What should be done when the assay design failed for one or more SNPs?
Three major causes of failure and the corresponding solutions: • Sequence around the SNP is not suitable for any design. Solution: There is no way to use PCR-RFLP to genotype this SNP. Other methods may have to be used. However, this kind of SNP is rare. • SNPSequer does not provide enough flanking sequences for the assay design. Check the *.DNinput.txt file to see if the SNP has a flanking sequence with correct length as the settings specified. For example, if the default setting is 2000 bp maximum PCR product size, then the sequence should have 1100 bp at both ends. If it is not at that setting, it is an indicator that SNPSequer had problem extracting the flanking sequences. Solution: Change the parameter in “Use” FastMode MediumMode SlowMode to fetch additional flanking sequence, if the SNP flanking sequences is not long enough in the supplied data.” The setting can be changed from FastMode to MediumMode or SlowMode. The three different SNP mapping modes:
