A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker - PubMed (original) (raw)

Review

A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker

Warren J Ewens et al. PLoS Genet. 2008.

Abstract

Quantitative trait transmission/disequilibrium tests (quantitative TDTs) are commonly used in family-based genetic association studies of quantitative traits. Despite the availability of various quantitative TDTs, some users are not aware of the properties of these tests and the relationships between them. This review aims at outlining the broad features of the various quantitative TDT procedures carried out in the frequently used QTDT and FBAT packages. Specifically, we discuss the "Rabinowitz" and the "Monks-Kaplan" procedures, as well as the various "Abecasis" and "Allison" regression-based procedures. We focus on the models assumed in these tests and the relationships between them. Moreover, we discuss what hypotheses are tested by the various quantitative TDTs, what testing procedures are best suited to various forms of data, and whether the regression-based tests overcome population stratification problems. Finally, we comment on power considerations in the choice of the test to be used. We hope this brief review will shed light on the similarities and differences of the various quantitative TDTs.

PubMed Disclaimer

Cited by

Candidate-gene association analysis for a continuous phenotype with a spike at zero using parent-offspring trios.
Klein N, Entwistle A, Rosenberger A, Kneib T, Bickeböller H. Klein N, et al. J Appl Stat. 2019 Dec 19;47(11):2066-2080. doi: 10.1080/02664763.2019.1704226. eCollection 2020. J Appl Stat. 2019. PMID: 35707573 Free PMC article.
Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies.
Ray D, Vergara C, Taub MA, Wojcik G, Ladd-Acosta C, Beaty TH, Duggal P. Ray D, et al. Genet Epidemiol. 2022 Jul;46(5-6):266-284. doi: 10.1002/gepi.22453. Epub 2022 Apr 22. Genet Epidemiol. 2022. PMID: 35451532 Free PMC article. Review.
Deconstructing a Syndrome: Genomic Insights Into PCOS Causal Mechanisms and Classification.
Dapas M, Dunaif A. Dapas M, et al. Endocr Rev. 2022 Nov 25;43(6):927-965. doi: 10.1210/endrev/bnac001. Endocr Rev. 2022. PMID: 35026001 Free PMC article.
Causal inference in genetic trio studies.
Bates S, Sesia M, Sabatti C, Candès E. Bates S, et al. Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24117-24126. doi: 10.1073/pnas.2007743117. Epub 2020 Sep 18. Proc Natl Acad Sci U S A. 2020. PMID: 32948695 Free PMC article.
Linkage Analysis of the Chromosome 5q31-33 Region Identifies JAKMIP2 as a Risk Factor for Graves' Disease in the Chinese Han Population.
Li J, Teng W, Yu Y, Hou X, Shan Z. Li J, et al. Med Sci Monit. 2019 Feb 23;25:1439-1451. doi: 10.12659/MSM.911489. Med Sci Monit. 2019. PMID: 30796769 Free PMC article.

References

1. Spielman RS, McGinnis RE, Ewens WJ. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet. 1993;52:506–516. - PMC - PubMed
1. Rabinowitz D. A transmission disequilibrium test for quantitative trait loci. Hum Hered. 1997;47:342–350. - PubMed
1. Monks SA, Kaplan NL. Removing the sampling restrictions from family-based tests of association for a quantitative-trait locus. Am J Hum Genet. 2000;66:576–592. - PMC - PubMed
1. Abecasis GR, Cardon LR, Cookson WO. A general test of association for quantitative traits in nuclear families. Am J Hum Genet. 2000;66:279–292. - PMC - PubMed
1. Allison DB. Transmission-disequilibrium tests for quantitative traits. Am J Hum Genet. 1997;60:676–690. - PMC - PubMed

A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker - PubMed (original) (raw)