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1.  A Bayesian approach to genetic association studies with family-based designs 
Genetic Epidemiology  2010;34(6):569-574.
For genomewide association studies with family-based designs, we propose a Bayesian approach. We show that standard TDT/FBAT statistics can naturally be implemented in a Bayesian framework. We construct a Bayes factor conditional on the offspring phenotype and parental genotype data and then use the data we conditioned on to inform the prior odds for each marker. In the construction of the prior odds, the evidence for association for each single marker is obtained at the population-level by estimating the genetic effect size in the conditional mean model. Since such genetic effect size estimates are statistically independent of the effect size estimation within the families, the actual data set can inform the construction of the prior odds without any statistical penalty. In contrast to Bayesian approaches that have recently been proposed for genomewide association studies, our approach does not require assumptions about the genetic effect size; this makes the proposed method entirely data-driven. The power of the approach was assessed through simulation. We then applied the approach to a genomewide association scan to search for associations between single nucleotide polymorphisms and body mass index in the Childhood Asthma Management Program data.
doi:10.1002/gepi.20513
PMCID: PMC3349938  PMID: 20818722
family-based association tests; Bayes factors; complex traits
2.  Using Canonical Correlation Analysis to Discover Genetic Regulatory Variants 
PLoS ONE  2010;5(5):e10395.
Background
Discovering genetic associations between genetic markers and gene expression levels can provide insight into gene regulation and, potentially, mechanisms of disease. Such analyses typically involve a linkage or association analysis in which expression data are used as phenotypes. This approach leads to a large number of multiple comparisons and may therefore lack power. We assess the potential of applying canonical correlation analysis to partitioned genomewide data as a method for discovering regulatory variants.
Methodology/Principal Findings
Simulations suggest that canonical correlation analysis has higher power than standard pairwise univariate regression to detect single nucleotide polymorphisms when the expression trait has low heritability. The increase in power is even greater under the recessive model. We demonstrate this approach using the Childhood Asthma Management Program data.
Conclusions/Significance
Our approach reduces multiple comparisons and may provide insight into the complex relationships between genotype and gene expression.
doi:10.1371/journal.pone.0010395
PMCID: PMC2869348  PMID: 20485529
3.  Recommendations for using standardised phenotypes in genetic association studies 
Human Genomics  2009;3(4):308-319.
Genetic association studies of complex traits often rely on standardised quantitative phenotypes, such as percentage of predicted forced expiratory volume and body mass index to measure an underlying trait of interest (eg lung function, obesity). These phenotypes are appealing because they provide an easy mechanism for comparing subjects, although such standardisations may not be the best way to control for confounders and other covariates. We recommend adjusting raw or standardised phenotypes within the study population via regression. We illustrate through simulation that optimal power in both population- and family-based association tests is attained by using the residuals from within-study adjustment as the complex trait phenotype. An application of family-based association analysis of forced expiratory volume in one second, and obesity in the Childhood Asthma Management Program data, illustrates that power is maintained or increased when adjusted phenotype residuals are used instead of typical standardised quantitative phenotypes.
doi:10.1186/1479-7364-3-4-308
PMCID: PMC3525193  PMID: 19706362
body mass index; confounding factors; covariate adjustment; forced expiratory volume; heritable quantitative traits

Results 1-3 (3)