SNP Genotyping Using Multiplex Single Base Primer Extension Assays

Single nucleotide polymorphisms (SNPs) are the most common form of polymorphisms present in the human genome. The single base primer extension (SBE) method is an effective and sensitive tool that can type over 30 known loci scattered throughout an organism’s genome in a single reaction. It allows the typing of tetra-allelic SNPs and has been adapted to a broad range of analytical necessities: single-cell analysis, molecular diagnosis of monogenic diseases, forensic mitochondrial DNA analysis on highly degraded human remains, and high-throughput SNP screening for population studies. Every SBE-based assay will need customized optimization efforts that are generally proportional to the number of desired SNPs typed in a single reaction. This chapter offers a detailed outline on which to base the design and optimization of any multiplex SBE assay that can then be tailored to the analytical conditions that characterize each specific application.