Coverage and efficiency in current SNP chips

Abstract

To answer the question as to which commercial high-density SNP chip covers most of the human genome given a fixed budget, we compared the performance of 12 chips of different sizes released by Affymetrix and Illumina for the European, Asian, and African populations. These include Affymetrix' relatively new population-optimized arrays, whose SNP sets are each tailored toward a specific ethnicity. Our evaluation of the chips included the use of two measures, efficiency and cost-benefit ratio, which we developed as supplements to genetic coverage. Unlike coverage, these measures factor in the price of a chip or its substitute size (number of SNPs on chip), allowing comparisons to be drawn between differently priced chips. In this fashion, we identified the Affymetrix population-optimized arrays as offering the most cost-effective coverage for the Asian and African population. For the European population, we established the Illumina Human Omni 2.5-8 as the preferred choice. Interestingly, the Affymetrix chip tailored toward an Eastern Asian subpopulation performed well for all three populations investigated. However, our coverage estimates calculated for all chips proved much lower than those advertised by the producers. All our analyses were based on the 1000 Genome Project as reference population.

Figure 1

LD efficiencies of different chips evaluated for European, Asian, and African reference populations. In the efficiency calculations, the r² threshold varied from 0.1 to 1 in steps of size 0.1.

Figure 2

Non-taggable SNPs' efficiencies of different chips evaluated for European, Asian, and African reference populations. In the efficiency calculations, the r² threshold was varied from 0.1 to 1 in steps of size 0.1.