The costs of individual genome sequencing are falling rapidly but are still a long way from the goal of a $1000 genome (Service, 2006). As an interim step, microarrays have made possible parallel genotyping of a million SNPs, the most common type of DNA polymorphism, as well as quantifying a million non-polymorphic DNA sequences useful for detecting CNVs, for less than $500. A microarray is a slide the size of a postage stamp that is dotted with short single-stranded DNA sequences called probes. It detects SNPs in the usual way: Fluorescently labelled single-stranded DNA from an individual is allowed to hybridise with a probe which will only happen if there is an exact match. The critical difference with microarray analysis is that an individual’s entire genome is first chopped into small pieces, amplified (genome-wide amplification) and labelled with a fluorescent tag, so that the individual’s genotypes can be determined simultaneously for millions of SNPs. Not only can microarrays be used to probe the entire genome, they can also be used to assess gene expression levels and to map ncRNA by
