Affymetrix last week launched its Axiom Genome-Wide Pan-African Array, which it claims offers genomic coverage of both common and rare alleles in populations of African ancestry, including West African, East African, and African American populations.
The array contains more than 2.2 million markers that are heterozygous in the African genome. It contains variants culled from the National Human Genome Research Institute's Catalog of Published Genome-Wide Association Studies, the Sanger Cancer Genome Census genes, major histocompatibilty complex genes, cardiovascular genes, and immune and inflammation pathway genes. The array also offers coverage across chromosomes X and Y, the mitochondrial genome, and drug metabolism genes.
According to the firm, the Axiom Pan-African Array offers about 90 percent coverage of HapMap Yoruba alleles with minor allele frequency greater than or equal to 2 percent. In addition, it has been validated in four African populations from the HapMap collection, including the Luhya from western Kenya; Maasai from eastern Kenya; Yoruba from Ibadan, Nigeria; and African ancestry in the Southwest US. In all cases, the Axiom Pan-African Array offers 15 percent to 20 percent more genomic coverage compared to other commercial arrays, the firm claims.
The array is designed to be used on the GeneTitan instrument with Axiom 2.0 Reagent Kits and Genotyping Console 4.1 for automated allele calling and quality control.
One customer is Rick Kittles, associate professor of medicine and director of the Institute of Human Genetics at the University of Illinois at Chicago. In a statement, he said that previous arrays on the market offered "poor genomic coverage" of African populations, an issue that has "significantly impacted our ability to understand the genetic factors that underlie the increased risk of African Americans for diseases such as cancer ... and cardiovascular and pulmonary disorders." Kittles said that his institute is currently using the Axiom Pan-African Array for prostate cancer, sickle-cell disease, and drug response research.