Assays designed to type for gene variants. Either differentially labeled (TaqMan®) probes (one for each variant) or a single probe and melting curve analysis can be used for this purpose. Alternative methods include dsDNA-binding dyes (in combination with melting curve analysis). TaqMan®-based allelic discrimination assays are analyzed by differences in threshold cycles or by endpoint fluorescence value for each allele. The results are plotted by fluorescence intensity or by Ct values for each allele at X and Y axes (see Osgood-McWeeney, 2000 and Figures 3-5 in Hu & Chen for examples). For increased specificity, MGB or LNA probes can be used (Kutyavin, 2000; Letertre, 2003; Johnson, 2004; Ugozzoli, 2004; Gibson NJ, 2006; Shen, 2009; Schleinitz, 2011). See ABI Allelic Discrimination with TaqMan® Probes and Getting Started Guides for ABI 7000 & 7900HT, LightScanner® and Amplifluor® SNPs Genotyping System. See SNPman (User Guide) for analysis of TaqMan allelic discrimination assay genotype calling for the ABI7300, LC480 and Bio-Rad CFX platforms (Konopac, 2011).