CrypticIBDcheck: An R Package For Checking Cryptic Relatedness In Nominally Unrelated Individuals

Resource type
Date created
2013
Authors/Contributors
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).
Document
Published as
Source Code for Biology and Medicine 2013, 8:5 doi:10.1186/1751-0473-8-5
Publication title
Source Code for Biology and Medicine
Document title
CrypticIBDcheck: An R Package For Checking Cryptic Relatedness In Nominally Unrelated Individuals
Date
2013
Volume
8
Issue
5
Publisher DOI
10.1186/1751-0473-8-5
Copyright statement
Copyright is held by the author(s).
Scholarly level
Peer reviewed?
Yes
Language
Member of collection
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1751-0473-8-5.pdf 812.77 KB