Which Bisulfite Conversion Kit should be used for Infinium Methylation Arrays?

Prior to performing the Infinium Methylation Assays, all DNA samples must undergo bisulfite conversion. The efficiency and accuracy of this step are critical to overall assay performance. In particular, adherence to Illumina‑recommended protocols is essential to for optimal results.

Recommended Bisulfite Conversion Kits for Infinium Methylation Assays

Illumina recommends the following bisulfite conversion kits from Zymo Research, which have been validated for use with Infinium Methylation assays.

Table 1.Validated and recommended EZ DNA / EZ-96 DNA Methylation Kits for use with Infinium Methylation Assays

• Approximate processing time: ~ 1.5 days

• Critical Workflow Requirements when using these kits: Follow the modified overnight/cycling incubation protocol as described in:

  • Instruction Manual - EZ DNA Methylation Kit Catalog Nos. D5001 & D5002 (Appendix: Bisulfite Conversion and PCR Optimization, page 10, Step 6. Alternative Incubation Conditions When Using the Illumina Infinium Methylation Assay).

• It should be noted that the Zymo EZ DNA Methylation kits (D5001, D5002, D5004) have not been validated and are not supported for use with Infinium EX Methylation Assay. Refer to Infinium EX Methylation DNA input guidelines and compatible bisulfite conversion kits for additional information.

Table 2.Validated and recommended EZ-96 DNA Methylation Lightning MagPrep Kits (uses magnetic beads for purification) for use with Infinium Methylation Assays.

• Approximate processing time: ~ 3 hours

• *User provides 96-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.

• Note: For questions regarding liquid-handling automation scripts and set-up, contact Zymo Research support at [e-mail].

Bisulfite Conversion Kits that are not recommended for use with Infinium Methylation Assays

The following bisulfite conversion kits from Zymo Research have not been validated and are not compatible with Infinium Methylation Assays.

Table 3.Bisulfite Conversion Kits that have not been validated and are not recommended for use with Infinium Methylation Assays.

• Note:No other bisulfite conversion kits have been validated by Illumina for use with Infinium Methylation Assays.

Additional Resources:

• Technical Note on EZ-96 DNA Methylation-Lightning Automation Kit validation: Automated bisulfite conversion for Infinium Methylation BeadChips

• 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].