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Table of Contents
Vol. 74, No. 1, 2012
Issue release date: November 2012
Section title: Original Paper
Free Access
Hum Hered 2012;74:17–26
(DOI:10.1159/000341636)

The Robustness of Generalized Estimating Equations for Association Tests in Extended Family Data

Suktitipat B.a,c,d · Mathias R.A.b · Vaidya D.b · Yanek L.R.b · Young J.H.b · Becker L.C.b · Becker D.M.b · Wilson A.F.a · Fallin M.D.b, c
aGenometrics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, bDepartment of Medicine, Johns Hopkins Medical Institutions, and cDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md., USA; dDepartment of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
email Corresponding Author

M. Daniele Fallin, PhD

615 N. Wolfe Street

Room 6509

Baltimore, MD 21205 (USA)

Tel. +1 410 955 3643, E-Mail dfallin@jhsph.edu


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.
  2. Horvath S, Xu X, Laird NM: The family based association test method: strategies for studying general genotype-phenotype associations. Eur J Hum Genet 2001;9:301–306.
  3. Lange C, DeMeo D, Silverman EK, Weiss ST, Laird NM: PBAT: tools for family-based association studies. Am J Hum Genet 2004;74:367–369.
  4. Chen WM, Abecasis GR: Family-based association tests for genomewide association scans. Am J Hum Genet 2007;81:913–926.
  5. Aulchenko YS, de Koning DJ, Haley C: Genomewide rapid association using mixed model and regression: A fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 2007;177:577–585.
  6. Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES: Mixed linear model approach adapted for genome-wide association studies. Nat Genet 2010;42:355–360.
  7. Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E: Efficient control of population structure in model organism association mapping. Genetics 2008;178:1709–1723.

    External Resources

  8. Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E: Variance component model to account for sample structure in genome-wide association studies. Nat Genet 2010;42:348–354.
  9. Liang K, Zeger SL: Longitudinal data analysis using generalized linear models. Biometrika 1986;73:13–22.

    External Resources

  10. Zeger SL, Liang KY: Longitudinal data analysis for discrete and continuous outcomes. Biometrics 1986;42:121–130.
  11. Cupples LA, Arruda HT, Benjamin EJ, D’Agostino RB Sr, Demissie S, DeStefano AL, Dupuis J, Falls KM, Fox CS, Gottlieb DJ, Govindaraju DR, Guo CY, Heard-Costa NL, Hwang SJ, Kathiresan S, Kiel DP, Laramie JM, Larson MG, Levy D, Liu CY, Lunetta KL, Mailman MD, Manning AK, Meigs JB, Murabito JM, Newton-Cheh C, O’Connor GT, O’Donnell CJ, Pandey M, Seshadri S, Vasan RS, Wang ZY, Wilk JB, Wolf PA, Yang Q, Atwood LD: The Framingham Heart Study 100K SNP genome-wide association study resource: overview of 17 phenotype working group reports. BMC Med Genet 2007;8(suppl 1):S1.
  12. Tregouet DA, Ducimetiere P, Tiret L: Testing association between candidate-gene markers and phenotype in related individuals, by use of estimating equations. Am J Hum Genet 1997;61:189–199.
  13. Vaidya D, Yanek LR, Moy TF, Pearson TA, Becker LC, Becker DM: Incidence of coronary artery disease in siblings of patients with premature coronary artery disease: 10 years of follow-up. Am J Cardiol 2007;100:1410–1415.

    External Resources

  14. R Development Core Team: R: A Language and Environment for Statistical Computing. Vienna, R Foundation for Statistical Computing, 2010.
  15. Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin – rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002;30:97–101.
  16. Kraja AT, Culverhouse R, Daw EW, Wu J, Van Brunt A, Province MA, Borecki IB: The Genetic Analysis Workshop 16 Problem 3: simulation of heritable longitudinal cardiovascular phenotypes based on actual genome-wide single-nucleotide polymorphisms in the Framingham Heart Study. BMC Proc 2009;3(suppl 7):S4.

    External Resources

  17. Huber P: The behavior of maximum likelihood estimates under nonstandard conditions. Proc Fifth Berkeley Symp Math Stat Prob 1967;1:221–233.
  18. White H: A heteroskedasticity-consistent covariance matrix estimator and a direct test for heteroskedasticity. Econometrica 1980;48:817–838.

    External Resources

  19. Vincent JC: GEE: generalized estimation equation solver, ported to R by Thomas Lumley (versions 3.13 and 4.4) and Brian Ripley (version 4.13). R package version 4.13–14. http://CRAN.R-project.org/package=gee, 2009.
  20. McArdle PF, O’Connell JR, Pollin TI, Baumgarten M, Shuldiner AR, Peyser PA, Mitchell BD: Accounting for relatedness in family based genetic association studies. Hum Hered 2007;64:234–242.