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Open Access Methodology

CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals

Annick Nembot-Simo, Jinko Graham and Brad McNeney*

Author Affiliations

Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, Canada

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Source Code for Biology and Medicine 2013, 8:5  doi:10.1186/1751-0473-8-5

Published: 6 February 2013

Abstract

Background

In 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.

Results

We 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.

Conclusions

The 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).

Keywords:
Cryptic relatedness; IBD estimation; Linkage disequilibrium; Gene drop simulation