clinically relevant events such as the FIP1L1-PDGFRA deletion on chromosome 4q12 in myeloid neoplasms, unusual or multi-partner rearrangements, and variants present in less than 5% of cells are generally not identified by conventional cytogenetics (4–6). Another major limitation of conventional cytogenetics is the requirement for cultured metaphase cells, which are generally not obtainable in solid tumors. Fluorescence in situ hybridization (FISH) offers considerable advantages over conventional cytogenetics, including increased resolution, the ability to test fixed interphase cells, faster turnaround time, and greater sensitivity. For solid tumors, FISH is often the method of choice for the detection of recurrent mutations, such as ALK rearrangements in lung cancer, MYCN amplification in neuroblastoma, and 1p/19q deletions in oligodendrogliomas (7–9). While FISH offers improved sensitivity compared with that of conventional cytogenetics, the evaluation of multiple loci requires multiple probes and FISH assays to be run, increasing the complexity of testing. DNA microarray technology has proved to be another reliable clinical method for the detection of structural variation, especially CNV and loss of heterozygosity (LOH). However, unlike FISH, DNA microarrays are unable to detect balanced translocations (10,11).
