2 Comparative genomic hybridization analysis using metaphase or microarray slides

Publisher Summary This chapter provides an overview of some of the comparative genomic hybridization (CGH) methods that are used in cytogenetic and genomics laboratories. It also discusses their usefulness for genome-wide analysis of chromosomal imbalances in the neuroblastoma cell line NUB7. The innovation of CGH analysis has allowed the identification of copy-number changes in a wide range of tumor samples and cell lines. This has greatly simplified the study of many tumors for which obtaining metaphase chromosome or interphase nuclei is technically challenging. The technique of “array CGH” has been developed, which combines the examination of chromosome changes with a similar microscope slide substrate platform to that used for microarray expression analysis. For array CGH, well-defined arrayed sequences of DNA have replaced the metaphase chromosomes as the hybridization targets on glass slides. The advantage of this approach is that it enables the researcher to quantitatively measure DNA copy-number changes at high resolution and use in silico analysis to accurately map them directly to chromosomal locations.