African american admixture panel

Manufactured by Illumina

The African American Admixture Panel is a genetic analysis tool designed to detect and quantify the ancestral proportions in individuals with African American ancestry. It targets ancestry-informative genetic markers to provide a comprehensive assessment of an individual's genetic makeup and admixture proportions.

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Lab products found in correlation

Puregene system, by Qiagen (1 mentions) Omni5 array, by Illumina (1 mentions) Jmp genomics, by SAS Institute (1 mentions) Axiom array, by Thermo Fisher Scientific (1 mentions) Axiom genotyping console, by Thermo Fisher Scientific (1 mentions)

2 protocols using african american admixture panel

Genomic Ancestry Analysis via MALD

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DNA was extracted from peripheral blood using the PureGene system (Gentra Systems, Minneapolis, MN). The MALD study was based on the streamlined panel of 1,509 ancestry informative marker (AIM) single nucleotide polymorphisms (SNPs) genotyped using the Illumina African American admixture panel covering all 22 autosomes and chromosome X. Genome-wide association study (GWAS) data was obtained from the Illumina Omni5 array inclusive of exome chip content. All genotyping was performed in the Center for Genomics and Personalized Medicine Research at WFSM.

Palmer N.D., Divers J., Lu L., Register T.C., Carr J.J., Hicks P.J., Smith S.C., Xu J., Judd S.E., Irvin M.R., Gutierrez O.M., Bowden D.W., Wagenknecht L.E., Langefeld C.D, & Freedman B.I. (2016). Admixture mapping of serum vitamin D and parathyroid hormone concentrations in the African American-Diabetes Heart Study. Bone, 87, 71-77.

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Genotyping Ancestry-Informative Markers

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More than 30,000 SNPs and ancestry informative markers (AIMs) on all 22 autosomal chromosomes were genotyped using a custom Affymetrix Axiom Array that we designed (Affymetrix, Santa Clara, CA). These SNPs were chosen because they were located within or near genes that previously had been found to associate with hypertension, cardiac disease, stress, and pigmentation phenotypes in other studies and on existing Affymetrix arrays (see S4 Table for a list of the 30,000+ SNPs and associated genes and other attributes). AIMs were identified from the Illumina African American Admixture panel (Illumina, San Diego, CA). We followed the recommendations set by Affymetrix’s Axiom Genotyping Console to call all SNP genotypes that had a genotyping success call rate ≥ 97%. SNP marker properties (minor allele frequency (MAF), call rate, Hardy-Weinberg Equilibrium (HWE) test) were calculated using PLINK [69 (link)] and JMP/Genomics (SAS 9.4). Only SNPs with a MAF >1%, a call rate >95%, and SNPs that were in HWE were included (p-value >0.001 for HWE test). This resulted in a final set of 27,559 SNPs and 3,197 AIMs for further analysis.

Quinlan J., Pearson L.N., Clukay C.J., Mitchell M.M., Boston Q., Gravlee C.C, & Mulligan C.J. (2016). Genetic Loci and Novel Discrimination Measures Associated with Blood Pressure Variation in African Americans Living in Tallahassee. PLoS ONE, 11(12), e0167700.

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