Abstract
A primary goal of The C onsortium on A sthma among A frican-ancestry P opulations in the A mericas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.
Highlights
The design of the African Diaspora Power Chip (ADPC) was a primary goal as part of the NIH-supported Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA)
Despite raising the minor allele frequency (MAF) threshold for TagSNPs to 1.6%, we report coverage of all variants with MAF greater than or equal to 1% to give a full picture of the low frequency coverage the African Diaspora Power Chip’ (ADPC) can provide
All selected variants of the ADPC, alone, are estimated to tag 12% of known variants at r2 = 0.9, 16% at r2 = 0.8, and 31% at r2 = 0.5. The combination of these two arrays is estimated to tag 29% of all CAAPA variants at r2 = 0.9, 37% at r2 = 0.8, and 56% at r2 = 0.5, an improvement of about 50% more variants tagged over the OmniExpress array across the three thresholds Table 2
Summary
The design of the African Diaspora Power Chip (ADPC) was a primary goal as part of the NIH-supported Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA). Previous GWAS studies in populations of African descent may have missed critical association signals because the single nucleotide polymorphisms (SNPs) genotyped on existing commercial arrays were selected for being informative among individuals of European ancestry, and generally do a poor job of tagging haplotypes and variants in individuals of non-European ancestry. Imputation of low-frequency variants is most efficient and accurate when the SNP to be imputed has a similar minor allele frequency as the genotyped SNP, so a relative lack of low frequency variants on an array can render imputation of similar frequency variants difficult [Marchini and Howie, 2010] To address this shortcoming, the ADPC was designed using the whole-genome sequencing results on 642 CAAPA samples, including 328 African Americans, 125 African Caribbean subjects, 164 African ancestry individuals with some Latino ancestry, and 25 individuals from Nigeria. 15.6 million variants have a MAF greater than or equal to 1%
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