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Association for Molecular Pathology

Webinars in 2014

The Role of the Pathologist in Reporting & Communicating Accurate and Succinct Results in the Genomic Era

November 7, 2014

 

Presenter: Colin C Pritchard, MD, PhD, University of Washington, Seattle, WA

 

Host: Benjamin Pinsky, MD, PhD, Stanford University School of Medicine, Palo Alto, CA

 

Description:
Next-generation DNA sequencing technology is transforming clinical genetics, including for diagnosis of hereditary genetic conditions, and in tumor-based testing for precision cancer therapy. This new testing approach presents considerable challenges for pathology reporting. This presentation will review considerations related to pathologist reporting of next-generation sequencing results with a focus on germline cancer risk panels, tumor mutation hotspot panels, and comprehensive tumor sequencing panels.

Learning Objectives:
1.  Describe methods for predicting if a poorly-characterized genetic variant is benign or pathogenic.
2.  Explain how the quantity of DNA sequenced impacts the detection of incidental findings, and how this influences clinical reporting considerations
3.  List two ways that clinical reporting considerations are different between hereditary (germline) sequencing panels and tumor sequencing panels

Level of Instruction: Intermediate

Contact Hours: 1.0


Nomenclature in the Context of Next Generation Sequencing Bio-Informatics

October 29, 2014

 

Presenter: Robert D. Daber, PhD, Bio-Reference Laboratories, Inc., Elmwood Park, NJ

 

Host:  Jordan Laser, MD, North Shore - Long Island Jewish Health System, Lake Success, NY

Description:

In this webinar we will explore the bio-informatics workflow as it relates to generating a final list of annotated variants. Most data processing steps occur inside a black box, yet variant identification and annotation depend upon the tools utilized during the data processing steps. We will review these basic steps, identify limitations and challenges and review basic nomenclature standards.

Learning Objectives:
1.  Review the general workflow of data as it originates from a sequencer and ends up as a list of reported variants
2.  Summarize general nomenclature and identify resources for nomenclature support
3.  Identify common problems and limitations in variant calling as it relates to nomenclature (i.e., problems associated with Indels)
4.  Identify methods to determine the accuracy and sensitivity of the variant detection workflows

Level of Instruction: Intermediate

Contact Hours: 1.0


Molecular Diagnostics for Global Health

September 23, 2014

 

Presenter: Ellen Jo Baron, PhD, D(ABMM), Cepheid, Sunnyvale, CA

 

Host: Benjamin Pinsky, MD, PhD, Stanford University School of Medicine

Description:
This presentation provides an overview of the major diseases confronting the world's poorest countries and the current use of molecular tests being implemented to aid in diagnosis of some of those diseases. Diagnostics for HIV and tuberculosis will be emphasized. Challenges to further molecular test utilization will be considered.

Objectives:
1. Characterize the relative burden of disease among different socio-economic regions of the world
2. Contrast laboratory staffing and practices between developed and resource-poor countries
3. List 2 diseases for which molecular tests are endorsed by the World Health Organization (WHO) and name some of the manufacturers
4. Describe the WHO monitored global rollout of GeneXpert molecular tuberculosis testing

Level of Instruction: Basic

Contact Hours: 1.0


 

FDA Laboratory Developed Test (LDT) Draft Guidance and the Potential Impact on Clinical Practice

September 16, 2014

 

Presenters: Roger Klein, MD, JD, AMP Professional Relations Committee Chair, and
Jennifer Leib, AMP Government Relations Consultant

Moderator:  Elaine Lyon, PhD, AMP President

Description:
Depending on how FDA finalizes its current views, the practice of medicine could be changed significantly. This webinar will provide an overview of the key concepts in the draft framework and an analysis of the potential impact on clinical practice.

