# Assay Design Use the following steps to create an assay design. Refer to the following Design Considerations for information on design options. ### Design Considerations **(Genotyping)** * **Total bead count** — Always consider total bead count when creating a design. Infinium I designs require two probes per SNP, which increases the bead count. Replication multiplies the number of beads needed for each probe by two or three depending on the Replication\_Count. Refer to [Input Target Files](https://help.connected.illumina.com/design-studio-array/product-guides/input-target-files) for more information on replication settings. * **Multiallelic targets** — Check the **convert multi-allelic** checkbox to convert multi-allelic loci to bi-allelic loci. DesignStudio supports design and analysis of bi-allelic designs only. If the designer is not able to determine clearly which minor allele to pick up based on MAF values, then that target is added to the identity error file and is excluded from the final design. * **Bi-allelic conversion —** During bi-allelic conversion, the system evaluates the Minor Allele Frequency (MAF) for each minor allele. If one minor allele has a MAF value **below** the defined threshold (currently set to 1%) and the other has a MAF value **above** the threshold, the allele with the MAF above the threshold will be designated as the minor allele for the purpose of bi-allelic conversion. ### Design Considerations **(Methylation)** * **MostImportant Flag —** User can mark any target MostImportant in Identity File in order to have that target replicated three times. * **Control Targets —** When a user marks checkbox to "Include SNP Probes for sample Identification", it adds the SNP control targets into the Design file. These targets are strictly for control purposes. Please refer to more [details here on this topic.](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000003719) [Design the Assay](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design/design-assay)\ [Review Design Summary](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design/review-design)\ [Add Custom Content to Commercial Arrays](https://help.connected.illumina.com/design-studio-array/product-guides/assay-design/add-custom) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/design-studio-array/product-guides/assay-design.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.