Screening for genomic rearrangements is a fundamental task in the genetic diagnosis of many inherited
disorders including cancer-predisposing syndromes. Several methods were developed for analysis of structural
genomic abnormalities, some are targeted to the analysis of one or few specific loci, others are designed to
scan the whole genome. Locus-specific methods are used when the candidate loci responsible for the specific
pathological condition are known. Whole-genome methods are used to discover loci bearing structural
abnormalities when the disease-associated locus is unknown. Three main approaches have been employed for
the analysis of locus-specific structural changes. The first two are based on probe hybridization and include
cytogenetics and DNA blotting. The third approach is based on PCR amplification and includes microsatellite or
single nucleotide polymorphism (SNP) genotyping, relative allele quantitation, real-time quantitative PCR, long
PCR and multiplex PCR-based methods such as multiplex ligation-dependent probe amplification and the
recently developed nonfluorescent multiplex PCR coupled to high-performance liquid chromatography analysis.
Whole-genome methods include cytogenetic methods, array-comparative genomic hybridization, SNP array
and other sequence-based methods. The goal of the present review is to provide an overview of the main
features and advantages and limitations of methods for the screening of structural genomic abnormalities
relevant to oncological research
