Clinical Genomics: A Guide to Clinical Next Generation Sequencing

Section 1: Methods Overview of technical aspects and chemistries of NGS: Dr Robi Mitra, Washington University School of Medicine. Non-selective methods (genome-wide): Dr Mark Bogoski, Harvard Medical School Capture based methods (exome, panels) Dr Birgit Funke, Harvard Medical School Amplification based methods (panels): Dr Madhuri Hegde, Emory Medical School Emerging technologies (Nanopore and others); impact on cost and turnaround time: Dr Elaine Mardis, Washington University School of Medicine. Section 2: Bioinformatics Base calling and alignment; quality metrics; depth of coverage: Dr Carl Volkerding, University of Utah, ARUP labs Single nucleotide variants (SNVs): Dr David Spencer, Washington University School of Medicine Insertions and deletions (Indels): Drs Eric Duncavage and Haley Abel, Washington University School of Medicine Large structural alterations (big deletions, translocations, and so on): Dr Charles Mullighan, St Jude's Cancer Institute Copy number variants (CNVs): Dr Mary-Claire King, University of Washington Section 3: Interpretation Reference data bases for disease associations: Dr Heidi Rehm, Harvard Medical School Reporting of results; level of evidence for associations; classes of associations: Dr Shashikant Kulkarni, Washington University School of Medicine Constitutional diseases (with individual chapters on hypertrophic cardiomyopathy, congenital deafness, blindness, cancer syndromes, and so on): Dr David Bick and Dr David Dimmock, Medical College of Wisconsin Cancer (with individual chapters on leukemia, lymphoma, lung cancer, colon cancer, and so on): Dr John Pfeifer, Washington University School of Medicine Section 4: Regulatory Issues Assay validation: Dr Ira Lublin, CDC and Dr Elizabeth Mansfield FDA QA/QC/PT issues: Dr Elaine Lyon, University of Utah, ARUP labs Consent and privacy issues: Dr James DuBois, Albert Gnaegi Center for Health Care Ethics Section 5: Reimbursement Billing: Andrew Drury and Kris Rickoff, Washington University School of Medicine

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