Abstract
Methods for single marker association analysis are presented for binary and quantitative traits. For a binary trait, we focus on the analysis of retrospective case–control data using Pearson’s chi-squared test, the trend test, and a robust test. For a continuous trait, typical methods are based on a linear regression model or the analysis of variance. We illustrate how these tests can be applied using a public available R package “Rassoc” and some existing R functions. Guidelines for choosing these test statistics are provided.
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References
Sasieni PD (1997) From Genotypes to Genes: Doubling the Sample Size. Biometrics 53: 1253–1261
Freidlin B, Zheng G, Li Z, Gastwirth JL (2002) Trend tests for case–control studies of genetic markers: power, sample size and robustness. Hum Hered 53: 146–152. (Erratum (2009) 68: 220)
Zang Y, Fung WK, Zheng G (2010) Simple algorithms to calculate asymptotic null distributions of robust tests in case–control genetic association studies in R. J Stat Softw 33(8): 1–24
The Wellcome Trust Case Control Consortium (WTCCC) (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661–678
Gastwirth JL (1966) On Robust Procedures. J Am Stat Assoc 61: 929–948
Gastwirth JL (1985) The Use of Maximin Efficiency Robust Tests in Combining Contingency Tables and Survival Analysis. J Am Stat Assoc 80: 380–384
Zheng G, Freidlin B, Gastwirth JL (2006) Comparison of robust tests for genetic association using case–control studies. In: Rojo J (ed) Optimality: The Second Eric L. Lehmann Symposium, IMS Lecture Notes-Monograph Series, Institute of Mathematical Statistics, Beachwood, Ohio
Li QZ, Zheng G, Li Z, Yu K (2008) Efficient approximation of P-value of the maximum of correlated tests, with applications to genome-wide association studies. Ann Hum Genet 72: 397–406
Joo J, Kwak M, Chen Z, Zheng G (2010) Efficiency robust statistics for genetic linkage and association studies under genetic model uncertainty. Stat Med 29: 158–180
Kuo CL, Feingold E (2010) What's the Best Statistic for a Simple Test of Genetic Association in a Case–control Study? Genet Epidemiol 34: 246–253
Zheng G, Joo J, Tian X, Wu CO, Lin J-P, Stylianou M, Waclawiw MA, Geller NL (2009) Robust genome-wide scans with genetic model selection using case–control design. Stat Its Interface 2: 145–151
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Zheng, G., Xu, J., Yuan, A., Gastwirth, J.L. (2012). Single Marker Association Analysis for Unrelated Samples. In: Elston, R., Satagopan, J., Sun, S. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 850. Humana Press. https://doi.org/10.1007/978-1-61779-555-8_18
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DOI: https://doi.org/10.1007/978-1-61779-555-8_18
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