Analysis of extended genomic rearrangements in oncological research.

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