4 Genetic association studies

Genetic association studies aim to identify genetic variants that explain subject differences in qualitative or quantitative traits. Genetic variants may include SNPs, CNVs, mosaicisms or polymorphic inversions, which can be obtained from SNP array data. In this chapter, we thoroughly discuss SNP association studies. We explain the different genetic models to be used in single SNP associations and how they are applied in a massive univariate testing when several SNPs are analyzed. Relating the simultaneous analysis of multiple SNPs, we discuss haplotype and genetic scores associations. We then move to the analysis of genome-wide association studies, where high-dimensional genomic data is treated. Issues concerning quality control of SNPs and individuals are discussed, as well as association tests and possible sources of confounding such as population stratification. We finish SNP analyses with tools that help to interpret results.

The R code to reproduce the results and figures of this chapter can be found here.