ArticleSource code for biology and medicine2013
CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals.
Article in Source code for biology and medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- A Log-Ratio Biplot Approach for Exploring Genetic Relatedness Based on Identity by State.Frontiers in genetics · 2019Article
- Graphics for relatedness research.Molecular ecology resources · 2017Article
- Cryptic relatedness in epidemiologic collections accessed for genetic association studies: experiences from the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study and the National Health and Nutrition Examination Surveys (NHANES).Frontiers in genetics · 2015Article
- PedWiz: a web-based tool for pedigree informatics.Frontiers in genetics · 2013Article
- Article
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3 authors.
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Abstract
backgroundIn population association studies, standard methods of statistical inference assume that study subjects are independent samples. In genetic association studies, it is therefore of interest to diagnose undocumented close relationships in nominally unrelated study samples.
resultsWe describe the R package CrypticIBDcheck to identify pairs of closely-related subjects based on genetic marker data from single-nucleotide polymorphisms (SNPs). The package is able to accommodate SNPs in linkage disequibrium (LD), without the need to thin the markers so that they are approximately independent in the population. Sample pairs are identified by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from one of several common close relationships.
conclusionsThe methods implemented in CrypticIBDcheck are particularly relevant to candidate-gene association studies, in which dependent SNPs cluster in a relatively small number of genes spread throughout the genome. The accommodation of LD allows the use of all available genetic data, a desirable property when working with a modest number of dependent SNPs within candidate genes. CrypticIBDcheck is available from the Comprehensive R Archive Network (CRAN).
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