Comparative genomic hybridization: emphasis on use of formalin-fixed paraffin-embedded tissue

Abstract

Comparative genomic hybridization (CGH) is a DNA-based technique that allows screening of the entire genome or individual chromosomes for the detection and location of chromosomal losses and gains. It accomplishes this without the need for cell culture and can therefore be employed on a wide range of routinely available specimens including fresh tissue and cell preparations, frozen tissue and formalin-fixed paraffin-embedded (FFPE) tissue. Therefore, large numbers of formalin-fixed tumours can be screened. This may then provide data regarding chromosomal gains and losses as both diagnostic tools and as markers of tumour progression. More specific investigation of the chromosomes can then be carried out by additional techniques such as fluorescent in situ hybridization, loss of heterozygosity analysis or DNA sequencing. CGH, however, is a difficult technique to perform and this is further confounded by the use of FFPE material. We describe some of the problems associated with using paraffin-embedded tissue as a source of DNA for use in CGH.