title: CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals.
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).
authors: Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, Canada. mcneney@sfu.ca.
authors: Annick
authors: A
authors: Nembot-Simo
authors: Jinko
authors: J
authors: Graham
authors: Brad
authors: B
authors: McNeney
references: Am J Hum Genet. 2001 Nov;69(5):1146-8
references: 11590549
references: Ann Hum Genet. 1975 Oct;39(2):173-88
references: 1052764
references: PLoS Genet. 2005 Sep;1(3):e32
references: 16151517
references: Bioinformatics. 2009 May 15;25(10):1287-92
references: 19289443
references: Bioinformatics. 2001 Aug;17(8):742-3
references: 11524377
references: Genet Epidemiol. 2009 Dec;33(8):668-78
references: 19333967
references: Nat Rev Genet. 2006 Oct;7(10):771-80
references: 16983373
references: Genet Epidemiol. 2010 Feb;34(2):119-24
references: 19582786
references: Bioinformatics. 2012 Dec 15;28(24):3329-31
references: 23052040
references: Genetics. 1999 Aug;152(4):1753-66
references: 10430599
references: Comput Stat Data Anal. 2009 Mar 15;53(5):1818-1828
references: 20161313
references: Genet Res (Camb). 2011 Feb;93(1):47-64
references: 21226974
references: Biometrics. 1999 Dec;55(4):997-1004
references: 11315092
references: PLoS One. 2012;7(2):e31560
references: 22347493
references: Genetics. 2003 Mar;163(3):1153-67
references: 12663552
references: Am J Hum Genet. 2007 Sep;81(3):559-75
references: 17701901