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 option, 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.

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.) 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.

For any feedback or questions regarding this article (Illumina Knowledge Article #9938), contact Illumina Technical Support [email protected].