Abstract
Cryptic relationships such as first-degree relatives often appear in studies that collect population samples such as the case–control genome-wide association studies (GWAS). Cryptic relatedness not only creates increased type 1 error rate but also affects other aspects of GWAS, such as population stratification via principal component analysis. Here we discuss two effective methods, as implemented in PREST and PLINK, to detect and correct for the problem of cryptic relatedness using high-throughput SNP data collected from GWAS or next-generation sequencing (NGS) experiments. We provide the analytical and practical details involved using three application examples.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Voight BF, Pritchard JK (2005) Confounding from cryptic relatedness in case-control association studies. PLoS Genet 1: 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: 172–18
Price AL, Zaitlen NA, Reich D, Patterson N (2010) New approaches to population stratification in genome-wide association studies. Nature Reviews Genetics 11: 459–46
McPeek MS, Sun L (2000) Statistical tests for detection of misspecified relationships by use of genome-screen data. Am J Hum Genet 66: 1076–109
Dimitromanolakis A, Paterson AD, Sun L (2009) Accurate IBD inference identifies cryptic relatedness in 9 hapmap populations. Abstract no. 1768 presented at the annual meeting of the American Society of Human Genetics
Sun L, Wilder K, McPeek MS (2002) Enhanced pedigree error detection. Hum Hered 54: 99–11
Purcell S, et al (2007) Plink: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559–57
The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851–861
Begleiter H, et al (1999) Description of the genetic analysis workshop 11 collaborative study on the genetics of alcoholism. Genet Epidemiol 17 Suppl 1: S25–3
Antoni G, et al (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
Browning SR, Browning BL (2010) High-resolution detection of identity by descent in unrelated individuals. Am J Hum Genet 86: 526–539
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., Dimitromanolakis, A. (2012). Identifying Cryptic Relationships. 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_4
Download citation
DOI: https://doi.org/10.1007/978-1-61779-555-8_4
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-554-1
Online ISBN: 978-1-61779-555-8
eBook Packages: Springer Protocols