Most genome-wide DNA microarrays were designed for individuals of European ancestry. The differences in LD structure and allele frequency among populations can lead to significantly worse coverage for other ancestry groups. For example, at imputation accuracy r2>0.8, the Affymetrix UK Biobank array covers 84% of the variants that have minor allele frequencies (MAF) > 1% in samples of European ancestry but only 46% of those for samples of African ancestry (Nelson et al., 2017). The large genetic diversity in African populations means that a larger number of variants are needed on arrays in order to provide similar coverage as in other populations (Barrett and Cardon, 2006). To address this issue, some groups, such as China Kadoorie Biobank (Chen et al., 2011), have designed population-specific arrays. Multi-ancestry arrays, such as the Multi-Ethnic Global Array (MEGA), Global Screening Array (GSA), and the H3Africa array (Mulder et al., 2018) were designed based on panels with more diverse ancestries, and are therefore recommended. An alternative strategy is to sequence whole genomes; low-depth sequencing has received recent attention for application in diverse samples due to cost-effectiveness and higher coverage with acceptable error rates ((Gilly et al., 2018; Peterson et al., 2017a); see Rare Variants).
