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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; 6) less than 2 discrepancies between SNP calls on duplicated samples. These thresholds resulted in 362 cases, 671 controls 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 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 1034 control and 1001 cases genotyped over 728222 SNPs used in the association analysis. Genome-wide association scan has been pre-computed by NCBI . |