Using DNA microarrays to study natural variation

The emerging field of genomics examines the relationship between genetic and phenotypic variation by describing and analyzing patterns of natural variation on a genome-wide scale. In this endeavor, an important tool is the use of microarrays, which enable simultaneous screening of thousands of assays. Microarrays were originally designed for the detection of differences between samples and are thus ideally suited to high-throughput studies of natural variation. Novel microarray platforms enable the high throughput survey of variation at multiple levels, including DNA sequences, gene expression, protein binding, and methylation. However, most microarray data analysis tools, notably normalization methods, were developed for experiments in which only few features differed between samples. In studies of natural variation, this assumption does not always hold, raising a number of new challenges.