ArticleGenetics, selection, evolution : GSE2015
Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis.
Article in Genetics, selection, evolution : GSE, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle.Animals : an open access journal from MDPI · 2020Article
- Combining micro-RNA and protein sequencing to detect robust biomarkers for Graves' disease and orbitopathy.Scientific reports · 2018Article
- Genetic Improvement in South African Livestock: Can Genomics Bridge the Gap Between the Developed and Developing Sectors?Frontiers in genetics · 2018Review
- The effect of mislabeled phenotypic status on the identification of mutation-carriers from SNP genotypes in dairy cattle.BMC research notes · 2017Article
- Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit.Genetica · 2016Article
- Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations.BMC genomics · 2016Article
- A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle.BMC genomics · 2016Article
- A frameshift mutation in GON4L is associated with proportionate dwarfism in Fleckvieh cattle.Genetics, selection, evolution : GSE · 2016Article
- "Noisy beets": impact of phenotyping errors on genomic predictions for binary traits in Beta vulgaris.Plant methods · 2016Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific haplotypes. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we present a procedure combining variable selection (i.e. the selection of predictive SNPs) and linear discriminant analysis for the identification of carriers of a haplotype on BTA19 (Bos taurus autosome 19) known to be associated with reduced cow fertility. A population of 3645 Brown Swiss cows and bulls genotyped with the 54K SNP-chip was available for the analysis.
resultsThe overall error rate for the prediction of haplotype carriers was on average very low (∼≤1%). The error rate was found to depend on the number of SNPs in the model and their density around the region of the haplotype on BTA19. The minimum set of SNPs to still achieve accurate predictions was 5, with a total test error rate of 1.59.
conclusionsThe paper describes a procedure to accurately identify haplotype carriers from SNP genotypes in cattle populations. Very few misclassifications were observed, which indicates that this is a very reliable approach for potential applications in cattle breeding.
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