP MAF ≥ 0.01; 4) SNP call rate ≥ 0.95 and HWE p value > 0.000001 5) plate effect p value test above 10^(-8) for a single plate and/or 10^(-4) for two plates; 4) Less than 2 discrepancies between SNP calls on duplicated samples. These thresholds resulted in 954 controls and 1195 cases genotyped over 845814 SNPs used in the association analysis. Genome-wide association scan has been pre-computed by NCBI . |
| Genome-Wide genotyping data has been produced with the Affymetrix 6.0 platform and with the Birdseed calling algorithm. This analysis includes only the subset of subjects with European ancestry. Data was filtered using criteria: 1) sample heterozygosity range from 0.26-0.285; 2) sample call rate greater than 97%; 3) SNP MAF ≥ 0.01; 4) SNP call rate ≥ 0.95, and HWE pvalue > 0.000001 5) plate effect pvalue test above 10^(-8) for a single plate and/or 10^(-4) for two plates; 4) Less than 2 discrepancies between SNP calls on duplicated samples. These thresholds resulted in 1378 controls and and 1351 cases genotyped over 729454 SNPs used in the assoiciation analysis. Genome-wide association scan has been pre-computed by NCBI . |