Single marker family-based association analysis conditional on parental information

Ren Hua Chung, Daniel D. Kinnamon, Eden R Martin

Research output: Chapter in Book/Report/Conference proceedingChapter


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) (Martin et al., 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 (Martin et al., 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 test 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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages17
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • EM algorithm
  • Extended pedigree
  • Family-based association test
  • Genome-wide association
  • Linkage disequilibrium
  • Nontransmission statistics
  • Nuclear family
  • Parallelization
  • Parental information
  • Population stratification
  • Rare variants
  • Transmission statistics

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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