title: Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray.
abstract: The Illumina Infinium HumanMethylation27 BeadChip (Illumina 27k) microarray is a high-throughput platform capable of interrogating the human DNA methylome. In a search for autosomal sex-specific DNA methylation using this microarray, we discovered autosomal CpG loci showing significant methylation differences between the sexes. However, we found that the majority of these probes cross-reacted with sequences from sex chromosomes. Moreover, we determined that 6-10% of the microarray probes are non-specific and map to highly homologous genomic sequences. Using probes targeting different CpGs that are exact duplicates of each other, we investigated the precision of these repeat measurements and concluded that the overall precision of this microarray is excellent. In addition, we identified a small number of probes targeting CpGs that include single-nucleotide polymorphisms. Overall, our findings address several technical issues associated with the Illumina 27k microarray that, once considered, will enhance the analysis and interpretation of data generated from this platform.
authors.affiliation: Program in Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.
authors.forename: Yi-an
authors.initials: YA
authors.lastname: Chen
authors.forename: Sanaa
authors.initials: S
authors.lastname: Choufani
authors.forename: Jose Carlos
authors.initials: JC
authors.lastname: Ferreira
authors.forename: Daria
authors.initials: D
authors.lastname: Grafodatskaya
authors.forename: Darci T
authors.initials: DT
authors.lastname: Butcher
authors.forename: Rosanna
authors.initials: R
authors.lastname: Weksberg
mesh_terms: D002877:Chromosomes, Human / Q000235:genetics*; D041321:Chromosomes, Human, X / Q000235:genetics*; D019295:Computational Biology; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics*; D003627:Data Interpretation, Statistical; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D011110:Polymorphism, Genetic / Q000235:genetics; D017385:Sequence Homology
chemical_list: D015342:DNA Probes