High-Throughput Gene Expression and Mutation Profiling: Current Methods and Future Perspectives

Following the completion of the human genome sequence at the beginning of the new millennium, a series of high-throughput methods have changed cancer research. Using these techniques, global analysis such as expression profiling could be carried out on a genomic scale. In breast cancer they led to the classification of the intrinsic subtypes, and the development of several prognostic and predictive ‘genomic tests' for patient stratification. During the last 2 years we have faced a similar dramatic revolution with the introduction of next generation sequencing (NGS). These techniques allow sequencing of the complete human exome or whole genome with a cost reduction in the order of 10,000-100,000 fold. Consequently, the number of known cancer genome sequences exploded with more than 6,000 samples, published between 2011 and 2013. These studies have led to important and surprising discoveries both for basic cancer research and clinical applications. They relate to understanding the development of cancer as well as the heterogeneity of the disease, and how to use this information to guide the development and application of therapies. Although it is foreseeable that the sequencing surveys of neoplasms will soon conclude, their introduction into clinical practice is just beginning.