An introduction to the discovery and analysis of genotype-phenotype associations

This chapter presents an introduction to genomic data and approaches to biomarker discovery: DNA variation markers and genome-wide association analysis. It will introduce fundamental concepts, such as linkage disequilibrium, the Hardy-Weinberg equilibrium and genetic interactions. The characteristics of the data and technical requirements will be discussed. This will include discussions on recent advances in cardiovascular and cancer research, concentrating on: (a) biomedical findings and clinical applications, (b) statistical and data mining methodologies applied, and (c) strengths and limitations. Chapter 9 will offer additional information on databases and software relevant to genome-wide association studies.

4.1 Introduction: sources of genomic variation

Alleles and genotypes represented in statistically detectable high rates in a population sample may be seen as factors that confer greater susceptibility to a particular disease or clinical response. Moreover, these loci may be strongly associated with other (phenotypically-neutral) loci, that is in linkage disequilibrium, which may also be over-represented in the population sample. Thus, one of the main objectives of genotype-phenotype association studies is to identify statistically detectable differences between phenotype-specific groups of individuals (e.g. between cases and controls) on the basis of their genotypes (Li, 2008). In recent ...

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