Several human diseases are associated with chromosomal abnormalities including germline alterations leading to developmental defects and somatic alterations leading to cancer. Originally, the diagnosis of such defects has been carried out by cytogenetic karyotype analysis using chromosome banding techniques, more recently, molecular cytogenetic analysis has been developed with advances in fluorescence in situ hybridization (FISH) based technology allowing even more refined identification of the chromosomal defects underlying the specific phenotypes. Characterization of the defects at the molecular level using classic molecular biology approaches (such as PCR, cloning, sequencing or Southern blotting hybridization) can be laborious and time consuming. Recent developments in microarray technology have allowed the study of some chromosomal aberrations with a relatively easy and high-throughput molecular biology hybridization-based approach (for review see (1)). This new approach has been called ‘molecular karyotyping’, or ‘segmental aneuploidy profiling’, a descriptive term that is in line with the lack of structural information in the data generated using microarray platforms (2). Several oligonucleotide array platforms originally developed for genotyping have also been used for copy number analysis (3–9) and oligonucleotide arrays have been
