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

Overview of attention for article published in Genome Biology, October 2016
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (93rd percentile)
  • Above-average Attention Score compared to outputs of the same age and source (62nd percentile)

Mentioned by

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48 X users
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4 patents
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1 Facebook page
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1 Redditor

Citations

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955 Dimensions

Readers on

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843 Mendeley
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1 CiteULike
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Title
Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
Published in
Genome Biology, October 2016
DOI 10.1186/s13059-016-1066-1
Pubmed ID
Authors

Ruth Pidsley, Elena Zotenko, Timothy J. Peters, Mitchell G. Lawrence, Gail P. Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J. Clark

Abstract

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. 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. 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.

X Demographics

X Demographics

The data shown below were collected from the profiles of 48 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 843 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Canada 2 <1%
Spain 1 <1%
Germany 1 <1%
United States 1 <1%
Unknown 838 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 176 21%
Researcher 160 19%
Student > Bachelor 89 11%
Student > Master 83 10%
Student > Doctoral Student 40 5%
Other 102 12%
Unknown 193 23%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 269 32%
Agricultural and Biological Sciences 129 15%
Medicine and Dentistry 65 8%
Computer Science 22 3%
Psychology 18 2%
Other 113 13%
Unknown 227 27%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 35. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 October 2022.
All research outputs
#1,138,924
of 25,373,627 outputs
Outputs from Genome Biology
#844
of 4,467 outputs
Outputs of similar age
#20,889
of 327,744 outputs
Outputs of similar age from Genome Biology
#22
of 58 outputs
Altmetric has tracked 25,373,627 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 95th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,467 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one has done well, scoring higher than 81% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 327,744 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 93% of its contemporaries.
We're also able to compare this research output to 58 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 62% of its contemporaries.