What are some things I can try to improve SNP Type assay performance?
Preamplification prior to genotyping might help alleviate issues with samples that contain inhibitor carryover from extraction, are of low quality or low concentration, vary in concentration from other samples, or come from a species whose genome size is large relative to the human genome. For a detailed preamplification protocol, see the SNP Genotyping User Guide (PN 68000098) or the Juno System User Guide (PN 100-7070).
Some regions of DNA are intrinsically more difficult to amplify. If amplification is inefficient, adding five amplification cycles to the thermal protocol may help.
If clusters are not sufficiently separated, increasing the EDTA concentration by diluting samples in TE buffer (10 mM Tris, 1 mM EDTA; pH 8.0) instead of DNA Suspension Buffer (10 mM Tris, 0.1 mM EDTA; pH 8.0; (TEKnova, PN T0221) might increase stringency of the reaction and improve assay specificity. Note that too much EDTA will inhibit the reaction completely.
Redesigning the assay to the opposite DNA strand might improve assay specificity.