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Derivation of HLA types from shotgun sequence datasets

Overview of attention for article published in Genome Medicine, December 2012
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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 (91st percentile)
  • Good Attention Score compared to outputs of the same age and source (73rd percentile)

Mentioned by

blogs
1 blog
twitter
8 tweeters
patent
1 patent

Citations

dimensions_citation
105 Dimensions

Readers on

mendeley
208 Mendeley
citeulike
3 CiteULike
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Title
Derivation of HLA types from shotgun sequence datasets
Published in
Genome Medicine, December 2012
DOI 10.1186/gm396
Pubmed ID
Authors

René L Warren, Gina Choe, Douglas J Freeman, Mauro Castellarin, Sarah Munro, Richard Moore, Robert A Holt

Abstract

The human leukocyte antigen (HLA) is key to many aspects of human physiology and medicine. All current sequence-based HLA typing methodologies are targeted approaches requiring the amplification of specific HLA gene segments. Whole genome, exome and transcriptome shotgun sequencing can generate prodigious data but due to the complexity of HLA loci these data have not been immediately informative regarding HLA genotype. We describe HLAminer, a computational method for identifying HLA alleles directly from shotgun sequence datasets (http://www.bcgsc.ca/platform/bioinfo/software/hlaminer). This approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.

Twitter Demographics

The data shown below were collected from the profiles of 8 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 208 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 5 2%
United Kingdom 3 1%
Hungary 2 <1%
Germany 2 <1%
India 1 <1%
Australia 1 <1%
Netherlands 1 <1%
Sweden 1 <1%
Kenya 1 <1%
Other 5 2%
Unknown 186 89%

Demographic breakdown

Readers by professional status Count As %
Researcher 55 26%
Student > Ph. D. Student 46 22%
Student > Master 23 11%
Other 18 9%
Student > Postgraduate 13 6%
Other 30 14%
Unknown 23 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 90 43%
Biochemistry, Genetics and Molecular Biology 41 20%
Computer Science 14 7%
Medicine and Dentistry 13 6%
Immunology and Microbiology 8 4%
Other 10 5%
Unknown 32 15%

Attention Score in Context

This research output has an Altmetric Attention Score of 15. 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 January 2016.
All research outputs
#753,819
of 10,501,255 outputs
Outputs from Genome Medicine
#234
of 825 outputs
Outputs of similar age
#27,101
of 306,929 outputs
Outputs of similar age from Genome Medicine
#7
of 26 outputs
Altmetric has tracked 10,501,255 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 825 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 21.7. This one has gotten more attention than average, scoring higher than 71% 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 306,929 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 91% of its contemporaries.
We're also able to compare this research output to 26 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 73% of its contemporaries.