Integrated Molecular Analyses of Biological Samples on a Bead-Based Microarray Platform

Molecular analyses of biological samples have traditionally been pursued in parallel, with those researchers studying genetic diversity having few technical approaches in common with those studying gene expression. Increasingly, scientists recognize the importance of integrating analytical technologies to further research, particularly into emerging fields such as epigenetics and the genetics of gene expression. In this chapter, we describe a suite of applications that take advantage of the Illumina® bead-based microarrays, all of which are read out on a single analytical instrument. The integration of whole genome genotyping, high throughput focused genotyping, whole transcriptome expression profiling, focused expression profiling of fresh or preserved tissues, allele-specific expression profiling and DNA methylation assays on the BeadArray™ Reader allows researchers to expand their perspectives, from whole genomes to single bases, from genetics to expression and on to epigenetics.