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.

Detailed Agenda:

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 Developing Liquid Biopsy Applications; Key Considerations in Preanalytical Phases

Greg Jones, Senior Director of Strategic Collaborations & Technical Affairs, Inivata

The collection, transport and storage of blood and plasma require careful consideration when developing liquid biopsy applications. As the promise of liquid biopsy is fulfilled and more options are available for testing, it is critical to understand why different methods have different performance characteristics. The link between assay performance characteristics and preanalytical variables will be discussed.  Real world examples of how optimization of performance and quality control are highly dependent on sample collection, transport and storage will be provided. Key considerations for analytical validation (AV) and clinical validation (CV) will also be discussed.

12:50 pm Interactive Q&A with Instructors and Participants

1:00 Close of Short Course

Instructors:

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.

Greg Jones, Senior Director of Strategic Collaborations & Technical Affairs, Inivata

Greg Jones is currently an employee of Inivata, Inc where he is responsible for coordinating external strategic collaborations and is the technical subject matter expert for the company.  Greg has 34 years of experience as the project lead in the development of IVDs including multiple BLA, PMA, 510K and LDT assays.  In his career he has been responsible for assuring that the assays developed meet regulatory requirements for satisfactory validation and transfer to manufacturing or to the testing laboratory.  He worked at MDxHealth, BioMerieux and Organon Teknika in product development and management roles.

1:00 - 1:30 Lunch for Short Course Participants

MONDAY, JUNE 17 | 1:30 – 4:30 PM

1:00 - 1:30 Lunch for Short Course Participants

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

Detailed Agenda:

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

Instructors:

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.

Christina Lockwood, 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, PhD, 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.