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Out of 96 SNPs, 86 assays were successful, giving an assay success rate of 89.6%.
The assay success rate was calculated based on the number of successful assays divided by total number of assays while the conversion rate was calculated based on number of polymorphic SNPs divided by total number of assays.
However, microarrays for diagnosis of disease-causing genetic mutations require a 100% assay success rate, suggesting that an alternative strategy for assay development is required.
When different spacer lengths were included as varying assay parameters, the assay success rate increased for methods C and D for assigning genotypes (Figure 4).
We found that the Illumina Infinium® design score accurately predicted assay success (Table 2) despite a few SNP drop outs (<3%) during assay manufacture which were independent of design score.
As expected, the methods for assigning genotypes (Figure 2) that require the greatest (0.1) separation of genotypes, methods B and D, had an approximately 10% lower assay success rate, than methods A and C, respectively (Figure 4).
Similar(31)
We assayed success of depletion (~ 98%) of major proteins by visualizing less abundant ones on silver-stained gels (data not shown).
The replicated samples produced only one discordant genotype among 107,412 genotypes indicating an assay replication success exceeding 99.99%.
Different parameters of genotyping performance, such as reproducibility, genotype call rate and assay development success rate were estimated [ 43].
Considering that our PCR assays were not optimized, the 93.6 percentage reproducible assay enrichment success rate can be considered high compared to competing platforms.
Illumina GoldenGate platform has shown exceptional performance with regard to throughput, reproducibility, genotype call rate and assay development success rate among several SNP genotyping assays involving human and a few plant species, [ 29, 34, 43].
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