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Chunk #55 — Discussion

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Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip.
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An often-quoted metric in assessing chips is the coverage of each chip: an estimate of the proportion of SNPs which have r 2>0.8 with at least one SNP on the chip. Although relatively simple to calculate (and even simpler to miscalculate), not least because it does not depend on study size, our results show that coverage can be a poor surrogate for power, and that relatively large differences between chips in coverage do not translate to large differences in power.