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Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Overview of attention for article published in Genome Biology (Online Edition), March 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (90th percentile)

Mentioned by

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49 tweeters

Citations

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78 Dimensions

Readers on

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260 Mendeley
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2 CiteULike
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Title
Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data
Published in
Genome Biology (Online Edition), March 2018
DOI 10.1186/s13059-018-1408-2
Pubmed ID
Authors

Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V. Berrens, Miguel R. Branco, Wolf Reik

Abstract

Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets.

Twitter Demographics

The data shown below were collected from the profiles of 49 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 260 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 260 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 64 25%
Student > Ph. D. Student 59 23%
Student > Master 26 10%
Student > Bachelor 18 7%
Student > Doctoral Student 16 6%
Other 30 12%
Unknown 47 18%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 106 41%
Agricultural and Biological Sciences 63 24%
Medicine and Dentistry 8 3%
Computer Science 6 2%
Chemistry 5 2%
Other 22 8%
Unknown 50 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 25. 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 18 December 2018.
All research outputs
#871,662
of 16,291,974 outputs
Outputs from Genome Biology (Online Edition)
#833
of 3,454 outputs
Outputs of similar age
#26,546
of 281,996 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 1 outputs
Altmetric has tracked 16,291,974 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,454 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 25.4. This one has done well, scoring higher than 75% of its peers.
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