Which bisulfite conversion kit should be used for the Infinium Methylation arrays?

This bulletin is intended for customers using Infinium Methylation BeadChips. Before carrying out the Infinium HD Methylation Assay, samples must first be bisulfite converted. The efficiency and accuracy of the bisulfite conversion step, including using the final elution volume recommended by Illumina, is critical to the accuracy and performance of the Infinium Methylation assay.

Illumina has validated and recommends only the following kits from Zymo Research.

EZ DNA / EZ-Methylation Kits

Bisulfite conversion completed in ~ 1.5 days

EZ-96 DNA Methylation Lightning MagPrep Kits (uses magnetic beads for purification)

Bisulfite conversion completed in ~ 3 hours

*User provides 96-well deep-well microplates and PCR plates **The EZ-96 DNA Methylation-Lightning Automation Kit is equivalent to the EZ-96 DNA Methylation-Lightning MagPrep Kit but contains buffer and reagent volumes needed for procedures using liquid-handling automation. Liquid-handling automation scripts and setup support are available through Zymo Research. For questions regarding automation, contact [e-mail]

Not recommended:

• EZ-96 DNA Methylation™ Kit (Shallow Well Format), Zymo Research Catalog Number D5003. (The final step of the bisulfite conversion before beginning the Infinium HD assay is the elution of the converted sample from the spin column. The Shallow Well format of the EZ-96 DNA Methylation Kit is not recommended for use with the Infinium Methylation HD Assay because the elution volume of 30 µl is too large for inclusion in the Infinium HD Assay.)

• The following kits have not been validated and are not recommended for use in preparing samples for the Infinium Methylation BeadChip

  • EZ DNA / EZ-96 DNA Methylation-Gold Kits

  • EZ DNA / EZ-96 DNA Methylation*-Direct* Kits

  • EZ DNA / EZ-96 DNA Methylation-Lightning Kits - Spin Column: D5030 - 96-well (Shallow): D5032 - 96-well (Deep): D5033

• No other bisulfite conversion kits have been validated.

Additional Resources:

• For information on how the Lightning kits were validated, refer to the Illumina Technical Note: Automated bisulfite conversion for Infinium Methylation BeadChips

• From Zymo: Bisulfite Conversion for Illumina Methylation Arrays: Troubleshooting & Best Practice Guidelines

For any feedback or questions regarding this article (Illumina Knowledge Article #1524), contact Illumina Technical Support [e-mail].