Infinium Methylation Assay scheme. a Infinium I assay. Two bead types correspond to each CpG locus: one bead type—to methylated (C), another bead type—to unmethylated (T) state of the CpG site. Probe design assumes same methylation status for adjacent CpG sites. Both bead types for the same CpG locus will incorporate the same type of labelled nucleotide, determined by the base preceding the interrogated ‘C’ in the CpG locus, and therefore will be detected in the same colour channel. b Infinium II assay. One bead type corresponds to each CpG locus. Probe can contain up to 3 underlying CpG sites, with degenerate R base corresponding to C in the CpG position. Methylation state is detected by single-base extension. Each locus will be detected in two colours. In the current version of the Infinium II methylation assay design, labelled ‘A’ is always incorporated at unmethylated query site (‘T’), and ‘G’ is incorporated at methylated query site (‘C’).