Pre-Conference Lunch Short Courses
MONDAY, June 17 | 10:00 AM – 1:00 PM
SC1: Preanalytical Variables: Effects of Blood Collection and Processing Procedures for Liquid Biopsies
Preanalytical variables are essential to consider when using liquid biopsies, as factors such as collection tubes, processing procedures, and extraction methods can affect yields and detection of low frequency variants. This is especially important in
cancer studies as detection of variants can have important clinical implications for patients. This course will cover the optimization and best practices of Liquid Biopsy.
Topics to be covered:
- The importance of considering preanalytical variables
- How to deploy controls and error correction to minimize physical and in silico inaccuracies
- Clinical and laboratory SOPs & workflows for specimen acquisition and processing
- Considerations when choosing between options
Who should attend this course:
Researchers and lab managers from pharma, biotech and academia working in fields such as molecular oncology, cancer biomarkers, molecular diagnostics, translational research, genetics, and research and development, who have an interest in preanalytical variables and biospecimen repositories.
10:00 am Welcome and Introductions
10:05 Why Preanalytical Variables Matter
Caitlin Stewart, PhD, Postdoctoral Research Fellow, Genomics, Memorial Sloan Kettering Cancer Center
This talk will explore processing procedures and extraction methods, best practices for collecting and processing cell-free DNA and cell-free RNA, and considerations when choosing between options.
11:20 Refreshment Break
11:35 Creating and Maintaining a Biospecimen Repository
Chih Long Liu, PhD, Research Associate, Division of Immunology and Rheumatology, Stanford University School of Medicine
A biospecimen repository comprises an essential component of many clinical studies. Successful management of one requires a well-designed infrastructure for specimen acquisition, processing, storage and retrieval, combined with effective training of personnel in the appropriate workflows and data management. Many groups setting out to build one underestimate the logistical complexity involved. Here, we will cover the basic components of a biospecimen repository and discuss logistical considerations in its deployment.
12:50 pm Interactive Q&A with Instructors and Participants
1:00 Close of Short Course
Caitlin Stewart, PhD, Postdoctoral
Research Fellow, Genomics, Memorial Sloan Kettering Cancer Center
Caitlin Stewart is a Postdoctoral Research Fellow working in Dana Tsui’s lab at Memorial Sloan Kettering Cancer Center. She works on technical development and optimization of sequencing and PCR based methods for cell-free (cf) nucleic acids and
translation of cfDNA assays for use in the clinic. She is particularly interested in understanding the underlying biology of cfDNA and exploring ways we can use this information to improve assays and ultimately, patient care. Caitlin did her PhD at
the Wellcome Trust Sanger Institute focusing on transcriptomics and small RNA and is using her knowledge of RNA methodology to explore and develop cfRNA assays.
Chih Long Liu, PhD, Research Scientist, Department of Medicine/Oncology, Stanford University School of Medicine
I am currently a research scientist and laboratory manager for Dr. Alizadeh in the Department of Medicine/Oncology at Stanford and maintain a secure LIMS that I have built for accrual, retention, and clinical annotation of the human subjects, their associated
specimens, and metadata, as well as analytical pipelines of liquid biopsies analyzed with next generation sequencing. My work and experience span numerous technological developments and their application to diverse fields, including microarray fabrication
and their use to profile an important immunological process (T cell activation), the application of protein and peptide arrays to profile the chromatin of neutrophil extracellular traps as immunogens of systemic lupus erythematosus, and development
of CIBERSORT, a highly-cited computational method for characterizing cell composition of complex tissues from their gene expression profiles. My recent work involves biomarker discovery from sequencing-based methods for the detection and analysis
of circulating tumor DNA in plasma samples from cancer patients.
1:00 - 1:30 Lunch for Short Course Participants
MONDAY, JUNE 17 | 1:30 – 4:30 PM
SC2: Advancing Liquid Biopsy Technologies from the Bench to the Clinic
This short course will provide a thorough grounding in the clinical application of the “liquid biopsy,” focusing in particular on the utility of circulating tumor DNA (ctDNA). An initial session will address the basic work in recognizing the
existence of cell free and circulating tumor nucleic acids, their significance in cancer patient care, and the recent adoption by clinical laboratories of novel ctDNA tests. This will be followed by a review from a clinical laboratory perspective
of the expectations for a robust clinical lab assay. And finally, an “in the trenches” look at adoption of patient testing in a major cancer center.
Topics to be covered:
- History of the ctDNA field
- Identify regulatory hurdles to adoption of ctDNA testing
- The pre-analytic and analytic variables important in clinical lab testing
- Understanding practical issues a lab director might face when introducing ctDNA assays
1:30 pm Welcome and Introductions
1:45 Circulating Tumor DNA in the Clinic: Background and Significance
Christopher D. Gocke, MD, Associate Professor, Pathology and Oncology; Director, Division of Molecular Pathology, Johns Hopkins University School of Medicine
2:30 Circulating Tumor DNA in the Clinic: Pre-Analytical and Analytic Best Practices
Christina Lockwood, PhD, Associate Professor, Director of Genetics and Solid Tumors Lab, Laboratory Medicine, University of Washington
3:15 Refreshment Break
3:30 Circulating Tumor DNA in the Clinic: Adoption and Case Based Lessons
Mark Routbort, MD, PhD, Professor, Department of Hematopathology, Division of Pathology/Lab Medicine, UT MD Anderson Cancer Center
4:10 Interactive Q&A with Instructors and Participants
4:30 End of Short Course
Christopher D. Gocke,
MD, Associate Professor, Pathology and Oncology; Director, Division of Molecular Pathology, Johns Hopkins University School of Medicine
Dr. Christopher Gocke is an Associate Professor of Pathology and Oncology at the Johns Hopkins University School of Medicine. He is Director of the Division of Molecular Pathology, Deputy Director of Personalized Medicine for the Department of Pathology,
and co-director of Johns Hopkins Genomics.
PhD, Associate Professor, Director of Genetics and Solid Tumors Lab, Laboratory Medicine, University of Washington
Dr. Lockwood is Director of the Genetics and Solid Tumors Laboratory and an associate professor of Laboratory Medicine at the University of Washington Medical Center. She is board-certified in clinical molecular genetics and clinical chemistry and received
her Ph.D. in Cellular and Molecular Biology at the University of Wisconsin. Dr. Lockwood completed clinical postdoctoral fellowship training at the Washington University School of Medicine in St. Louis where she was also a faculty member. Dr.
Lockwood’s clinical expertise is the application of molecular methods to advance precision medicine for prenatal screening, genetic disorders, and molecular oncology. Her research focuses on the development and implementation of innovative genomic
methods to guide patient care. She has most recently fostered clinical deployment of cell-free DNA diagnostics in pregnancy and oncology
Mark Routbort, MD, Professor, Department
of Hematopathology, Division of Pathology/Lab Medicine, 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.