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The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

Overview of attention for article published in BMC Genomics, July 2016
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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 (88th percentile)
  • High Attention Score compared to outputs of the same age and source (98th percentile)

Mentioned by

twitter
27 tweeters
patent
1 patent

Citations

dimensions_citation
50 Dimensions

Readers on

mendeley
315 Mendeley
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1 CiteULike
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Title
The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity
Published in
BMC Genomics, July 2016
DOI 10.1186/s12864-016-2836-6
Pubmed ID
Authors

Johannes Dapprich, Deborah Ferriola, Kate Mackiewicz, Peter M. Clark, Eric Rappaport, Monica D’Arcy, Ariella Sasson, Xiaowu Gai, Jonathan Schug, Klaus H. Kaestner, Dimitri Monos

Abstract

The ability to capture and sequence large contiguous DNA fragments represents a significant advancement towards the comprehensive characterization of complex genomic regions. While emerging sequencing platforms are capable of producing several kilobases-long reads, the fragment sizes generated by current DNA target enrichment technologies remain a limiting factor, producing DNA fragments generally shorter than 1 kbp. The DNA enrichment methodology described herein, Region-Specific Extraction (RSE), produces DNA segments in excess of 20 kbp in length. Coupling this enrichment method to appropriate sequencing platforms will significantly enhance the ability to generate complete and accurate sequence characterization of any genomic region without the need for reference-based assembly. RSE is a long-range DNA target capture methodology that relies on the specific hybridization of short (20-25 base) oligonucleotide primers to selected sequence motifs within the DNA target region. These capture primers are then enzymatically extended on the 3'-end, incorporating biotinylated nucleotides into the DNA. Streptavidin-coated beads are subsequently used to pull-down the original, long DNA template molecules via the newly synthesized, biotinylated DNA that is bound to them. We demonstrate the accuracy, simplicity and utility of the RSE method by capturing and sequencing a 4 Mbp stretch of the major histocompatibility complex (MHC). Our results show an average depth of coverage of 164X for the entire MHC. This depth of coverage contributes significantly to a 99.94 % total coverage of the targeted region and to an accuracy that is over 99.99 %. RSE represents a cost-effective target enrichment method capable of producing sequencing templates in excess of 20 kbp in length. The utility of our method has been proven to generate superior coverage across the MHC as compared to other commercially available methodologies, with the added advantage of producing longer sequencing templates amenable to DNA sequencing on recently developed platforms. Although our demonstration of the method does not utilize these DNA sequencing platforms directly, our results indicate that the capture of long DNA fragments produce superior coverage of the targeted region.

Twitter Demographics

The data shown below were collected from the profiles of 27 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 315 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 <1%
United Kingdom 2 <1%
Brazil 2 <1%
Canada 1 <1%
France 1 <1%
Benin 1 <1%
China 1 <1%
Netherlands 1 <1%
Unknown 303 96%

Demographic breakdown

Readers by professional status Count As %
Researcher 77 24%
Student > Ph. D. Student 75 24%
Student > Master 29 9%
Student > Bachelor 27 9%
Other 17 5%
Other 51 16%
Unknown 39 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 120 38%
Biochemistry, Genetics and Molecular Biology 91 29%
Medicine and Dentistry 12 4%
Immunology and Microbiology 10 3%
Engineering 8 3%
Other 23 7%
Unknown 51 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 16. 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 05 February 2021.
All research outputs
#1,632,441
of 19,606,303 outputs
Outputs from BMC Genomics
#486
of 9,828 outputs
Outputs of similar age
#29,919
of 270,994 outputs
Outputs of similar age from BMC Genomics
#2
of 51 outputs
Altmetric has tracked 19,606,303 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 91st percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 9,828 research outputs from this source. They receive a mean Attention Score of 4.5. This one has done particularly well, scoring higher than 95% 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 270,994 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 88% of its contemporaries.
We're also able to compare this research output to 51 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 98% of its contemporaries.