Array Manifest Why are there multiple assays targeting the same SNP marker

What are the possible reasons for multiple assays targeting the same SNP?

1. Multiple assays may be targeted against the same target in order to ensure that at least one of the assays designed will end up on the array. For any Infinium array being designed, there is no guarantee that all attempted probes will end up in the final product. The minimum guarantee for custom arrays is that at least 80% of the requested probes will end up on the final product; for a commercial beadchip, the yield is > 90%. These losses are inherent to the manufacturing process for a BeadChip and are expected. So for important SNPs, some users will request multiple iterations of an assay against the same SNP, in order to increase the chance that at least one will make it onto the array. Alternatively, users may include multiple assays against the same target simply to be more confident in the results.

2. The SNP being designed for may be a multi-allelic SNP (eg,. [A/C/T],[A/C/G/T]) rather than a bi-allelic SNP (eg, [A/T], [T/G]). Infinium was designed to determine only biallelic SNPs, but users who want to determine the genotypes for multi-allelic SNPs can try to "game" the system by designing multiple assays against the SNP, submitting designs for them as bi-allelic SNPs but with different combinations of 2 bases. Note: Illumina does not directly support such designs, nor does Illumina provide any tools to analyze such assays to determine genotype or copy number.

3. BeadChip designs are often created by groups of scientists, and separate portions of the designs are submitted by multiple individuals during the design phase. Often, the individual submissions will contain overlapping submissions which go unnoticed until the separate design results are combined for the final design.

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