Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

Background In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new conte...

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Vydáno v:Genome Biology Ročník 17; číslo 1; s. 208
Hlavní autoři: Pidsley, Ruth, Zotenko, Elena, Peters, Timothy J., Lawrence, Mitchell G., Risbridger, Gail P., Molloy, Peter, Van Djik, Susan, Muhlhausler, Beverly, Stirzaker, Clare, Clark, Susan J.
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 07.10.2016
Springer Nature B.V
Témata:
Animal Genetics and Genomics
Bioinformatics
Biomedical and Life Sciences
Consortia
CpG islands
CpG Islands - genetics
Deoxyribonucleic acid
Design
Disease
DNA
DNA fingerprinting
DNA methylation
DNA Methylation - genetics
DNA microarrays
DNA probes
Enhancer Elements, Genetic - genetics
Enhancers
Epigenetics
Evolutionary Biology
Gene expression
Genetic diversity
genetic variation
genome
Genome, Human
Genomes
High-Throughput Nucleotide Sequencing
Human Genetics
Humans
Hybridization
Life Sciences
loci
microarray technology
Microbial Genetics and Genomics
Oligonucleotide Array Sequence Analysis - methods
Plant Genetics and Genomics
Prostate cancer
Regulatory sequences
Researchers
Sequence Analysis, DNA - methods
HM450
Validation
Enhancers
EPIC
Whole-genome bisulphite sequencing (WGBS)
DNA methylation
Microarray
ISSN:1474-760X, 1474-7596, 1474-760X
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Shrnutí:Background In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform. Results EPIC covers over 850,000 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58 % of FANTOM5 enhancers, only 7 % distal and 27 % proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and WGBS show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform. Finally, we provide an annotated list of probes whose signal could be affected by cross-hybridisation or underlying genetic variation. Conclusion The EPIC array is a significant improvement over the HM450 array, with increased genome coverage of regulatory regions and high reproducibility and reliability, providing a valuable tool for high-throughput human methylome analyses from diverse clinical samples.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-016-1066-1