Rick W. Staub¹, Michael G. Carrico¹, Jeffrey J. Tollett², Steve Nye³, Michael Pirrung⁴ and John M. Shumaker^2
1 Identigene, Inc., Houston, TX
² Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
³ Pharmacia Biotech, Milwaukee, WI
⁴ Department of Chemistry, Duke University, Durham, NC

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We have developed a rapid assay for human identity typing based on arrayed primer extension (APEX) analysis of many unlinked single nucleotide polymorphisms (SNPs). APEX utilizes a 2-D array of unique primer sites to direct a template-dependent polymerase extension in a space-specific fashion. Fluorescently labeled nucleotides identify the base following the 3' of each primer. A CCD-based detection system images the labeled primers on the array and a software system converts the image into genotype information. Multiplex amplifications of several loci can be analyzed together on one array. APEX analysis promises to be a powerful means for automating the human identification process by eliminating the need for the labor-intensive step of gel electrophoresis of any sort. Additionally, it is a significant improvement over mini-sequencing systems which perform one reaction per well in plate assays since the APEX arrays can be expanded to type very large numbers of SNPs simultaneously (presently, 2500 elements/cm²). Theoretical calculations of match probabilities and exclusion powers for SNPs with allele frequencies between 0.4 and 0.6 indicate that 40-50 such loci should be adequate for any human identification typing needs, including paternity testing.