September 12, 2018Tanuja Koppal, PhD
Q: Can you share some details on the work that you are doing to apply clinical genomics to drive precision medicine?
A: Certainly! I’m delighted to be part of a team that is expanding precision medicine efforts at Baylor College of Medicine and the Texas Medical Center. Specifically, we are building an academic precision oncology laboratory within the Breast Center that will lead and support cutting-edge translational research, including the design and execution of clinical trials. We are utilizing a variety of core pathology and advanced molecular technologies, from next-generation sequencing to mass spectrometry, to facilitate individualized patient management plans and better define theragnostic strategies for specific patient populations, such as those who have metastatic breast cancer. Our approach affords both discovery and surveillance arms that span cancer detection, molecular profiling, and monitoring of disease. For the latter, we seek to demonstrate a substantial lead time in adaptive treatment and trial placement relative to current monitoring of disease progression.
Q: Are there new trends and technologies in genomics that you are excited about or you consider to be game-changers?
A: We are now at a point where improvement in patient outcomes will be driven in large part by the integration of complex molecular data into the clinical space, tailored to a patient’s genetic information and corresponding functional phenotype. Cancer (as with any other disease) is a dynamic process and really should be monitored as such. I know that the ability to synthesize and act on panoptic molecular consequences— genomic, proteomic, metabolomic— will be a major move forward. Add to that the network complexities that are further intertwined with the microbiome, immune response, drug history, and combination drug therapies, and much more! I am excited about the “multi-omic” approach in clinical diagnostics that we are harnessing here at Baylor College of Medicine.
In addition, the development of novel approaches to sequencing nucleic acids is gaining traction now and may help democratize sequencing ability/access, spurring further innovation in research and patient care. I’ve been fascinated with real-time, native single-molecule sequencing and its potential, once it becomes widely available.
Q: What are some of the changes that have taken place in recent years on the technical and informatics front that have enabled the growing use of genomics technologies?
A: Continuous advances in bioinformatics and big data analytics are helping tackle the problem of efficiently deciphering and interpreting the observed aberrations en masse rather than as individual components. At the very least, this should provide impetus for the design of in silico clinical trials followed by functional validations. This will help in further demonstrating clinical utility, which of course will feed demand in utilizing genomic technologies as a tool in diagnosis and management.
Q: As laboratory director in the BCM Breast Center, can you share your perspectives on some of the challenges you encounter in clinical diagnosis and therapeutic intervention?
A: There are a number of logistical and operational challenges associated with high-complexity genomic/molecular diagnostics that require close interactions between a number of vested parties at all stages. This requires a very streamlined and efficient workflow. Laboratory/assay development costs remain a concern, particularly for some very complex patient cohorts that we are supporting, such as metastatic breast cancer that requires serial monitoring. Such comprehensive testing at scale (and with much required automation) across individuals and clinical trial populations is particularly challenging and expensive, necessitating a tiered and narrowly focused approach with complementary techniques/molecular platforms supported through various grant mechanisms.
Q: What attempts are being made to tackle these issues in terms of investing in new technologies or expertise?
A: The Breast Center fosters an integrated framework between all shareholders in our precision medicine initiatives, including the following: an in-house biobank staffed with full-time research coordinators who manage patient consent and sample accruals for basic and clinical research, a dedicated genomics-molecular/core pathology lab, a mouse PDX core facility, focused resources that support biostatistics and informatics in clinical trial management, a high-performance computing center, and so forth. Of course, our collaborations extend beyond the center itself, taking advantage of expertise within Baylor, commercial entities, and surrounding institutions. Additionally, we host a monthly CME-accredited molecular tumor board meeting to discuss challenging cases. This multidisciplinary gathering highlights our expertise and workflow and has proven to be an invaluable resource in patient management and care.
Q: Any advice specifically for our readers who are lab managers in clinical genomics and diagnostics laboratories?
A: The recent advances in clinical genomics have really fostered a paradigm shift in genetic testing and personalized medicine, and it is an exciting time to be able to bring these next-generation diagnostic tools to fruition in the clinic. Particularly in academic medical centers, the formation of a close working partnership between physicians and labs to best leverage internal expertise and resources is critical.
George Miles, MD, PhD, is an assistant professor in the Department of Molecular and Human Genetics at Baylor College of Medicine, Houston, Texas. He is the laboratory director for the Precision Oncology Laboratory within the Lester and Sue Smith Breast Center/Dan L. Duncan Comprehensive Cancer Center. He completed an MD and PhD at Texas A&M University, College Station, Texas, followed by a pathology residency and fellowship at the National Cancer Institute, National Institutes of Health, Bethesda, Maryland, and a molecular genetic pathology fellowship at Washington University School of Medicine, St. Louis, Missouri. He is board-certified in anatomic and molecular genetic pathology. He is a physician scientist with expertise in cancer genomics and molecular diagnostic assay development that spans academic, government, and private industry settings and is involved in a number of ongoing clinical trials.