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Copy Number Variation in the Horse Genome

Overview of attention for article published in PLoS Genetics, October 2014
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  • Good Attention Score compared to outputs of the same age (72nd percentile)
  • Above-average Attention Score compared to outputs of the same age and source (54th percentile)

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Title
Copy Number Variation in the Horse Genome
Published in
PLoS Genetics, October 2014
DOI 10.1371/journal.pgen.1004712
Pubmed ID
Authors

Sharmila Ghosh, Zhipeng Qu, Pranab J. Das, Erica Fang, Rytis Juras, E. Gus Cothran, Sue McDonell, Daniel G. Kenney, Teri L. Lear, David L. Adelson, Bhanu P. Chowdhary, Terje Raudsepp

Abstract

We constructed a 400K WG tiling oligoarray for the horse and applied it for the discovery of copy number variations (CNVs) in 38 normal horses of 16 diverse breeds, and the Przewalski horse. Probes on the array represented 18,763 autosomal and X-linked genes, and intergenic, sub-telomeric and chrY sequences. We identified 258 CNV regions (CNVRs) across all autosomes, chrX and chrUn, but not in chrY. CNVs comprised 1.3% of the horse genome with chr12 being most enriched. American Miniature horses had the highest and American Quarter Horses the lowest number of CNVs in relation to Thoroughbred reference. The Przewalski horse was similar to native ponies and draft breeds. The majority of CNVRs involved genes, while 20% were located in intergenic regions. Similar to previous studies in horses and other mammals, molecular functions of CNV-associated genes were predominantly in sensory perception, immunity and reproduction. The findings were integrated with previous studies to generate a composite genome-wide dataset of 1476 CNVRs. Of these, 301 CNVRs were shared between studies, while 1174 were novel and require further validation. Integrated data revealed that to date, 41 out of over 400 breeds of the domestic horse have been analyzed for CNVs, of which 11 new breeds were added in this study. Finally, the composite CNV dataset was applied in a pilot study for the discovery of CNVs in 6 horses with XY disorders of sexual development. A homozygous deletion involving AKR1C gene cluster in chr29 in two affected horses was considered possibly causative because of the known role of AKR1C genes in testicular androgen synthesis and sexual development. While the findings improve and integrate the knowledge of CNVs in horses, they also show that for effective discovery of variants of biomedical importance, more breeds and individuals need to be analyzed using comparable methodological approaches.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 80 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 1%
Czechia 1 1%
Canada 1 1%
South Africa 1 1%
Unknown 76 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 21 26%
Researcher 19 24%
Student > Bachelor 10 13%
Student > Master 6 8%
Professor 3 4%
Other 5 6%
Unknown 16 20%
Readers by discipline Count As %
Agricultural and Biological Sciences 37 46%
Biochemistry, Genetics and Molecular Biology 13 16%
Veterinary Science and Veterinary Medicine 8 10%
Computer Science 1 1%
Unknown 21 26%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 03 October 2016.
All research outputs
#7,212,870
of 25,394,764 outputs
Outputs from PLoS Genetics
#4,691
of 8,960 outputs
Outputs of similar age
#74,211
of 273,407 outputs
Outputs of similar age from PLoS Genetics
#108
of 244 outputs
Altmetric has tracked 25,394,764 research outputs across all sources so far. This one has received more attention than most of these and is in the 71st percentile.
So far Altmetric has tracked 8,960 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 17.8. This one is in the 46th percentile – i.e., 46% of its peers scored the same or lower than it.
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 273,407 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 72% of its contemporaries.
We're also able to compare this research output to 244 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 54% of its contemporaries.