Table 1.
HumanHap550 and HumanHap650Y Coverage
Figure 1.
Coverage of the HapMap (A) or SeattleSNPs (B) Datasets As Measured by the Proportion of Common Variation in Each Dataset That Is Captured by a SNP in Either HumanHap550 (CEU; CHB + JPT) or HumanHap650Y (YRI) at Various r2 Thresholds
Lines show coverage for the CEU (red), CHB + JPT (green), and YRI (blue) populations.
Figure 2.
Total Power to Detect a Single Common Risk Allele in the HapMap Data Using HumanHap550 for CEU (A) and CHB + JPT (B) and HumanHap650Y for YRI (C) in a Study Size of 1,000 cases and 1,000 Controls under a Multiplicative Disease Model
Power is calculated for a 5% false discovery rate after a Bonferroni correction for multiple testing (red line). The solid black line represents the power to detect a risk allele if all the common HapMap SNPs in each respective population are genotyped using the same significance cutoff. Also shown are the powers for different frequency ranges as dashed lines, where the lower line indicates the power for risk allele frequencies from 5%–10% and the upper line indicates the power for risk allele frequencies from 40%–50%.
Figure 3.
The Minimum Risk Detectable at 80% Power with p ≤ 0.05 after a Bonferroni Correction for Multiple Testing (χ2 ≥ 28.5687) for Various Sample Sizes under Multiplicative (Red) and Additive (Blue) Models
Power is calculated as the ability to detect a single common risk allele in the HapMap data in a whole genome association study within CEU samples.
Figure 4.
Total Power to Detect a Single Common Risk Allele outside of the HapMap Data Using 1,000 cases and 1,000 Controls under a Multiplicative Model
The power is estimated using the common SNPs in 68 resequenced SeatleSNPs genes that were not characterized in the HapMap Project for (A) 23 CEU samples using HumanHap550 and (B) 24 YRI samples using HumanHap650Y. Power is calculated for a 5% false discovery rate after a Bonferroni correction for multiple testing (red line). The solid black line shows the power to detect a common risk allele in the HapMap data (i.e., solid red lines in Figure 2).
Figure 5.
Power to Detect At Least One Risk Allele in CEU (HumanHap550) and YRI (HumanHap650Y) in 1,000 Cases and 1,000 Controls under a Multiplicative Model
Curves represent the cases where there is a single risk locus (red), two independent loci (blue), or four independent loci (green). The red lines are the single risk loci as shown in Figure 4. Under the multiple loci cases, the relative risk represents the minimum risk for all risk alleles and the corresponding power represents a lower bound on the power.
Table 2.
Minimum Risk Detectable at a p-Value ≤ 0.05 after a Bonferroni Correction for Multiple Testing (χ2 ≥ 28.5687 for CEU and χ2 ≥ 28.8976 for YRI) with 80% Power under the Multiplicative Model for Various Sample Sizes and Number of Unlinked Disease Loci
Table 3.
Minimum Risk Detectable at a p-Value ≤ 0.05 after a Bonferroni Correction for Multiple Testing (χ2 ≥ 28.5687 for CEU and χ2 ≥ 28.8976 for YRI) with 80% Power under the Additive Model for Various Sample Sizes and Number of Unlinked Disease Loci
Table 4.
HumanHap550 and HumanHap650Y Data Quality