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Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies

Overview of attention for article published in BMC Genomics, November 2015
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  • High Attention Score compared to outputs of the same age and source (80th percentile)

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Title
Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies
Published in
BMC Genomics, November 2015
DOI 10.1186/s12864-015-2202-0
Pubmed ID
Authors

Patrycja Daca-Roszak, Aleksandra Pfeifer, Jadwiga Żebracka-Gala, Dagmara Rusinek, Aleksandra Szybińska, Barbara Jarząb, Michał Witt, Ewa Ziętkiewicz

Abstract

Infinium HumanMethylation 450 BeadChip Arrays by Illumina (Illumina HM450K) are among the most popular CpG microarray platforms widely used in biological and medical research. Several recent studies highlighted the potentially confounding impact of the genomic variation on the results of methylation studies performed using Illumina's Infinium methylation probes. However, the complexity of SNPs impact on the methylation level measurements (β values) has not been comprehensively described. In our comparative study of European and Asian populations performed using Illumina HM450K, we found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. Characteristic tri-modal or bi-modal patterns of β values distribution among individual samples were observed for CpGs with SNPs in the first and second position, respectively. To better understand how SNPs affect methylation readouts, we investigated their impact in the context of SNP position and type, and of the Illumina probe type (Infinium I or II). Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes. In addition, it provides important practical clues for discriminating between differences due to the methylation status and to the genomic polymorphisms, based on the inspection of methylation readouts in individual samples. This approach is of special importance when Illumina Infinium assay is used for any comparative population studies, whether related to cancer, disease, ethnicity where SNP frequencies differentiate the studied groups.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 106 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 4 4%
Unknown 102 96%

Demographic breakdown

Readers by professional status Count As %
Researcher 20 19%
Student > Ph. D. Student 15 14%
Student > Bachelor 14 13%
Student > Master 14 13%
Student > Doctoral Student 12 11%
Other 18 17%
Unknown 13 12%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 33 31%
Agricultural and Biological Sciences 25 24%
Medicine and Dentistry 12 11%
Computer Science 6 6%
Immunology and Microbiology 3 3%
Other 12 11%
Unknown 15 14%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 01 October 2021.
All research outputs
#6,155,043
of 22,834,308 outputs
Outputs from BMC Genomics
#2,627
of 10,655 outputs
Outputs of similar age
#95,374
of 386,751 outputs
Outputs of similar age from BMC Genomics
#75
of 388 outputs
Altmetric has tracked 22,834,308 research outputs across all sources so far. This one has received more attention than most of these and is in the 72nd percentile.
So far Altmetric has tracked 10,655 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 74% 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 386,751 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 74% of its contemporaries.
We're also able to compare this research output to 388 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 80% of its contemporaries.