Dartmouth Cancer Center researchers develop process for quicker gene analysis

Precision medicine is a rapidly advancing field that is unlocking potential therapies for a variety of diseases and conditions—particularly cancer—by looking for mutations in a patient’s genetic code. Identifying those mutations creates the opportunity for personalized treatment, specific to the patient and the condition. But with more than 20,000 genes in the human genome, analyzing the mountains of data produced by genetic sequencing is time consuming.

Now, researchers at the Dartmouth Cancer Center have developed computer algorithms to speed up that analysis. “We have implemented a unique system that combines lab testing and data analysis in a timely fashion that will have a direct impact on patient care,” says by Parth S. Shah, MD, Director of Genomic Informatics in the Center for Clinical Genomics and Advanced Technology (CGAT) at the Dartmouth Hitchcock Medical Center, who led the team that developed the data analysis process.

Until now, molecular profiling efforts for both cancer and hereditary diseases only looked at the most commonly altered genes known to impact the diagnosis of disease and a patient’s response to therapy. “Whole exome sequencing” allows the laboratory to sequence all 20,000+ genes to get a complete look at a patient’s entire genetic code and to allow oncologists to pinpoint better treatments. However, this type of sequencing generates an enormous amount of data making it incredibly challenging to analyze.

 “Whole exome sequencing, when applied in a clinical setting, is a game changer for the entire Dartmouth Health system,” says Gregory J. Tsongalis, PhD, Medical Director of CGAT. “To the best of our knowledge, the Dartmouth Cancer Center is the only cancer center in the country routinely doing clinical whole exome sequencing on solid tumors. Other centers are doing this on a research basis only. Sequencing is being run on specific tumor types at the moment, with the future goal of running it on all cancer patients.” Tsongalis also notes that some insurance companies cover the service while others do not, but this is slowly changing.

Having a comprehensive molecular profile allows providers to select the most appropriate and best-targeted therapy for their patients. “The data we get from this sequencing will significantly advance our capabilities in precision medicine, including the identification of extremely rare genetic changes, which are not detectable by routine testing,” says Laura J. Tafe, MD, Assistant Director of CGAT and lead investigator on the somatic cancer testing whole exome sequencing project.

Tafe also directs the Dartmouth Cancer Center’s Molecular Tumor Board, a goal of which is to identify patients who may be eligible for clinical trials based on cancer sequencing data. “With whole exome sequencing we’ll be able to find more patients eligible for precision-based treatment options,” Tafe explains.

While a major focus of this effort has been on cancer, the new test is also being applied to the detection of variants associated with hereditary disease conditions. “The ability to look across the entire genome instead of just at a few genes, makes the diagnosis of complex hereditary diseases more feasible,” said Wahab A. Khan, PhD, Assistant Director of CGAT and lead investigator for the germline whole exome sequencing project. “We will play an unprecedented role in defining and detecting rare hereditary disease conditions seen in our rural population,” said Khan.

In addition, the massive amounts of data generated will allow researchers not only at Dartmouth Health, but worldwide to probe the underlying mechanisms of disease in an attempt to develop better diagnostic testing and therapeutics.

Through CGAT, the Dartmouth Cancer Center is now able to provide the most advanced, cutting-edge testing, currently available in only a handful of institutions in the world, locally at DHMC. Testing makes sure patients have the best possible chance of being matched to the most suitable treatment strategy for them.