Abstract
Candidate gene association studies aim to establish or characterise association between the genetic variation occurring within a specific gene or locus and a phenotype. If the phenotype is quantitative, then the effect size is often measured as the difference between the genotype specific means or a per allele effect. When the phenotype is binary and the disease is either present or absent, the effect is summarised as a genotype specific risk or relative risk. This chapter focuses on methodology employed when a single or small number of genetic loci are being investigated for an association with a specific phenotype.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Risch, N., Merikangas, K. (1996) The future of genetic studies of complex diseases. Science 273:1516–1517.
Cordell, H.J., Clayton, D.G. (2005) Genetic epidemiology 3 – Genetic association studies. Lancet 366:1121–1131.
Dobson, A.J. (2002) Normal Linear Models. In: An Introduction to Generalised Linear Models, 2nd Edition. Chapman and Hall/CRC: Boca Raton, FL, pp. 85–114.
Vignal, C., Bansal, A.T., Balding, D.J., et al. (2009) Genetic association of the major histocompatibility complex with rheumatoid arthritis implicates two non-DRB1 loci. Arthritis Rheum 60:53–62.
Antoniou, A., Pharoah, P.D.P., Narod, S., et al. (2003) Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: A combined analysis of 22 studies. Am J Hum Genet 72:1117–1130.
Cancer Research UK FactSheet. http://info.cancerresearchuk.org/cancerstats/types/breast/incidence/
Cox, A., Dunning, A.M., Garcia-Closas, M., et al. (2007) A common coding variant in CASP8 is associated with breast cancer risk. Nat Genet 39:352–358.
Amos, C.I., Wu, X., Broderick, P., Gorlov, I.P., et al. (2008) Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet 40:616–622.
Jewell, N.P. (2004) Study Designs. In: Statistics for Epidemiology. Chapman and Hall/CRC: Boca Raton, FL, pp. 43–56.
Dobson, A.J. (2002) Binary Variables and Logistic Regression. In: An Introduction to Generalised Linear Models, 2nd Edition. Chapman and Hall/CRC: Boca Raton, FL, pp. 115–134.
Sutton, A.J., Abrams, K.R., Jones, D.R., Sheldon, T.A., Song, F. (2004) Methods for Meta-Analysis in Medical Research. Wiley: New York.
Sutton, A.J., Abrams, K.R., Jones, D.R., Sheldon, T.A., Song, F. (2004) Publication Bias. In: Methods for Meta-Analysis in Medical Research. Wiley: London, pp. 109–132.
Iles, M.M. (2010) Genome Wide Association. In: M.D. Teare (ed.) Genetic Epidemiology. Springer: New York.
Clayton, D., Chapman, J., Cooper, J. (2004) The use of unphased multilocus genotype data in indirect association studies. Genet Epidemiol 27:415–428.
Guo, Y., Li, J., Bonham, A.J., Wang, Y., Deng, H. (2009) Gains in power for exhaustive analyses of haplotypes using variable-sized sliding window strategy: A comparison of association-mapping strategies. Eur J Hum Genet 17:785–792.
Browning, B.L., Browning, S.R. (2009) A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210–223.
Price, A.L., Patterson, N., Hancks, D.C., Myers, S., Reich, D., et al. (2008) Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genet 4:e1000294. doi:10.1371/journal.pgen.1000294.
Balding, D.J. (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7:781–791.
Chen, Y., Shen, H., Yang, F., Liu, P.-Y., et al. (2009) Choice of phenotype in osteoporosis genetic research. J Bone Miner Metab 27:121–126.
NIH Consensus Development Panel on Osteoporosis Prevention, Diagnosis, and Therapy (2001) Osteoporosis prevention, diagnosis, and therapy. JAMA 285:785–795.
Morrison, N.A., Qi, J.C., Tokita, A., Kelly, P.J., et al. (1994) Prediction of bone density from vitamin D receptor alleles. Nature 367:284–287.
Cooper, G.S., Umbach, D.M. (1996) Are vitamin D receptor polymorphsims associated with bone mineral density? J Bone Miner Res 11:1241–1248.
Thakkinstian, A., D’Este, C., Eisman, J., Nguyen, T., Attia, J. (2004) Meta-analysis of molecular association studies: Vitamin D receptor gene polymorphisms and BMD as a case study. J Bone Miner Res 19:419–428.
Gong, G., Stern, H.S., Cheng, S.C., Fong, N., Mordeson, J., Deng, H.W., et al. (1999) The association of bone mineral density with vitamin D receptor gene polymorphisms. Osteoporos Int 9:55–64.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Teare, M.D. (2011). Candidate Gene Association Studies. In: Teare, M. (eds) Genetic Epidemiology. Methods in Molecular Biology, vol 713. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-416-6_8
Download citation
DOI: https://doi.org/10.1007/978-1-60327-416-6_8
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60327-415-9
Online ISBN: 978-1-60327-416-6
eBook Packages: Springer Protocols