January 6-10, 2014
Genomics Course for Pathology Trainees
We have developed a highly integrative, practical and focused approach to genomics teaching for residents and trainees in the Department of Pathology and Laboratory Medicine to be offered as a 1 week intensive program in Jan 2014. Simple genetic tests with a limited detection threshold are gradually being replaced by multiplex, deeply interrogative assays which coincide with the recent revolutions in massively parallel sequencing and advanced molecular profiling technology. This is further propelled by simultaneous ongoing discoveries of novel cancer pathway aberrations that drive the development and clinical application of novel targeted therapeutics. More questions are being asked of the pathologist and biopsied tissues are getting smaller. This course provides the residents a review and refresher of relevant topics in genomics and epigenomics followed by a survey of available clinically significant molecular diagnostic assays as well as bioinformatic tools.
Genomic medicine and lab medicine, especially pathology, are natural and symbiotic partners in the future of patient care. In many cases, molecular diagnostic assays complement rather than supplement “glass-based” pathology. For example, correct identification of tumor cells and estimation of tumor fraction facilitates downstream analysis. In an era of personalized medicine, understanding of the genomic and epigenomic makeup of a disease lesion, via the appropriate application of advanced molecular tests and bioinformatic analytic tools, represents a logical progression from special stains to epitope-specific antibodies to genetic tests, for making an accurate and informative diagnosis. We will draw from the community of local experts at UBC, the Michael Smith Genome Sciences Centre, the Centre for Disease Control and the BC Cancer Agency in the fields of molecular pathology, molecular biology, microbiology, bioinformatics and genomics to offer an immersive introductory program on current state of the art and emergent technologies and their applications.
The core competencies students will obtain and the course outline are listed below:
- Solid understanding of the concepts of human molecular biology including the human genome, resources to navigate it, the nature and extent of human genetic variation as it applied to pathology and genetic disorders
- Available and emerging molecular assays for diagnosis
- understanding the nature of the test, its limitations and assumptions for interpretation
- appreciate that specific molecular variants can lead to unique histopathology, biochemical findings, and biological behaviour with direct impact on clinical management of patients
- understand that careful evaluation of the tissue (for extraction of genetic material) and proper pathologic diagnosis are necessary prerequisites for molecular assays
- Understand qualitative differences between human genomes and prokaryotic genomes and highlight the role of genomics in the field of microbiology and infectious diseases
- Understanding the role of computation and bioinformatics in emergent assays
UBC Pathology Genomics/Bioinformatics core 2014
- Provide clinical trainees and graduate students in the Department of Pathology & Laboratory Medicine with an inclusive yet focused and practical course on molecular diagnostic assays relevant to anatomical pathology, hematopathology, medical biochemistry, medical microbiology, and neuropathology.
- Acknowledge that this is a rapidly-evolving field with constantly changing technology as well as expectations and demands from the end-users. The course will include the most up-to-date topics and will also briefly touch on issues such as ethical/medico-legal concerns (including DTC genomics such as 23andMe). However, given the limited time frame of the course these topics may be discussed in detail in subsequent lectures.
- The course will review basic concepts of molecular genetics and how aberrations in the genome/epigenome can lead to phenotypic changes from congenital malformations to cancers, liquid and solid. This is followed by survey of the available molecular diagnostic assays used to identify these changes and review of tests “on the horizon”.
- The course will devote significant amount of time and resources into survey of open source bioinformatic tools and resources and how they can be utilized in laboratory medicine – in clinical practice or as part of research project.
- Survey of relevant topics on pathogen genomics (eg. rapid identification of pathogens in an outbreak), microbiome, and liquid- based diagnostics (biochemistry) will be included.
- There will be a discussion on “careers” in molecular diagnostics with active participation by current fellows
- Highlight the local expertise and resources in advanced translational genomics to trainees and clinical staff to foster collaborations.
- Guest speaker should be experienced in advanced molecular diagnostics and highlight his/her contribution(s) to the field. Also, there should be interactions with the trainees to facilitate career development.
“The UBC Pathology Genomics Core Teaching course is a self-approved group learning activity (Section 1) as defined by the Maintenance of Certification program of the Royal College of Physicians and Surgeons of Canada.”