ArticleTropical animal health and production2022
Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa.
Article in Tropical animal health and production, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed, 1 citations in OpenAlex.
- Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.Genetics, selection, evolution : GSE · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Imputation may be used to rescue genomic data from animals that would otherwise be eliminated due to a lower than desired call rate. The aim of this study was to compare the accuracy of genotype imputation for Afrikaner, Brahman, and Brangus cattle of South Africa using within- and multiple-breed reference populations. A total of 373, 309, and 101 Afrikaner, Brahman, and Brangus cattle, respectively, were genotyped using the GeneSeek Genomic Profiler 150 K panel that contained 141,746 markers. Markers with MAF ≤ 0.02 and call rates ≤ 0.95 or that deviated from Hardy Weinberg Equilibrium frequency with a probability of ≤ 0.0001 were excluded from the data as were animals with a call rate ≤ 0.90. The remaining data included 99,086 SNPs and 360 Afrikaner, 75,291 SNPs and 288 animals Brahman, and 97,897 SNPs and 99 Brangus animals. A total of 7986, 7002, and 7000 SNP from 50 Afrikaner and Brahman and 30 Brangus cattle, respectively, were masked and then imputed using BEAGLE v3 and FImpute v2. The within-breed imputation yielded accuracies ranging from 89.9 to 96.6% for the three breeds. The multiple-breed imputation yielded corresponding accuracies from 69.21 to 88.35%. The results showed that population homogeneity and numerical representation for within and across breed strategies, respectively, are crucial components for improving imputation accuracies.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.