Abstract
Pedigree relationship errors often occur in family data collected for genetic studies, and unidentified errors can lead to either increased false positives or decreased power in both linkage and association analyses. Here we review several allele sharing, as well as likelihood-based statistics, that were proposed to efficiently extract genealogical information from available genome-wide marker data, and the software package PREST that implements these methods. We provide detailed analytical steps involved using two application examples, and we discuss various practical issues including results interpretation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Boehnke M, Cox NJ (1997) Accurate inference of relationships in sib-pair linkage studies. Am J Hum Genet 61(2):423–429
Voight BF, Pritchard JK (2005) Confounding from cryptic relatedness in case-control association studies. PLoS Genet 1(3):e32
Thornton T, McPeek MS (2010) Roadtrips: case-control association testing with partially or completely unknown population and pedigree structure. Am J Hum Genet 86(2):172–184
Goring HH, Ott J (1997) Relationship estimation in affected sib pair analysis of late-onset diseases. Eur J Hum Genet 5(2):69–77
O’Connell JR, Weeks DE (1998) Pedcheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet 63(1):259–266
Ehm M, Wagner M (1998) A test statistic to detect errors in sib-pair relationships. Am J Hum Genet 62(1):181–188
McPeek MS, Sun L (2000) Statistical tests for detection of misspecified relationships by use of genome-screen data. Am J Hum Genet 66(3):1076–1094
Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2001) Grr: graphical representation of relationship errors. Bioinformatics 17(8):742–743
Sieberts SK, Wijsman EM, Thompson EA (2002) Relationship inference from trios of individuals, in the presence of typing error. Am J Hum Genet 70(1):170–180
Sun L, Wilder K, McPeek MS (2002) Enhanced pedigree error detection. Hum Hered 54(2):99–110
Rabiner L (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77:2257–2286
Sun L (2001) Two statistical problems in human genetics. PhD thesis, University of Chicago
Thompson EA (1975) The estimation of pairwise relationships. Ann Hum Genet 39(2):173–188
Thompson EA (1986) Pedigree analysis in human genetics. The Johns Hopkins University Press, Baltimore
Dimitromanolakis A, Paterson AD, Sun L (2009) Accurate IBD inference identifies cryptic relatedness in 9 hapmap populations. Abstract no. 1768
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) Plink: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 57:289–300
Craiu RV, Sun L (2008) Choosing the lesser evil: trade-o_ between false discovery rate and non-discovery rate. Statistica Sinica 18:861–879
Sun L, Craiu RV, Paterson AD and Bull SB (2006) Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genet Epidemiol 30:519–530
Begleiter H, Reich T, Nurnberger JJ, Li TK, Conneally PM, Edenberg H, Crowe R, Kuperman S, Schuckit M, Bloom F, Hesselbrock V, Porjesz B, Cloninger CR, Rice J, Goate A (1999) Description of the genetic analysis workshop 11 collaborative study on the genetics of alcoholism. Genet Epidemiol 17 Suppl 1:S25–30
Antoni G, Morange P, Luo Y, Saut N, Burgos G, Heath S, Germain M, Biron-Andreani C, Schved J, Pernod G, Galan P, Zelenika D, Alessi M, Drouet L, Visvikis-Siest S, Wells P, Lathrop M, Emmerich J, Tregouet D, Gagnon F (2010) A multi-stage multi-design strategy provides strong evidence that the bai3 locus is associated with early-onset venous thromboembolism. J Thromb Haemost DOI 10.1111/j.1538-7836.2010.04092.x
Epstein MP, Duren WL, Boehnke M (2000) Improved inference of relationship for pairs of individuals. Am J Hum Genet 67(5):1219–1231
McPeek MS (2002) Inference on pedigree structure from genome screen data. Statistica Sinica 12:311–335
Sun L, Abney M, McPeek MS (2001) Detection of mis-specified relationships in inbred and outbred pedigrees. Genet Epidemiol 21 Suppl 1:S36–41
Broman KW, Weber JL (1998) Estimation of pairwise relationships in the presence of genotyping errors. Am J Hum Genet 63(5):1563–1564
Ray A, Weeks DE (2008) Relationship uncertainty linkage statistics (ruls): affected relative pair statistics that model relationship uncertainty. Genet Epidemiol 32(4):313–324
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Sun, L. (2012). Detecting Pedigree Relationship Errors. In: Elston, R., Satagopan, J., Sun, S. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 850. Humana Press. https://doi.org/10.1007/978-1-61779-555-8_3
Download citation
DOI: https://doi.org/10.1007/978-1-61779-555-8_3
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-554-1
Online ISBN: 978-1-61779-555-8
eBook Packages: Springer Protocols