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Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
Published on: May 6, 2022
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Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes
Wanding Zhou1, Peter W Laird1, Hui Shen1
1Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA.
Nucleic Acids Research
|December 8, 2016
Summary
This study thoroughly characterizes Illumina
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- Illumina Infinium DNA Methylation BeadChips are widely used for genome-scale DNA methylation analysis.
- Current methods for masking probes on these arrays rely on subjective criteria.
- The MethylationEPIC (EPIC) array requires comprehensive characterization.
Purpose of the Study:
- To extensively characterize probes on the EPIC and HM450 microarrays.
- To establish empirical criteria for excluding underperforming probes.
- To explore novel applications of array probes, including SNP analysis and bisulfite conversion control.
Main Methods:
- Probe characterization including mappability, copy number, and polymorphism influence.
- Analysis of a previously unrecognized color channel switch for Type I probes.
- Identification and utilization of SNP probes for ethnicity prediction and bisulfite conversion controls.
Main Results:
- Extensive characterization of EPIC and HM450 array probes against the latest genome build.
- Empirical evidence supporting new exclusion criteria for underperforming probes.
- Demonstration of novel probe uses: 1052 SNP probes added to EPIC array for ethnicity prediction and 62,371 probes for bisulfite conversion control.
Conclusions:
- This work provides a robust basis for probe exclusion criteria, improving DNA methylation array data quality.
- Novel applications of array probes enhance their utility for SNP analysis, ethnicity prediction, and quality control.
- The characterization and novel uses presented will benefit researchers utilizing Illumina methylation arrays.
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