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

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) (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.
Pages391-407
Number of pages17
Volume1666
DOIs
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1666
ISSN (Print)1064-3745

Fingerprint

Pedigree
Siblings
Genotype
Viverridae
Nuclear Family

Keywords

  • 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

Cite this

Chung, R. H., Kinnamon, D. D., & Martin, E. R. (2017). Single marker family-based association analysis conditional on parental information. In Methods in Molecular Biology (Vol. 1666, pp. 391-407). (Methods in Molecular Biology; Vol. 1666). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7274-6_19

Single marker family-based association analysis conditional on parental information. / Chung, Ren Hua; Kinnamon, Daniel D.; Martin, Eden R.

Methods in Molecular Biology. Vol. 1666 Humana Press Inc., 2017. p. 391-407 (Methods in Molecular Biology; Vol. 1666).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chung, RH, Kinnamon, DD & Martin, ER 2017, Single marker family-based association analysis conditional on parental information. in Methods in Molecular Biology. vol. 1666, Methods in Molecular Biology, vol. 1666, Humana Press Inc., pp. 391-407. https://doi.org/10.1007/978-1-4939-7274-6_19
Chung RH, Kinnamon DD, Martin ER. Single marker family-based association analysis conditional on parental information. In Methods in Molecular Biology. Vol. 1666. Humana Press Inc. 2017. p. 391-407. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7274-6_19
Chung, Ren Hua ; Kinnamon, Daniel D. ; Martin, Eden R. / Single marker family-based association analysis conditional on parental information. Methods in Molecular Biology. Vol. 1666 Humana Press Inc., 2017. pp. 391-407 (Methods in Molecular Biology).
@inbook{f942881f180b4add87c0c4da50fc046a,
title = "Single marker family-based association analysis conditional on parental information",
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) (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.",
keywords = "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",
author = "Chung, {Ren Hua} and Kinnamon, {Daniel D.} and Martin, {Eden R}",
year = "2017",
doi = "10.1007/978-1-4939-7274-6_19",
language = "English (US)",
volume = "1666",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "391--407",
booktitle = "Methods in Molecular Biology",

}

TY - CHAP

T1 - Single marker family-based association analysis conditional on parental information

AU - Chung, Ren Hua

AU - Kinnamon, Daniel D.

AU - Martin, Eden R

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

KW - EM algorithm

KW - Extended pedigree

KW - Family-based association test

KW - Genome-wide association

KW - Linkage disequilibrium

KW - Nontransmission statistics

KW - Nuclear family

KW - Parallelization

KW - Parental information

KW - Population stratification

KW - Rare variants

KW - Transmission statistics

UR - http://www.scopus.com/inward/record.url?scp=85030687088&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85030687088&partnerID=8YFLogxK

U2 - 10.1007/978-1-4939-7274-6_19

DO - 10.1007/978-1-4939-7274-6_19

M3 - Chapter

VL - 1666

T3 - Methods in Molecular Biology

SP - 391

EP - 407

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -