Balkan Journal of Medical Genetics

ARRAY COMPARATIVE GENOMIC HYBRIDIZATION: A NEW GENOMIC APPROACH FOR HIGH-RESOLUTION ANALYSIS OF COPY NUMBER CHANGES
Dimova Iv
*Corresponding Author: Dr. Ivanka Dimova, Department of Medical Genetics, Medical University Sofia, 2 Zdrave str, 1431 Sofia, Bulgaria; Tel.Fax: +359-2-952-03-57; E-mail: idimova73@yahoo.com
page: 11

INTRODUCTION

A variety of chromosomal aberrations that underlie the development and progression of cancer and genetic pathways defined at the chromosomal level, are mirrored by genetic changes at the level of the gene [1]. Comparative genomic hybridization (CGH), a molecular cytogenetic technique that detects and maps changes in copy number of DNA sequences, has been widely used in dissecting the molecular complexity of chromosomal changes in solid tumors [2]. In CGH, differentially labeled total genomic DNA from a “test” and a “reference” cell population are co hybridized to normal metaphase chromosomes using blocking DNA to suppress signals from repetitive sequences. The resulting ratio of the fluorescence intensities at a location on the “cytogenetic map”, provided by the chromosomes, is approximately proportional to the ratio of the copy numbers of the corresponding DNA sequences in the test and reference genomes. The use of metaphase chromosomes, however, limits detection of events, involving small regions of the genome, resolution of closely spaced aberrations and linking ratio to genomic/ genetic markers. Therefore, more laborious locus-by-locus techniques have been required for higher resolution studies. Hybridization to an array of mapped sequences instead of metaphase chromosomes could overcome the limitations of conventional CGH if adequate performance could be achieved. Copy number would be related to the test/reference fluorescence ratio on the array targets, and genomic resolution could be determined by the map distance between the targets, or by the length of the cloned DNA segments. Microarray-based formats for CGH [array comparative genomic hybridization (aCGH)] are being widely used in preference to chromosome-based CGH [3,4]. Conventional CGH has a limited resolution and can only detect losses of ~10 Mb or greater. High-level amplifications have a maximum resolution of 3 Mb. The resolution of CGH has been improved dramatically by replacing the metaphase chromosomes as the hybridization target with mapped and sequenced clones [bacterial artificial chromosomes (BAC), bacteriophage P1 genomic library-derived artificial chromosomes (PAC) and cosmids] arrayed onto glass slides [3-6]. The availability of the draft human genome sequence has further directed aCGH for gene discovery. This means that the individual clones which define regions of gain or loss on the array can be linked to the human genome sequence, and a list of candidate genes generated directly and immediately.

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