Making the leap from sequence data to actionable targets in clinical oncology
By Sara Cassidy, M.S., Ph.D.
The ever-shrinking cost of DNA sequencing improves accessibility for an increasing number of people and, importantly, for the diagnosis and treatment of disease. This is particularly salient in cancer genetics, as cancer is often the result of mutation in not one gene, but many. Moreover, personalized genomics is the foundation of precision medicine; however, having the DNA sequence in hand is only half of the equation. Effective interpretation of that sequence, and identification of causative and actionable mutations in disease states, is still a major hurdle to the delivery of personalized genomics. In other words, what good is cheap genome sequencing if you can’t make good on the resulting data?
A recent publication by the Clinical Genomics group at The Jackson Laboratory for Genomic Medicine in the journal Human Genomics is bridging this gap by building a database of clinically actionable variants in cancer (the JAX Clinical Knowledgebase, JAX-CKB) to support the JAX Cancer Treatment Profile (JAX-CTP). Here is how it works: A patient’s physician submits a sample of tumor or tissue for analysis using the JAX-CTP, which is a flexible sequencing platform for cancer-associated genes and gene fusions. The cancer-linked variant results from the JAX-CTP are then fed to the JAX-CKB, which identifies patient-specific therapeutic strategies and potential treatment approaches, including current clinical trials. The JAX-CKB pulls data from clinical literature, clinicaltrials.gov and other sources. The output is an easy-to-interpret clinical report linking mutations with specific therapies and current trials. The relatively quick turnaround time—14 days from the receipt of tumor sample—allows the JAX-CKB to have real relevance in patient’s therapy strategies.
Although the JAX-CKB is currently proprietary and largely manually curated, Susan Mockus, Ph.D., manager of clinical analytics & curation, hopes that sharing methods for the pipeline will foment improvements to this strategy and ultimately better outcomes for patients.
The paper, titled “The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies,” is freely available through BioMed Central and found here.