The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes
Open accessAbstract
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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Cites
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Wang, L.-B., Karpova, A., Gritsenko, M. A., Kyle, J. E., Cao, S., Li, Y., Rykunov, D., Colaprico, A., Rothstein, J. H., Hong, R., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.01.006 · Cited by 661
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation
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“We chose this DNAm site as a positive control as it showed a strong cis-mQTL in several datasets on chr22 and hasn’t been proposed to be excluded from the analyses by probe annotation efforts 59,66–68 .”
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Metadata
- Authors
- Zhou, W., Laird, P. W., & Shen, H.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-10-24
- Volume
- 45
- Issue
- 4
- Pages
- gkw967
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2537310520
- Cited by
- 760
- References
- 28
- FWCI
- 13.09
- Type
- journal article
- Language
- en
- Open access
- gold
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