ArticleGenetics, selection, evolution : GSE2011
Identification of Mendelian inconsistencies between SNP and pedigree information of sibs.
Article in Genetics, selection, evolution : GSE, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Short communication: genomic kinship, opposing homozygotes and genetic diversity in a selected population of Australian Angus cattle.Journal of animal science · 2025Article
- First large-scale genomic prediction in the honey bee.Heredity · 2023Article
- Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm.BMC plant biology · 2020Article
- Assessment of kinship detection using RNA-seq data.Nucleic acids research · 2019Article
- Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset.Poultry science · 2019Article
- Optimized grouping to increase accuracy of prediction of breeding values based on group records in genomic selection breeding programs.Genetics, selection, evolution : GSE · 2019Article
- 'apparent': a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information.BMC bioinformatics · 2019Article
- Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond.Molecular ecology resources · 2017Article
- Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population.BMC genomics · 2015Article
- The effect of rare alleles on estimated genomic relationships from whole genome sequence data.BMC genetics · 2015Article
- Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle.Frontiers in genetics · 2015Article
- hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups.BMC bioinformatics · 2014Article
- The effect of linkage disequilibrium and family relationships on the reliability of genomic prediction.Genetics · 2013Article
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3 authors.
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Abstract
backgroundUsing SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement.
methodsStraightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP) genotypes between parent and offspring (PAR-OFF). Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT). The second test compares pedigree and SNP-based relationships (SIBREL). All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals.
resultsBoth SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL) identified 18 (22) additional inconsistent animals.Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error), were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error), were considerably higher for SIBREL compared to SIBCOUNT.
conclusionsTests to remove Mendelian inconsistencies between sibs should be preceded by a test for parent-offspring inconsistencies. This parent-offspring test should not only consider parent-offspring pairs based on pedigree data, but also those based on SNP information. Both SIB tests could identify pairs of sibs with Mendelian inconsistencies. Based on type I and II error rates, counting opposing homozygotes between sibs (SIBCOUNT) appears slightly more precise than comparing genomic and pedigree relationships (SIBREL) to detect Mendelian inconsistencies between sibs.
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