Disrupting Cytogenetics in the Clinic
To select the right treatment for each cancer patient, we need fast, accurate and cost-effective ways to characterize tumors. Now, with newly developed algorithms and protocols, mate pair sequencing could well be the tool we’ve been seeking.
George Vasmatzis |
The entry of next-generation sequencing (NGS) into clinical practice has been disruptive. We can now analyze many more samples, with much less money, and in more depth than ever before, allowing us to comprehensively interrogate the entire genome of cancer cells. In the past, we could only assess one known gene at time, but now NGS allows us to look at the entire genome in a single assay – completely changing how we do translational research and how we will do clinical genomic testing.
Traditionally, we have taken a bottom-up approach in biomarker discovery. Basic scientists look at an interesting pathway in the cell that may be associated with tumor behavior. They find a limited number of genes or proteins related to that pathway, and study them to find out how they work, and whether they might have potential as biomarkers. Along with John Cheville, I direct the Biomarker Discovery Program at the Mayo Clinic’s Center for Individualized Medicine. Here, rather than starting from a gene or protein of interest, we start with a practical clinical question that fills a physician and patient need, and aim to identify a biomarker and develop a test to answer that clinical need. We refer to this process as product-driven biomarker discovery. Economically, we believe this makes a lot of sense – the clinical need dictates the experimental design, validation and assay development, rather than a more random approach.
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