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  • Hands-on training: Implementing NGS for Clinical Diagnostics

    Implementing Next-Generation Sequencing for Clinical Diagnostics

    Monday, June 24, 2:00-5:00 pm
    Hotel Kabuki, San Francisco, CA

    More details: http://www.clinicalgenomeconference....?id=121826#SC1

    Registration info: https://chidb.com/register/2013/clg/reg.asp

    The rapid evolution of next-generation sequencing and the resulting move into routine clinical practice requires arguably as much skill in navigating bureaucracy as mapping and interpreting base pairs. Significant challenges for clinical diagnostics include the rapid evolution of platforms, protocols, kits, and reagents as well as genome analysis, interpretation and ethics. This short course provides practical information on implementing clinical sequencing, genomic data analysis and interpretation, ethics, CLIA certification and CAP standards. This course has been created in collaboration between Cambridge Healthtech Institute and the College of American Pathologists.

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

    Instructors:

    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 PathologistsRecently, there has been a remarkable growth in the number of laboratories offering clinical tests using next-generation sequencing (NGS) technologies as well as an expansion in the volume and types of NGS clinical tests. Currently, all NGS-based clinical tests are considered to be laboratory-developed tests that must be conducted under Clinical Laboratories Improvement Act (CLIA) regulations. The College of American Pathologists (CAP) has deemed status under CMS to accredit laboratories for CAP/CLIA certification and importantly, CAP’s standards are considered to be of the highest level in the field. In 2012, CAP published its first set of standards--the CAP Checklist for NGS--that labs seeking accreditation and offering NGS-based tests need to follow. This session will cover the CAP NGS Work Group’s process and methodologies of development of standards for both the wet bench (DNA, RNA sample preparation, sequence generation) and the dry bench (bioinformatics analysis) workflows of NGS tests that include requirements for documentation, validation, data storage, quality assurance, reporting and interpretation. Dr. Aziz will also discuss CAP’s standard for noninvasive prenatal screening and proficiency tests currently under development.

    Data Interpretation and Ethics in Clinical Genomic Sequencing
    Wayne W. Grody, M.D., Ph.D., Professor, Medical Genetics and Molecular Diagnostics; Director, Clinical Genomics Center, School of Medicine, University of California, Los Angeles
    The advent of massively parallel or “next generation” DNA sequencing has finally brought into reach the long-anticipated “Thousand Dollar Genome,” or the ability to sequence an individual’s entire genome at reasonable cost. Many are predicting that this achievement will supplant the single-gene genetic testing that largely comprises molecular medicine today. But if so, how will we handle the massive amounts of data produced, distinguish benign variants from pathologic mutations, and convey their clinical implications to doctors and patients? This presentation will discuss these new challenges in test interpretation and genetic counseling, current controversies over return of incidental findings, new approaches to informed consent, and the impacts of gene patents on test access.

    The Impact of Next-Generation Sequencing on Diagnosing Inherited Disorders
    Karl V. Voelkerding, M.D., Professor of Pathology, University of Utah; Medical Director, Genomics and Bioinformatics, ARUP Laboratories
    Next-generation sequencing (NGS) has, in a relatively short time frame, moved from a research technology to one that is increasingly being applied in the clinical diagnostic realm. This presentation will focus on how NGS is being specifically applied to enhance the diagnosis of inherited disorders. In this context, the application of NGS spans the spectrum from single genes to multigene panels to genome-scale analyses, the latter through the use of exome- and whole-genome sequencing. Discussed will be technical considerations for implementing NGS inclusive of workflow and platform options and the key and evolving diversity of NGS data analysis tools. Technical limitations and pitfalls that laboratories need to be aware of will be addressed. An introduction to analyzing exome- and whole-genome data for the identification of causal and candidate genes will be provided accompanied by use-case examples.

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