Figure 1
The overview of software flow for image analysis on the UHT instrument. Top – Depiction of 2-color fluorescent readouts analyzed by the UHT Image™ software. Intensities from the two fluorescent channels presented in pseudo-colors are compared to determine genotypes. Three hundred eighty-four replicates of 4 × 4 tag arrays are produced on a single glass plate. Each 4 × 4 tag array has 4 control locations and 12 probe locations for 12 SNPs. The top left location is a positive control for both colors. The top right and bottom left locations are positive controls for the two different alleles, and the bottom right location is a negative control and has a probe that lacks a complementary tag sequence in the reaction. The controls are also used to mark the array boundaries for the image analysis software. Center – The UHT® GetGenos software assigns genotype calls to individual SNP signal from every DNA sample. The results can be displayed as a P-plot (Figure 1) by QCreview™ software for manual review (arrow to the right) or used to measure clustering parameters for auto-validation by the neural network (arrow down). Bottom – Schematic representation of SNP signal call clusters measured on the P-plot. The neural network uses 64 parameters described in Additional file: 1 to auto-classify P-plot as "Pass" or "Fail".