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A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample

Overview of attention for article published in BMC Genomics, April 2018
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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 (83rd percentile)
  • High Attention Score compared to outputs of the same age and source (91st percentile)

Mentioned by

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22 tweeters

Citations

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2 Dimensions

Readers on

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19 Mendeley
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Title
A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample
Published in
BMC Genomics, April 2018
DOI 10.1186/s12864-018-4640-y
Pubmed ID
Authors

Lisa Olohan, Laura-Jayne Gardiner, Anita Lucaci, Burkhard Steuernagel, Brande Wulff, John Kenny, Neil Hall, Anthony Hall

Abstract

Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses.

Twitter Demographics

The data shown below were collected from the profiles of 22 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 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 19 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 5 26%
Student > Master 3 16%
Student > Ph. D. Student 3 16%
Unspecified 2 11%
Professor 2 11%
Other 4 21%
Readers by discipline Count As %
Agricultural and Biological Sciences 13 68%
Biochemistry, Genetics and Molecular Biology 4 21%
Unspecified 2 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 13. 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 12 February 2019.
All research outputs
#1,276,738
of 13,630,849 outputs
Outputs from BMC Genomics
#551
of 7,939 outputs
Outputs of similar age
#44,142
of 272,198 outputs
Outputs of similar age from BMC Genomics
#2
of 23 outputs
Altmetric has tracked 13,630,849 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 7,939 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done particularly well, scoring higher than 93% 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 272,198 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 83% of its contemporaries.
We're also able to compare this research output to 23 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 91% of its contemporaries.