The ability of chips to detect other types of variations in the genome, such as copy number variations and structural rearrangements, is also quite good. Chips designed to detect structural changes are rapidly supplanting traditional karyotyping techniques as the first line laboratory investigation for children with developmental and congenital abnormalities.13 Another clinical use of gene chips is for expression profiling.14 In this application, RNA is harvested from a sample (a tumor, for example), processed, and incubated with the chip. The location of binding in the microarray provides an idea of the type of RNA expressed and the signal intensity at the binding site provides a measure of the expression level of that particular RNA species. This type of analysis can give insights into gene expression patterns in healthy or diseased tissues, as well as the genome’s response to environmental influences including medications. Patterns of gene expression have proven to be useful guides for prognostication and treatment selection; examples include the FDA-approved MammaPrint® and Oncotype DX™ assays for prognosis and treatment selection in breast cancer.15
