ABSTRACT
This chapter discusses single nucleotide polymorphism (SNP) association studies. It explains 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, the chapter also discusses haplotype and genetic scores associations. It examines the analysis of genome-wide association studies, where high-dimensional genomic data is treated. The chapter describes issues concerning quality control of SNPs and individuals, as well as association tests and possible sources of confounding such as population stratification. It illustrates how to perform SNP association analyses and single SNP association analyses, multiple SNPs analyses, environmental interactions and genome-wide association analyses. The chapter explores quality control, population stratification and multiple comparisons issues. A SNP is a categorical variable that encodes one of three possible genotypes per individual at a given genomic locus.