Level of Instruction: Basic

Contact Hours: 1.0


 

NGS 101 Webinar #2:
Viewing and Interpreting Sequencing Data

September 11, 2014

 

Presenter: Patrik Vitazka, MD, PhD, GeneDx, Inc, Gaithersburg, MD

Host: Christopher Watt, MD, PhD, University of Pennsylvania, Philadelphia, PA

Description:
NGS sequencing, depending on the design and size of the analyzed genomic region, yields between tens to thousands of DNA variants. Handling of sequencing variants involves visualization of sequencing reads (alignments), identification of sequencing artifacts, filtering and prioritization of variants, interpretation and assignment of pathogenicity to variants, and finally correlation of variants with clinical presentation of the patient's disease. This webinar will provide an overview of useful tools, web-based data sets (e.g., 1,000 Genomes Project, NHLBI ESP database, HGVS LSDBs), predictor tools for splicing a functional protein, and genetic disease databases (e.g., HGMD, OMIM, PubMed) used for viewing and interpreting NGS sequencing data.

Learning Objectives:
1. Observe, evaluate, and categorize NGS sequencing data
2. Prioritize and predict pathogenicity of genomic variants
3. Correlate variants with a disease
4. Review available tools for handling NGS data

Level of Instruction: Basic

Contact Hours: 1.0


 

NGS 101 for the Clinic

July 23, 2014

 

Presenter: Birgit H. Funke, PhD, FACMG, Harvard Medical School, Boston, MA

 

Host: Devon Chabot-Richards, MD, University of New Mexico

 

Description:

This webinar provides a basic overview on facets of clinical NGS ranging from choosing and designing test contents to NGS sample preparation, sequencing technologies and post-analytic bioinformatic data analysis. Limitations of NGS technologies and how to work around them will also be discussed. Finally, practical guidance on important considerations prior to implementing NGS for clinical applications will be presented.

 

Learning Objectives:

1.   Evaluate which NGS technology platforms match different laboratory needs.
2.   Prepare for technical limitations of NGS.
3.   Recognize the differences and commonalities between the different NGS platforms.

Level of Instruction: Basic

 

Number of Contact hours: 1.0


 

 

AMP 2014 Annual Meeting Advocacy Day: What to Expect and How to Participate
May 21, 2014

 

 

Presenters: Elaine Lyon, PhD, ARUP Laboratories, AMP President; and Jennifer Leib, Healthfutures, LLC, AMP Profession Relations Committee

 

Host: Roger D. Klein, MD, JD, Cleveland Clinic Foundation, AMP Professional Relations Committee Chair

 

Description:

The 2014 AMP Annual Meeting location is a brief ride to Capitol Hill in Washington, DC! This is a perfect opportunity to introduce policymakers to AMP, educate Congressional staff on molecular pathology, and ask Congress to address AMP's concerns with the coverage and reimbursement of the new molecular pathology CPT codes. AMP Advocacy Day will be a limited-attendance, no-fee event, held prior to the annual meeting. It will feature a full day of meetings with members of Congress and/or their staff and a Congressional briefing on "Realizing the Dream of Precision Medicine," the theme of the 2014 Annual Meeting. This webinar will provide an overview of the day's activities and share information on how to participate.

 

Learning Objectives:

1. Review briefly the structure of Congress, the legislative process, and federal advocacy.
2. Describe AMP's priority policy issue areas, specifically coverage and reimbursement of molecular pathology tests.
3. Describe the events planned and overall goals for AMP Advocacy Day

Level of Instruction: Basic

 

Number of Contact hours: 1.0



Development of Consensus Reference Material Tools for Development and Validation of Clinical NGS Tests

May 08, 2014

 

 

Presenters: Lisa Kalman, PhD, Centers for Disease Control, Atlanta, GA; Birgit Funke, PhD, Harvard Medical School, Boston, MA; Melissa Landrum, PhD, NIH/NLM/NCBI, Bethesda, MD; and Justin Zook, PhD, NIST, Gaithersburg, MD

Host: Christopher D. Watt, MD, PhD, Hospital of the University of Pennsylvania, Philadelphia, PA

