Despite using a small number of individuals for SNP discovery, over 85% of SNP with working assays were found to be polymorphic in economically important breeds such as Poll Dorset, Merino, Italian Sarda, African Dorper, Scottish Blackface, Suffolk, Romney and Rambouillet.
Out of 768 SNP assays, 710 assays (92.4%) were converted to working assays (Table 3).
Out of 86 working assays, 20 SNPs (23%) had design scores in the range of 0.4 to 0.6.
All results presented here for the two rice arrays exclude up front SNPs which did not convert to working assays, to the best of our ability to determine.
The majority (95%) of the selected SNPs with working assays, generated data with the European bison and the Greater Koudou samples (35/37 and 27/37 SNPs, respectively) (Table 5).
In the present study, we also demonstrated that the high-throughput GoldenGate technology could be successfully used for genotyping predicted SNPs by conversion into working assays.
QC filtering: as with any new genotyping product, a number of intended SNP assays fail to convert to working assays in the multiplexed environment for reasons which cannot always be determined.
Working assays were established for a total of 110 SNPs, including 5 from the extended class I region, 1 from the extended class II region, and 104 from the classical MHC.
Human genotyping products from Affymetrix and Illumina, now in their fifth generation or later, are largely free of SNPs and probes which did not 'convert' to working assays, as previous generation products have identified these SNPs empirically and they have been removed from later generation products.
The Illumina SNP selection is based on an absence of neighbouring polymorphisms (60 bp flanking sequence on each side between SNPs), repetitive elements or palindromes, since these are known to affect the conversion rate of SNPs into working assays [ 42, 43].
