# Methylation Control Panel FAQ for the Illumina 5 Base WGS and Enrichment kits

**For the Enrichment workflow, what is the Methylation Control Panel and what is its purpose?**

* The reagents SFMC (used in the cfDNA workflow) and GDMC (used in the gDNA workflow) contain control genomes, composed of methylated pUC19 plasmid and unmethylated lambda DNA. The Small Genome Control Panel enriches for fragments from the control genomes. While use of the panel is optional, without that panel, the methylation true positive rate and false positive rate will be difficult to decipher.
* Note: The control panel is diluted and added to the enrichment reaction alongside the custom enrichment panel.

**Does the Methylation Control Panel enrich for the full pUC19 and lambda genomes, or only certain regions? If only certain regions, which ones?**

* It covers the entire pUC19 and Lambda genomes.

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#### **Does the Methylation Control Panel come with the Enrichment kit, or is it sold separately? Specifically, how should this be ordered?**

* The Methylation Control Panel is sold separately from the Enrichment kit and is available to order from DesignStudio. If using, purchase the Methylation Control Panel **in addition to** the desired custom panel. (ie, the Methylation Control Panel probes are not added to the custom design, because they have different reference genomes.)
* To order the Methylation control Panel in [DesignStudio](https://designstudio.illumina.com/), follow these instructions:

1. Select **Start A New Design** on the DesignStudio homepage
2. Select Sample Type as **DNA**, Assay Technology as **Illumina Custom Enrichment Panel v2**, and Assay Type as **Control Panels**.
3. In the popup box, select the radio button to the left of the Methylation Control Panel's Design ID, then select **OK**.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-4e765f59aef3581b98684959ac8939945c32d80a%2Fimage1.png?alt=media)

4. In the subsequent popup box, select **Copy** to copy the Methylation Control Panel design to your personal DesignStudio account. From there, select **Get Pricing**. Note that the design will have a warning that "This design has a lower total panel size (bp) than the recommended 75kb: 51122 (75000bp minimum)," but this will not prevent ordering.

**How many enrichment reactions or samples does the Methylation Control Panel support?**

* This depends on the panel size being used, as it affects the dilution calculations.

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