Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray
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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.
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Autosomal sex-specifically methylated loci are very few in number.
“True, autosomal sex-specifically methylated loci are very small in number”
From A data-driven approach to preprocessing Illumina 450K methylation array data (2013) · cites this paper as [17]
Section 2.1 reports that, among 26,486 autosomal CpGs tested in blood lymphocytes, only seven of the 19 apparent sex-specific findings were not considered technical artifacts. That supports the claim that such loci were very few in this study, but not an unqualified claim about all autosomal loci or tissues. (LLM, conf=0.84)
Experimental — accuracy not yet measuredAutosomal sex-specifically methylated loci may represent autosomal probes mapping to sex-chromosome sequences.
“and potentially represent autosomal probes mapping to sequences on the sex-chromosome [17].”
From A data-driven approach to preprocessing Illumina 450K methylation array data (2013) · cites this paper as [17]
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References 30 · Cited by 90
- Authors
- Chen, Y.-A., Choufani, S., Ferreira, J. C., Grafodatskaya, D., Butcher, D. T., & Weksberg, R.
- Affiliations
- Hospital for Sick Children (CA)
- University of Toronto (CA)
- Corresponding author
- Weksberg, Rosanna
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2011-04
- Volume
- 97
- Issue
- 4
- Pages
- 214-222
- ISSN
- 0888-7543 (ISSN-L)
- OpenAlex
- W2043546047
- Cited by
- 90
- References
- 30
- Citations by year
- 2025: 2 · 2024: 8 · 2022: 15 · 2021: 1 · 2020: 2 · 2019: 4 · 2018: 1 · 2017: 3 · 2016: 2 · 2015: 7 · 2014: 10 · 2013: 16 · 2012: 17
- FWCI
- 5.82
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Genomics (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Funders
- Canadian Institutes of Health Research (CIHR)
- POPH (Operational Program for Human Potential)
- FSE (European Social Fund)
- MCTES (Ministry of Science, Technology and Higher Education)
- Autism Training Research Program (McGill University, Montreal)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- DNA methylation microarrays, CpG methylation, probe specificity, single nucleotide polymorphisms, measurement precision
- MeSH terms
- Chromosomes, Human, Data Interpretation, Statistical, Humans, Polymorphism, Genetic, DNA Probes, Sequence Homology, CpG Islands, DNA Methylation, Computational Biology, Oligonucleotide Array Sequence Analysis, Chromosomes, Human, X
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