Illumina Methylation Assay - Advantages and Disadvantages

Advantages and Disadvantages

Advantages

1. No PCR is required, which means that there will be no selective bias towards shorter fragments.
2. Ability to survey up to 12 samples per chip allows for high throughput processing.
3. Allows integration of data between other platforms such as gene expression and microRNA profiling.
4. The method looks at ~2 CpG sites per CpG island, providing genome-wide coverage of methylation patterns

Disadvantages

1. Not every gene annotated in the NCBI database was included in the design of this assay, which covers 14,495 genes out of the 17,052 GeneIDs present to date (Human build 36.3).
2. According to Staaf et al. (2008), “the Infinium II assay seemed to have dye intensity biases between the two channels used in fluorescence detection. Furthermore, this bias was not eliminated even after the data had gone through normalization algorithms used in the BeadStudio software.” This concern, while valid for the GoldenGate methylation assay, is not relevant to the HumanMethylation27k chips, where both probes in a pair extend and fluoresce within the same channel.