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Statistical Human Genetics pp 359–370Cite as

Single-Marker Family-Based Association Analysis Conditional on Parental Information

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 850))

Abstract

Family-based designs have been commonly used in association studies. Different family structures such as extended pedigrees and nuclear families, including parent–offspring triads and families with multiple affected siblings (multiplex families), can be ascertained for family-based association analysis. Flexible association tests that can accommodate different family structures have been proposed. The pedigree disequilibrium test (PDT) (Am J Hum Genet 67:146-154, 2000) can use full genotype information from general (possibly extended) pedigrees with one or multiple affected siblings but requires parental genotypes or genotypes of unaffected siblings. On the other hand, the association in the presence of linkage (APL) test (Am J Hum Genet 73:1016-1026, 2003) is restricted to nuclear families with one or more affected siblings but can infer missing parental genotypes properly by accounting for identity-by-descent (IBD) parameters. Both the PDT and APL are powerful association tests in the presence of linkage and can be used as complementary tools for association analysis. This chapter introduces these two tests and compares their properties. Recommendations and notes for performing the tests in practice are provided.

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Author information

Authors and Affiliations

  1. John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA

    Ren-Hua Chung & Eden R. Martin

Authors
  1. Ren-Hua Chung
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  2. Eden R. Martin
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Corresponding author

Correspondence to Eden R. Martin .

Editor information

Editors and Affiliations

  1. School of Medicine, Dept. Epidemiology & Biostatistics, Case Western Reserve University, Cornell Road 2103, Cleveland, 44106, Ohio, USA

    Robert C. Elston

  2. Dept. Epidemiology & Biostatistics, Memorial Sloan-Kettering Cancer Center, East 63rd Street 307, New York, 10021, New York, USA

    Jaya M. Satagopan

  3. School of Medicine, Dept. Epidemiology & Biostatistics, Case Western Reserve University, Cornell Road 2103, Cleveland, 44106, Ohio, USA

    Shuying Sun

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© 2012 Springer Science+Business Media, LLC

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Chung, RH., Martin, E.R. (2012). Single-Marker Family-Based Association Analysis Conditional on Parental Information. 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_19

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  • DOI: https://doi.org/10.1007/978-1-61779-555-8_19

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-554-1

  • Online ISBN: 978-1-61779-555-8

  • eBook Packages: Springer Protocols

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