SC12: Clinical Informatics: Returning Results from Big Data
Room Location: 103
Mark Routbort, MD, PhD, Director, Computational and Integrational Pathology; Associate Professor, Hematopathology; Medical Director, Laboratory Informatics, UT MD Anderson Cancer Center (AMP Informatics Subdivision Representative to the AMP 2017 Clinical Practice Committee; Member)
Somak Roy, MD, Director, Molecular Informatics, Genetics Services, & MGP Fellowship, Molecular and Genomic Pathology, University of Pittsburgh Medical Center (AMP Member)
Detailed agenda:
5:30 - 6:40 Supporting Precision Oncology: Data, Workflow, Software
Mark Routbort, MD, PhD, Director, Computational and Integrational Pathology; Associate Professor, Hematopathology; Medical Director, Laboratory Informatics, UT MD Anderson Cancer Center (AMP Informatics Subdivision Representative to the AMP 2017 Clinical Practice Committee; Member)
The proliferation of biomarker-based therapy and "basket" clinical cancer trials reflects a growing need to support longitudinal genomic profiling and matching of patients to a large set of pathway-based therapies. Historically, many tumor characterization data elements are reported in unconstrained free-text documents, providing a barrier to scalable decision support. In addition, the common use of distinct methodologic approaches ranging from immunohistochemistry to direct nucleic acid sequencing to measure the same underlying pathway alterations provides deep challenges to informatics solutions. This session will compare and contrast some of the different approaches to implementing or deriving structured genomic and biomarker data, drawing on experience from the NCI-MATCH precision oncology trial and the heterogeneous data environment at UT MD Anderson.
6:40 - 7:00 Dinner
7:00 - 8:10 Genomic Data Visualization: Potential Applications in Clinical Laboratory Practice.
Somak Roy, MD, Director, Molecular Informatics, Genetics Services, & MGP Fellowship, Molecular and Genomic Pathology, University of Pittsburgh Medical Center (AMP Member)
Data visualization is a well-known approach for exploring large datasets to gain meaningful insights and direct further analysis. More recently, it has been profoundly utilized in biomedical research for exploring results of petabyte-scale genomic analyses. However, this powerful approach is under-utilized in routine clinical practice in molecular pathology laboratories that routinely generate large volumes of complex datasets. This talk will introduce some key concepts in data visualization, current technologies and how this approach can allow better utilization of laboratory-generated data for result interpretation, laboratory quality assurance and clinical assay development using simple and illustrative examples.
8:10 - 8:30 Q & A
Meet the instructors:
Mark Routbort, M.D., Ph.D., Director, Computational and Integrational Pathology; Associate Professor, Hematopathology; Medical Director, Laboratory Informatics, UT MD Anderson Cancer Center
Dr. Mark Routbort is a practicing molecular pathologist and bioinformatician at the University of Texas MD Anderson Cancer Center, where he develops and supports the computational pipelines and reporting tools for next generation sequencing in the clinical Molecular Diagnostics Laboratory. Receiving a Master's degree in Biochemistry and Molecular Biology from the University of Chicago, and later his MD and PhD degrees at Duke University, he joined the faculty at MD Anderson in 2004, where he has focused his informatics efforts on initiatives directed at improving pathologist and lab workflow, and on improving the generation, storage, reporting, and retrieval of pathology and laboratory data. In these roles, he publishes and maintains several open source pathology informatics-related toolsets (http://github.com/routbort ). He currently serves as Director of Computational and Integrational Pathology for the Division of Pathology and Laboratory Medicine, facilitating the transactional and integrational use of genomic data both internally and with large scale multi-institutional collaborations like NCI-MATCH and AACR Project GENIE.
Somak Roy, MD, Director, Molecular Informatics, Genetics Services, & MGP Fellowship, Molecular and Genomic Pathology, University of Pittsburgh Medical Center (AMP Member)
Somak Roy, MD., is Assistant Professor of Pathology at the University of Pittsburgh Medical Center (UPMC). He serves as the Director of Molecular Informatics and genetics Services at the Division of Molecular and Genomic Pathology at UPMC. Dr. Roy is a board-certified molecular and anatomic pathologist. His clinical and translational work focuses on the following; 1) Use of modern computational infrastructure and innovative software technology for high-throughput sequence analysis, genomic data visualization, and optimizing molecular laboratory workflow. 2) molecular characterization of urothelial carcinoma to identify clinically relevant, theranostic biomarkers. Since 2014, he has been a member of Informatics Subdivision in the Association of Molecular Pathology (AMP). He served as a representative to the Clinical Practice Committee from 2014-2016 and currently to the Program Committee. Dr. Roy is chaired the AMP workgroup that developed the guidelines for validation of clinical NGS bioinformatics pipeline.
Back To Short Courses