> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000002975.md).

# Why Multiple Assays May Target the same SNP Marker in BeadArray Manifests

When reviewing a BeadArray manifest, it is not uncommon to find multiple assays associated with the same SNP marker. The presence of duplicate or multiple probes targeting a single SNP can be intentional and may arise for several reasons during the assay design and array manufacturing process. Possible reasons why a BeadChip design may contain multiple assays targeting the same SNP: 1. **To increase the likelihood of successful inclusion on the array**During the design process, multiple assays may be included for the same SNP to improve the chances that at least one assay will be successfully incorporated into the final array. For any Infinium custom arrays, there is no guarantee that all submitted probes will be present in the final product. Some assay loss is inherent to the BeadChip manufacturing process and is expected. Therefore, for high-priority SNPs, users may request multiple iterations of an assay against the same SNP to increase the chance that at least one assay will be present on the array. Alternatively, users may include multiple assays against the same target to provide additional confidence in the genotyping results. 2. **To interrogate multi-allelic SNPs**

The target SNP may be multi-allelic (eg, \[A/C/T] or \[A/C/G/T)] rather than bi-allelic (eg, \[A/T] or \[T/G]). Since Infinium technology was designed specifically to genotype bi-allelic SNPs, users who would like to investigate multi-allelic SNPs may submit multiple assay designs for the same SNP. In such cases, each assay is designed to target a different bi-allelic combination of alleles, allowing the multi-allelic SNP to be interrogated using several separate assays.

**Note:** Illumina does not directly support the design or analysis of multi-allelic SNP assays and does not provide tools to analyze and determine genotype or copy number from such custom assay configurations.

3. **Overlapping submissions during the design process**

BeadChip designs are often developed in collaboration with multiple scientists or groups. During the design phase, different contributors may submit separate sets of markers for inclusion on the array, which can result in overlapping assay submissions. These duplicate entries may not be identified until the individual design outputs are combined into the final BeadChip design, resulting in multiple assays targeting the same SNP.

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #2975), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002975%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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