Description: The genetic testing laboratory community has expressed an urgent need for reference materials for clinical Next Generation Sequencing (NGS). This webinar will describe the efforts of the Center for Disease Control and Prevention's (CDC) Genetic Testing Reference Material Coordination (GeT-RM) Program, the National Center for Biotechnology Information (NCBI), and the National Institute of Standards and Technology (NIST), in collaboration with members of the genetic testing community, to develop characterized human genomes for use as reference materials. The reference material data is hosted on the versatile GeT-RM web browser, developed by NCBI. Users can view calls, capture reagents, regions of interest, alignments and gene concordance scores within the browser site; download reference data from the site to compare to variants calls made from these samples in their own laboratory; or upload their variant calls to the GeT-RM browser and manually review differences. During the webinar we will demonstrate the functionalities of the GeT-RM browser, describe the NIST data and how it was produced. We'll also discuss ways in which the browser and data can be used for development and validation of a clinical NGS assay.

 

Learning Objectives:

1.    Review efforts by CDC, NCBI, NIST, and the genetic testing community to develop characterized genomic DNA samples and tools for development and validation of clinical NGS assays
2.    Review the GeT-RM browser, and how it can be used to view and analyze NGS data
3.    Describe methods used by the NIST-hosted Genome in a Bottle Consortium to characterize a publicly available human genome and define a large set of high quality SNP, indel, and homozygous reference genotypes.
4.    Identify how the sequence data and GeT-RM browser can be used by clinical laboratories for assay development and validation.


Level of Instruction: Beginner to Intermediate

 

Number of Contact hours: 1.0



Interpretation of Sequence Variants
April 24, 2014

 

 

Presenters: C. Sue Richards, PhD, Oregon Health & Sciences University, Portland, OR; Elaine Lyon, PhD, ARUP Laboratories, Salt Lake City, UT; and Madhuri Hegde, PhD, Emory University, Atlanta, GA

Host: Jill M. Hagenkord, MD, 23andMe, Mountain View, CA

Description: Over the last year a workgroup composed of ACMG, AMP, and CAP representatives has developed new guidelines on the "Interpretation of Sequence Variants". This effort focused on interpreting Mendelian variants identified by single gene testing, gene panels, and exome analysis in clinically validated genes. The workgroup developed a set of standard terms for classifying variants. The interpretation of a variant is based on multiple lines of evidence and a menu approach for scoring. The results of this effort as a proposed recommendation will be presented. The three speakers will discuss the evidence-based approach for classifying variants, how to report variants, and how to apply the evidence rules and scoring to real case examples.

Learning Objectives:

1. Describe the evidence required to classify sequence variants.
2. Describe the reporting requirement for sequence variants detected by Sanger and Next Generation sequencing.
3. Practice the art of variant classification through selected cases.

 

Level of Instruction: Advanced

Number of Contact Hours: 1.0



Next-Gen Sequencing for the Detection of Chromosomal Rearrangements: From Discovery to Clinical Practice
March 27, 2014

 

 

Presenter: Marina N. Nikiforova, MD, FCAP, University of Pittsburgh Medical Center, Pittsburgh, PA

Host: Jordan S. Laser, MD, North Shore - LIJ Health System New York, New Hyde Park, NY

Description:

This webinar will review the pathogenesis of chromosomal rearrangements and associated gene fusions in human cancer and describe the role of Next-Generation Sequencing (NGS) in the exploration of this area. It will provide an overview of currently available NGS tools (e.g., whole genome sequencing, RNA-seq, and gene panels) and describe the targeted amplification-based NGS strategy for the detection of gene fusions and gene expression that can be routinely used in the clinical laboratory

Learning Objectives:

1. Present an overview on classification and pathogenesis of chromosomal rearrangements and gene fusions.
2. Discuss the use of next-gen sequencing in the discovery of novel fusion types.
3. Describe current NGS approaches for detection of gene fusions in the clinical lab.

 

Level of Instruction: Beginner to Intermediate

Number of Contact Hours: 1.0