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Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation

Overview of attention for article published in BMC Genomics, December 2015
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (86th percentile)
  • High Attention Score compared to outputs of the same age and source (92nd percentile)

Mentioned by

blogs
1 blog
twitter
5 tweeters
facebook
1 Facebook page

Citations

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29 Dimensions

Readers on

mendeley
114 Mendeley
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Title
Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation
Published in
BMC Genomics, December 2015
DOI 10.1186/1471-2164-16-s13-s1
Pubmed ID
Authors

Maxim Ivanov, Ancha Baranova, Timothy Butler, Paul Spellman, Vladislav Mileyko

Abstract

The assessment of cell-free circulating DNA fragments, also known as a "liquid biopsy" of the patient's plasma, is an important source for the discovery and subsequent non-invasive monitoring of cancer and other pathological conditions. Although the nucleosome-guided fragmentation patterns of cell-free DNA (cfDNA) have not yet been studied in detail, non-random representation of cfDNA sequencies may reflect chromatin features in the tissue of origin at gene-regulation level. In this study, we investigated the association between epigenetic landscapes of human tissues evident in the patterns of cfDNA in plasma by deep sequencing of human cfDNA samples. We have demonstrated that baseline characteristics of cfDNA fragmentation pattern are in concordance with the ones corresponding to cell lines-derived. To identify the loci differentially represented in cfDNA fragment, we mapped the transcription start sites within the sequenced cfDNA fragments and tested for association of these genomic coordinates with the relative strength and the patterns of gene expressions. Preselected sets of house-keeping and tissue specific genes were used as models for actively expressed and silenced genes. Developed measure of gene regulation was able to differentiate these two sets based on sequencing coverage near gene transcription start site. Experimental outcomes suggest that cfDNA retains characteristics previously noted in genome-wide analysis of chromatin structure, in particular, in MNase-seq assays. Thus far the analysis of the DNA fragmentation pattern may aid further developing of cfDNA based biomarkers for a variety of human conditions.

Twitter Demographics

The data shown below were collected from the profiles of 5 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 114 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 3%
United Kingdom 1 <1%
Ireland 1 <1%
Netherlands 1 <1%
Canada 1 <1%
Unknown 107 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 33 29%
Researcher 32 28%
Unspecified 15 13%
Other 10 9%
Student > Bachelor 7 6%
Other 17 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 46 40%
Agricultural and Biological Sciences 27 24%
Unspecified 18 16%
Medicine and Dentistry 11 10%
Computer Science 3 3%
Other 9 8%

Attention Score in Context

This research output has an Altmetric Attention Score of 10. 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 21 February 2016.
All research outputs
#957,273
of 8,605,160 outputs
Outputs from BMC Genomics
#591
of 6,020 outputs
Outputs of similar age
#44,136
of 317,528 outputs
Outputs of similar age from BMC Genomics
#28
of 377 outputs
Altmetric has tracked 8,605,160 research outputs across all sources so far. Compared to these this one has done well and is in the 88th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 6,020 research outputs from this source. They receive a mean Attention Score of 4.2. This one has done particularly well, scoring higher than 90% 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 317,528 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 86% of its contemporaries.
We're also able to compare this research output to 377 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 92% of its contemporaries.