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Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

Overview of attention for article published in BMC Genomics, February 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (78th percentile)

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11 tweeters

Citations

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Title
Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits
Published in
BMC Genomics, February 2016
DOI 10.1186/s12864-016-2443-6
Pubmed ID
Authors

I. M. MacLeod, P. J. Bowman, C. J. Vander Jagt, M. Haile-Mariam, K. E. Kemper, A. J. Chamberlain, C. Schrooten, B. J. Hayes, M. E. Goddard

Abstract

Dense SNP genotypes are often combined with complex trait phenotypes to map causal variants, study genetic architecture and provide genomic predictions for individuals with genotypes but no phenotype. A single method of analysis that jointly fits all genotypes in a Bayesian mixture model (BayesR) has been shown to competitively address all 3 purposes simultaneously. However, BayesR and other similar methods ignore prior biological knowledge and assume all genotypes are equally likely to affect the trait. While this assumption is reasonable for SNP array genotypes, it is less sensible if genotypes are whole-genome sequence variants which should include causal variants. We introduce a new method (BayesRC) based on BayesR that incorporates prior biological information in the analysis by defining classes of variants likely to be enriched for causal mutations. The information can be derived from a range of sources, including variant annotation, candidate gene lists and known causal variants. This information is then incorporated objectively in the analysis based on evidence of enrichment in the data. We demonstrate the increased power of BayesRC compared to BayesR using real dairy cattle genotypes with simulated phenotypes. The genotypes were imputed whole-genome sequence variants in coding regions combined with dense SNP markers. BayesRC increased the power to detect causal variants and increased the accuracy of genomic prediction. The relative improvement for genomic prediction was most apparent in validation populations that were not closely related to the reference population. We also applied BayesRC to real milk production phenotypes in dairy cattle using independent biological priors from gene expression analyses. Although current biological knowledge of which genes and variants affect milk production is still very incomplete, our results suggest that the new BayesRC method was equal to or more powerful than BayesR for detecting candidate causal variants and for genomic prediction of milk traits. BayesRC provides a novel and flexible approach to simultaneously improving the accuracy of QTL discovery and genomic prediction by taking advantage of prior biological knowledge. Approaches such as BayesRC will become increasing useful as biological knowledge accumulates regarding functional regions of the genome for a range of traits and species.

Twitter Demographics

The data shown below were collected from the profiles of 11 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 88 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Denmark 1 1%
Unknown 87 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 31 35%
Researcher 19 22%
Student > Master 15 17%
Unspecified 10 11%
Student > Postgraduate 3 3%
Other 10 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 65 74%
Unspecified 9 10%
Biochemistry, Genetics and Molecular Biology 8 9%
Veterinary Science and Veterinary Medicine 2 2%
Mathematics 2 2%
Other 2 2%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. 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 13 September 2018.
All research outputs
#2,100,118
of 12,379,581 outputs
Outputs from BMC Genomics
#1,189
of 7,331 outputs
Outputs of similar age
#60,989
of 277,995 outputs
Outputs of similar age from BMC Genomics
#1
of 1 outputs
Altmetric has tracked 12,379,581 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 7,331 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done well, scoring higher than 83% of its peers.
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We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them