Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes

Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition,...

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Bibliographic Details
Published in:Nucleic acids research Vol. 45; no. 4; pp. gkw967 - e22
Main Authors: Zhou, Wanding, Laird, Peter W., Shen, Hui
Format: Journal Article
Language:English
Published: England Oxford University Press 28.02.2017
Subjects:
Alleles
CpG Islands
DNA Methylation
DNA Probes
Gene Dosage
Gene Frequency
Genomics - methods
HeLa Cells
Humans
Methods Online
Molecular Sequence Annotation - methods
Oligonucleotide Array Sequence Analysis - methods
Polymorphism, Single Nucleotide
Repetitive Sequences, Nucleic Acid
ISSN:0305-1048, 1362-4962, 1362-4962
Online Access:Get full text
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Summary:Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3΄ nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes. We show empirical evidence for exclusion criteria for underperforming probes, providing a sounder basis than current ad hoc criteria for exclusion. In addition, we describe novel probe uses, exemplified by the addition of a total of 1052 SNP probes to the existing 59 explicit SNP probes on the EPIC array and the use of these probes to predict ethnicity. Finally, we present an innovative out-of-band color channel application for the dual use of 62 371 probes as internal bisulfite conversion controls.
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkw967