Hello everyone,

I want to ask a question about the probe annoations in the package IlluminaHumanMethylation27kanno.ilmn12.hg19 (27k) and the package IlluminaHumanMethylation450kanno.ilmn12.hg19 (450k).

I found for many methylation probes, their loci annotations in the 27k package and the 450k package are different. For example, if I check the loci for the probes cg00000292, cg00002426, and cg00003994 using the 27k package as

IlluminaHumanMethylation27kanno.ilmn12.hg19::Locations[c('cg00000292', 'cg00002426', 'cg00003994'),]

And also check their loci using the 450k package as

IlluminaHumanMethylation450kanno.ilmn12.hg19::Locations[c('cg00000292', 'cg00002426', 'cg00003994'),]

For the 27k result for these 3 probes, it is

DataFrame with 3 rows and 3 columns
                   chr       pos      strand
           <character> <integer> <character>
cg00000292       chr16  28797601           +
cg00002426        chr3  57718583           +
cg00003994        chr7  15692387           +

While for the 450k result for these 3 probes, it is

DataFrame with 3 rows and 3 columns
                   chr       pos      strand
           <character> <integer> <character>
cg00000292       chr16  28890100           +
cg00002426        chr3  57743543           +
cg00003994        chr7  15725862           -

It means the same probe IDs have different loci in 27k and 450k. I know the probe chemistry of Illumina 27k and 450k are different, but is it mean even the coordinates for the same probe ID are also different? If so, is it possible to combine the shared probes (with the same probe IDs) from samples detected on 27k and 450k together? Thank you so much!

Hi,

It seems that the manufacturer (Illumina) simply moved the target locus, which often occurs across array designs. In the case of cg00000292, the change is somewhat dramatic, but one can infer that, on the 27k, it may be targeting a promoter region; whereas, on the 450k, it is targeting exon 1 (of ATP2A1).

What do you mean by 'combine' these together? I would personally keep separate the analysis of both arrays, unless you are just doing univariate analysis (analysing each probe separately). However, even in the case where you are doing univariate analysis, the arrays should be processed separately, in my opinion. To 'combine' them, in this case, I would just assign a unique ID to each probe, perhaps by simply adding a '_27k' or '_450k' prefix.

There is, however, a function in the minfi Bioconductor package that claims to be able to combine arrays - please take a look: https://rdrr.io/bioc/minfi/man/combineArrays.html

Kevin