@article{miclaus_wolfinger_czika_2009, title={SNP Selection and Multidimensional Scaling to Quantify Population Structure}, volume={33}, ISSN={["1098-2272"]}, DOI={10.1002/gepi.20401}, abstractNote={AbstractIn the new era of large‐scale collaborative Genome Wide Association Studies (GWAS), population stratification has become a critical issue that must be addressed. In order to build upon the methods developed to control the confounding effect of a structured population, it is extremely important to visualize and quantify that effect. In this work, we develop methodology for single nucleotide polymorphism (SNP) selection and subsequent population stratification visualization based on deviation from Hardy‐Weinberg equilibrium in conjunction with non‐metric multidimensional scaling (MDS); a distance‐based multivariate technique. Through simulation, it is shown that SNP selection based on Hardy‐Weinberg disequilibrium (HWD) is robust against confounding linkage disequilibrium patterns that have been problematic in past studies and methods as well as producing a differentiated SNP set. Non‐metric MDS is shown to be a multivariate visualization tool preferable to principal components in conjunction with HWD SNP selection through theoretical and empirical study from HapMap samples. The proposed selection tool offers a simple and effective way to select appropriate substructure‐informative markers for use in exploring the effect that population stratification may have in association studies. Genet. Epidemiol. 33:488–496, 2009. © 2009 Wiley‐Liss, Inc.}, number={6}, journal={GENETIC EPIDEMIOLOGY}, author={Miclaus, Kelci and Wolfinger, Russ and Czika, Wendy}, year={2009}, month={Sep}, pages={488–496} }
 @article{czika_weir_2004, title={Properties of the multiallelic trend test}, volume={60}, ISSN={["0006-341X"]}, DOI={10.1111/j.0006-341X.2004.00166.x}, abstractNote={Summary.  Disease genes can be mapped on the basis of associations between genetic markers and disease status, with the case–control design having the advantage of not requiring individuals from different generations. When the marker loci have multiple alleles, there has been debate on whether the power of tests for association increases or decreases. We show here that the multiple‐allele version of Armitage's trend test has increased power over the two‐allele version under the requirement of equifrequent alleles, but not in general. The trend test has the advantage of remaining valid even when the sampled population is not in Hardy–Weinberg equilibrium. A departure from Hardy–Weinberg means that association tests depend on gametic and nongametic linkage disequilibrium between marker and disease loci, and we illustrate the magnitude of these effects with simulated data.}, number={1}, journal={BIOMETRICS}, author={Czika, W and Weir, BS}, year={2004}, month={Mar}, pages={69–74} }
 @misc{czika_berry_2002, title={Using all alleles in the multiallelic versions of the SDT and combined SDT/TDT}, volume={71}, number={5}, journal={American Journal of Human Genetics}, author={Czika, W. and Berry, J. J.}, year={2002}, pages={1235–1236} }