Clinical OMICs - Issue 8 - (Page 8)

(continued from previous page) will soon provide oncologists with information they need to identify and utilize treatment options based on the patient's genomic profile," says Helen Fernandes, Ph.D., associate professor of pathology and laboratory medicine, Weill Cornell Medical College. Dr. Fernandes, however, adds that NGS will become established in the clinic only after certain challenges are addressed. NGS Assays "We need to understand the role of several mutations in the pathogenesis and outcomes of tumors before the information can be used for patient care," explains Dr. Fernandes. "For a start, we focus our efforts on a panel of 50 genes that could provide actionable information to our clinicians." This panel, notes Dr. Fernandes, poses a practical difficulty. It must be used with an assay sensitive enough to identify a mutation present in less than 5% of a heterogenous population of tumor cells. The most common starting material typically comes from core biopsies embedded in paraffin for preservation. "We were able to successfully use this somewhat compromised material to amplify and analyze multiple genes simultaneously," continues Dr. Fernandes. The test that has been validated in the clinical lab is able to use 10 ng of starting DNA to generate sequences covering 2,800 hotspots in the 50-gene panel. The power of this approach was demonstrated in a pilot study aiming to identify sequence variants in head and neck squamous cell carcinoma (HNSCC) with and without human papilloma virus (HPV). Surprisingly, tumors with increased HPV viral copy number are associated with better response to chemotherapy and prolonged survival. Dr. Fernandes' team utilized NGS to systematically analyze somatic variants in virus-infected and virus-free To develop a system capable of generating actionable sequencing reports for oncologists, researchers at the Mt. Sinai School of Medicine are leveraging predictive network models that can comb through vast amounts of publicly available knowledge and integrate information at the DNA, RNA, and protein levels. The researchers also build a decision tree for each FDA-approved treatment as well as drugs that have not yet been approved but appear to have potential benefits. 8 Clinical OMICs August 13, 2014 www.clinicalomics.com http://www.clinicalomics.com

Table of Contents for the Digital Edition of Clinical OMICs - Issue 8

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Clinical OMICs - Issue 8