Illumina has changed the production process for Infiniumâ„¢ MethylationEPIC and therefor has posted the new manifest Infinium MethylationEPIC v1.0 B5. Beadchips with serial numbers greater than or equal to 204220330001 originate from production batches using the new manufacturing process.
Illumina identified 998 loci that showed different performance compared to prior methylation arrays. They decided to mark these affected loci (8 affected loci have already missed in manifest B3 and B4, therefore only 990 loci are flagged) in the new manifest B5 (column "MFG_CHANGE_FLAGGED" = TRUE). This gives the customer the choice to remove these loci from further analysis.
For more details see Illumina Release Notes
In case of questions contact Matthias Schick.