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Agnosticism and equity in genome-wide association studies

Nature Genetics volume 38, pages 605–606 (2006)Cite this article

Two new studies evaluate the extent to which widely used SNP platforms capture common variation in different populations, and they present strategies for improving power in whole-genome association studies using fixed marker sets. Their results suggest that genome-wide association studies are finally ready to move from theory to practice.

Barrett and Cardon11 present a practical analysis of the coverage of common variation, comparing the 500,000 randomly selected SNPs on the Affymetrix GeneChip13 with the 300,000 selected tag SNPs on the Illumina BeadChip14,15. They performed this analysis using the HapMap Phase II data as a reference data set, exploring how strongly the SNPs on the chips are correlated with the known common variants in each of the HapMap populations. They find that both platforms provide reasonably good coverage in non-African populations (more than 60% of common SNPs are correlated with one or more SNPs on the chip at r2 > 0.8), with substantially lower coverage in the HapMap African population (less than 40% coverage at the same threshold r2). Pe'er et al.12 present similar findings; moreover, they show that although coverage is improved in all populations using multi-marker predictors, the coverage disparity remains, with a substantially lower percentage of coverage in the African group than in non-African groups. It is well known that African populations have both higher genetic diversity and shorter-range linkage disequilibrium, so this finding is not a surprise. However, the coverage estimates raise the question of whether the time is right to conduct genome-wide association studies with existing tools in genetically diverse groups, such as African Americans, or if it would be better to wait for the next generation of tools.

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  1. Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

    Christopher S Carlson

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Carlson, C. Agnosticism and equity in genome-wide association studies. Nat Genet 38, 605–606 (2006). https://doi.org/10.1038/ng0606-605

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