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Monday, June 11

1:30 pm Short Course Registration

2:00- 5:00 Short Course One

The Diagnostic Odyssey for Genome Sequencing 

The move to push genome sequencing into routine clinical practice requires arguably as much skill in navigating bureaucracy as mapping and interpreting base pairs. This short course provides practical information on crafting clinical sequencing and analysis pipeline strategies while navigating the route of CAP and CLIA certification by those who have sailed through these uncharted waters.

2:00 Chairperson's Opening Remarks

Mary Ann Brown, Exective Director, Conferences, Cambridge Healthtech Institute

2:10 CLIA 101: Basic CLIA Information

Gary Yamamoto, Laboratory Consultant, United States Department of Health and Human Services (US DHHS), Centers for Medicare and Medicaid Services (CMS)

The Clinical Laboratory Improvement Amendments of 1988 (CLIA) requires all clinical laboratories be certified by the US Department of Health and Human Services, Centers for Medicare & Medicaid Services (CMS).  To become certified, clinical laboratories must be in compliance with the CLIA requirements and are subject to onsite inspections.  This presentation will cover the CLIA certification process, a summary of the CLIA regulations with an emphasis on the requirements that should be considered when setting up a CLIA certified genomic laboratory, and what you could expect during a CLIA survey.

Nazneen_Aziz2:45 Development of Laboratory Standards for Next-Generation Sequencing as a Clinical Tool

Nazneen Aziz, Ph.D., Director of Molecular Medicine, Transformation Program Office, College of American Pathologists

The rapid evolution of next generation sequencing (NGS) technologies presents significant opportunities and challenges for researchers and clinicians for improving health outcomes; particularly with respect to an increased emphasis on personalized and preventive medicine.   Adoption of NGS in the clinical laboratory setting requires the adoption of many processes and procedures, such as, the analytic and clinical validation of the test, CLIA/CAP certification, standards for reference materials for proficiency testing, and questions regarding reimbursement and informed consent.  This talk will cover what is practically needed for clinical adoption of NGS such as regulatory and professional standards, development, availability, and access to reference materials, and the laboratory professional's role for ensuring high quality test results that are useful for informing clinical decision making. Dr. Aziz will focus on the laboratory accreditation standards being developed at CAP for NGS in collaboration with ACMG and AMP.

3:20 Networking Refreshment Break

Worthey_Elizabeth3:35 Implementing Tools and Platforms to Support Interpretation of Clinical Diagnostic Whole Genome Sequencing Data

Elizabeth A. Worthey, Ph.D., Assistant Professor, The Human and Molecular Genetics Center, Pediatrics, Bioinformatics, Medical College of Wisconsin 

A variety of analysis tools and pipelines are required to support the clinical interpretation of clinical diagnostic whole genome sequence data.  Tools for data tracking, pipelines for tertiary sequence analysis providing functional data for clinical interpretation of variants, tools to identify likely deficiencies or limitations in the data, platforms to integrate and perform QA on disparate data types, systems to hold, organise, and query vast quantities of reference data, and tools to support clinicians and provide visualisation to increase efficiency and effectiveness are all required for successful clinical implementation of WGS. This presentation will cover all of these aspects, with guidelines and findings gleaned from 18 months of running this type of program at the Medical College of Wisconsin: Dr. Worthey will focus on the tools and systems required, the possible pitfalls and potential solutions in this type of analysis, and the process of implementing these tools and pipelines within a CAP and CLIA environment.

4:10 Panel Discussion

4:45 Short Course Wrap-Up

5:00 End of Short Course One


5:00 Shared Dinner for Short Courses One and Two 

4:30 pm Short Course Registration

5:30-8:30 Short Course Two

6:00-6:30 Early Main Conference Registration


The Saga of Genomic Interpretation for Physicians, Payers, Patients 

To succeed, clinical genome sequencing must have the ability to enhance medical decision making. Primary care physicians are often on the front line of responding to "what does this mean/what do I do?" questions. Their informed response is a saga of detailed reports including 1) physicians who order the genomic test 2) laboratory testing personnel who run the test and generate the data 3) bioinformaticists who prepare reports by aligning, annotating, and analyzing the genomic data 4) molecular pathologists who interpret the data and confirm clinical relevance 5) physicians who communicate results back to the patients 6) genetic counselors who advise patients and 7) patients who respond to treatment. Step by step informed decisions will lead to the success of the clinical genomics saga.

5:30 Chairperson's Opening Remarks

Mary Ann Brown, Exective Director, Conferences, Cambridge Healthtech Institute

Ashley_Euan5:40 Clinical Interpretation of Whole Genome Sequencing

Euan Ashley, Ph.D., Assistant Professor, Cardiovascular Medicine, Stanford University School of Medicine

The cost of human genome sequencing has fallen significantly and the availability of such information to the practicing clinician is near term. We have recently developed a pipeline for the analysis of personal genomes suitable for health-care applications. In this talk, I will provide examples of the application of whole genome sequencing to the care of patients and families.

Levin_Elissa6:15 Delivering the Message: Translating Complex Genomic Data for Providers and Patients

Elissa Levin, Vice President, Genomic Services, Navigenics, Inc.

One of the greatest challenges we face in the era of personalized medicine is how to deliver complex genomic data to both providers and patients in a manner that is accessible, understandable, and current. Navigenics, a personalized genomic testing service that has offered testing services through a dynamic reporting and educational platform for the past five years, focuses on clinically relevant testing to inform clinical decision-making and motivate behavior change. I will review our experience with physicians and patients, as well as the inclusion of genetic counseling to facilitate the integration of genomic data into clinical care.

6:50 Networking Refreshment Break

Smith_David7:05 Implementing Next-Generation Sequencing at the Mayo Clinic: The Coming Revolution!

David I. Smith, Ph.D., Professor, Department of Laboratory Medicine and Pathology; Chairman, Technology Assessment Group, Center for Individualized Medicine, Mayo Clinic

I am going to review the recent developments in Next-Generation sequencing that have resulted in dramatic increases in sequence output. As the cost for full genome sequencing continues to drop it will herald a revolution in the practice of medicine. These technologies can be used for so much more than whole genome sequencing. I will then discuss how the Mayo Clinic is approaching these technologies and the development of molecular tests based upon Next-Generation sequencing. I will finally discuss how we are setting up the necessary facilities to both do Next-Generation sequencing and to analyze the resulting data.

                 7:40 A Pilot Study on Interpretation, Attitudes and Behavioral Impact of Personal Genomes in Knowledgeable Professionals

Francisco De La VegaFrancisco M. De La Vega, D.Sc., Department of Genetics, Stanford University School of Medicine

We are studying the perceptions, behavioral changes, and the genome interpretation capabilities of a group of highly motivated knowledgeable professionals in genetics, by sequencing their genome and providing back both the raw data and interpretation on medically relevant variants.  I will present current results of this study focusing on the design and informed consent procedure, as well as the lessons learned from various genome interpretation platforms that we provided to the participants.


8:15 Short Course Wrap-Up

8:00 End of Short Course Two