Introduction

The sequencing of even a few members of a bacterial species has underlined the remarkable genetic diversity that underpins these organisms. These have suggested that in many taxa, there could be innumerable genetically unique members and that their genetic characterisation is best initiated by obtaining information on those genomic attributes that are unique to each member. However, genome sequencing using the Sanger methodology–described in the previous chapter–is expensive and time-consuming, and therefore not a practical option when it comes to sequencing ‘every’ genetically unique isolate of some relevance. However, various alternatives have been remarkably successful, and these have led to the field of ‘phylogenomics’ or ‘genomic epidemiology’.

DNA microarrays: The concept

The first approach that permits ‘phylogenomics’ is the use of DNA microarrays to probe sequence variations between different isolates.

DNA microarrays are based on the concept of hybridisation of a nucleic acid to one of complementary sequence–a fundamental principle underlying many molecular biology methods for detecting and quantifying nucleic acids of a defined sequence. These microarrays are slides containing many nucleic acid probes, allowing thousands to millions of hybridisation experiments to be run in parallel. The technology can be used to detect the presence and absence of genes or more subtle polymorphisms in a genome (comparative genome hybridisation or CGH, the subject of this chapter), calculate relative expression levels of all genes encoded in a genome and compare these levels across several conditions and genetic backgrounds (gene expression microarray), and even measure, semi-quantitatively, the levels of binding of a DNA-binding protein to various parts of the genome (chromatin immuniprecipitation chip or ChIP-chip).

Irrespective of the application, there are certain general points to be noted while analysing and interpreting microarray data. A few of these–they are not exhaustive–are as follows:

1 The general idea of a microarray: In a DNA microarray experiment, fluorescently-labelled nucleic acid sample is hybridised against unlabelled, complementary probe sequences.