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Accuracy of genome-wide imputation in Braford and Hereford beef cattle

Overview of attention for article published in BMC Genetics, December 2014
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Title
Accuracy of genome-wide imputation in Braford and Hereford beef cattle
Published in
BMC Genetics, December 2014
DOI 10.1186/s12863-014-0157-9
Pubmed ID
Authors

Mario L Piccoli, José Braccini, Fernando F Cardoso, Medhi Sargolzaei, Steven G Larmer, Flávio S Schenkel

Abstract

BackgroundStrategies for imputing genotypes from the Illumina-Bovine3K, Illumina-BovineLD (6K), BeefLD-GGP (8K), a non-commercial-15K and IndicusLD-GGP (20K) to either Illumina-BovineSNP50 (50K) or to Illumina-BovineHD (777K) SNP panel, as well as for imputing from 50K, GGP-IndicusHD (90iK) and GGP-BeefHD (90tK) to 777K were investigated. Imputation of low density (<50K) genotypes to 777K was carried out in either one or two steps. Imputation of ungenotyped parents (n¿=¿37 sires) with four or more offspring to the 50K panel was also assessed. There were 2,946 Braford, 664 Hereford and 88 Nellore animals, from which 71, 59 and 88 were genotyped with the 777K panel, while all others had 50K genotypes. The reference population was comprised of 2,735 animals and 175 bulls for 50K and 777K, respectively. The low density panels were simulated by masking genotypes in the 50K or 777K panel for animals born in 2011. Analyses were performed using both Beagle and FImpute software. Genotype imputation accuracy was measured by concordance rate and allelic R2 between true and imputed genotypes.ResultsThe average concordance rate using FImpute was 0.943 and 0.921 averaged across all simulated low density panels to 50K or to 777K, respectively, in comparison with 0.927 and 0.895 using Beagle. The allelic R2 was 0.912 and 0.866 for imputation to 50K or to 777K using FImpute, respectively, and 0.890 and 0.826 using Beagle. One and two steps imputation to 777K produced averaged concordance rates of 0.806 and 0.892 and allelic R2 of 0.674 and 0.819, respectively. Imputation of low density panels to 50K, with the exception of 3K, had overall concordance rates greater than 0.940 and allelic R2 greater than 0.919. Ungenotyped animals were imputed to 50K panel with an average concordance rate of 0.950 by FImpute.ConclusionFImpute accuracy outperformed Beagle on both imputation to 50K and to 777K. Two-step outperformed one-step imputation for imputing to 777K. Ungenotyped animals that have four or more offspring can have their 50K genotypes accurately inferred using FImpute. All low density panels, except the 3K, can be used to impute to the 50K using FImpute or Beagle with high concordance rate and allelic R2.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 4%
Brazil 1 4%
United States 1 4%
Colombia 1 4%
Unknown 24 86%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 25%
Student > Master 7 25%
Researcher 5 18%
Student > Doctoral Student 5 18%
Student > Postgraduate 2 7%
Other 2 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 19 68%
Unspecified 3 11%
Biochemistry, Genetics and Molecular Biology 3 11%
Veterinary Science and Veterinary Medicine 1 4%
Computer Science 1 4%
Other 1 4%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 29 December 2014.
All research outputs
#2,096,158
of 4,691,823 outputs
Outputs from BMC Genetics
#209
of 495 outputs
Outputs of similar age
#64,929
of 156,097 outputs
Outputs of similar age from BMC Genetics
#17
of 37 outputs
Altmetric has tracked 4,691,823 research outputs across all sources so far. This one has received more attention than most of these and is in the 52nd percentile.
So far Altmetric has tracked 495 research outputs from this source. They receive a mean Attention Score of 3.2. This one has gotten more attention than average, scoring higher than 53% 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 156,097 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 55% of its contemporaries.
We're also able to compare this research output to 37 others from the same source and published within six weeks on either side of this one. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.