Genetic association mapping at the crossroads: Which test and why? Overview and practical guidelines

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Abstract
Until about a decade ago, genetic association testing essentially meant case control association analysis using genetic markers. Concerns about population stratification propelled family‐based tests of association into widespread use and challenged the classic case control design. The literature now contains a vast collection of different family‐based methods, most of which are based on the transmission/disequilibrium test (TDT). Some methods extend the original TDT to accommodate multiallelic markers, variable pedigree constellations, multiple loci, etc. Other methods go beyond the original design of the TDT to detect genetic association via haplotype sharing. Most recently, we have witnessed a revival of case control methods that control for population stratification. The purpose of this review is to help orient readers to the rapidly developing methods of association testing and enhance their understanding of the basic principles of these approaches. We present an overview of the development of genetic association tests, with practical guidelines on which test might be the most suitable for a given study.