Innovation Spotlight Stages

New AMP Educational Content 

Hosted by: AMP Training and Education Committee

Speakers: Erin Graf, Susan Hsiao, Cinthya Zepeda Mendoza, and Preeti Pancholi

AMP Education and the AMP Training and Education Committee are committed to bringing the most relevant and useful content to our members and extended audience. This includes AMP certificate programs (self-paced thematically bundled webinars designed to help you develop knowledge and skills needed for success in molecular pathology and diagnostics), the AMP Horizons Series (forward-looking information about emerging science and technology that will likely soon impact the practice of molecular pathology) and other initiatives. Join us at the Innovation Stage where we’ll showcase new AMP Education initiatives.

Attendees will receive coupon codes for some of the AMP Programs presented.

Accurate detection of CNVs and gene amplifications in tumor samples

Hosted by: SOPHiA Genetics

Speaker: Emily Paul, PhD

There are incredible challenges faced when looking at the gene amplifications on somatic NGS-based applications as low tumor content weakens the coverage signal and FFPE sample degradation increases coverage noise. Given these criteria, the utmost precision in noise filtering and analysis is required. SOPHiA AI is able to identify Copy Number Variations (CNVs) routinely in a variety of solutions, ranging from targeted, germline applications to large, complex, somatic ones. This presentation will provide
an overview of key concepts in CNV detection and explore analytical technologies that allow to overcome limitations and reach advanced performance.

State of the Art Clinical Copy Number Variant Analysis in Next-Gen Sequencing
Data: Gene Panels, Whole Exome, Whole Genome 

Hosted by: Golden Helix

Copy Number Variations (CNVs) are associated with a variety of genetic disorders, including autoimmune diseases, autism, and cancer. Golden Helix has developed an industry-leading CNV calling solution, called VS-CNV, which enables clinicians and researchers to detect CNVs ranging from small single exon events to large chromosomal deletions and duplications, removing the need for additional assays such as MLPA. The solution also allows clinicians to annotate CNVs against a wide array of useful data sources and perform filtering based on these annotations to obtain a small set of clinically relevant variations. In this spotlight, Golden Helix President & CEO, Andreas Scherer, Ph.D., and VP of Product & Engineering, Gabe Rudy, will discuss VS-CNV’s analysis capabilities with a focus on the application of these various CNV annotations for filtering false positive and clinically irrelevant CNVs. The talk will also include a discussion of CNV interpretation in accordance with the AMP guidelines for the interpretation of somatic variants.

Enabling the Next Generation of Diagnostics with Enzyme Design and Control

Hosted by: New England Biolabs

Nucleic acid enzymes have long powered the chemistries of molecular diagnostics, and as the field moves to rapid POC and field settings, new demands are placed on DNA polymerases, reverse transcriptases, and other key enzymes. Through protein engineering, discovery, and novel mechanisms for control of enzymatic activities, New England Biolabs can provide unique reagents, customizable formats, and solutions to enable this new generation of diagnostic applications. Methods and reagents for isothermal amplification and RT-qPCR can benefit from enzyme innovation, and we will present how our approach to building better tools has benefited both core and developing applications of molecular diagnostics.

Comprehensive Genomic Profiling is becoming a new Standard-of-Care in Oncology

Hosted by: Illumina

Speaker: Phil Febbo, Chief Medical Officer, Illumina

The value behind a comprehensive assessment of the genomic alterations in a tumor has been consistently increasing with the availability of new therapeutic agents and better predictability of response. The regulatory environment and reimbursement for this type of assay evolved drastically over the last few years. We will discuss the value of adopting comprehensive genomic profiling in today's oncology care.

Consistent Testing Terminology: Eliminating Patient Confusion and Facilitating Access

Hosted by: AMP Professional Relations Committee

Speakers: Nikki Martin, LUNGevity; Lisa Schlager, Facing Our Risk of Cancer Empowered (FORCE)

There are more than 20 terms that can be used to describe comprehensive biomarker testing to patients such as genetic testing, germline testing, somatic testing, genomic testing, molecular testing, molecular profiling, tumor profiling, mutational testing, genotyping, etc.  The patient advocacy community has been working with professional societies and industry to align around the use of consistent testing terminology when communicating with patients. These efforts will help eliminate confusion around the testing required after diagnosis. Learn from two patient advocacy groups about the confusion patients face regarding testing terminology, and the collaborative effort to identify one, two or three testing terms to be used consistently across all cancer types. 

Resources for the Next Generation of Technologists 

Hosted by: AMP Training and Education Committee

Speakers: Technologist Representatives from the AMP Training & Education Committee

The goal of this presentation is to help you to progress in your career by:

    · Providing resources for Continuing Education and improvement.
    · Outlining paths for Molecular certification.
    · Describing opportunities and paths for advancement.

We will highlight the newly updated “Laboratory Careers in Molecular Pathology” page on the AMP website.

Novartis Innovation Spotlight 

Hosted by: Novartis Pharmaceuticals Corporation

Join us as Dr Jean Lopategui discusses PIK3CA mutations in HR+/HER2- advanced breast cancer and how to detect them.

Testing Methods to Identify NTRK Gene Fusions Including NGS, FISH, and IHC

Hosted by: Bayer

Faculty Presenter Michelle Shiller, DO, AP/CP, MGP Co-Director Cancer Genetics Baylor Sammons Cancer Center Molecular Pathologist-PathGroup/Pathologist Biomedical Laboratories A tumor’s underlying genomic profile has become increasingly important in oncology.
One genomic alteration of interest are NTRK gene fusions. This session will cover NTRK gene fusions, the frequency of NTRK gene fusions across many tumor types, and provide an overview of detecting NTRK gene fusions in cancer.

Meet the Authors: “Recommendations for Clinical CYP2C9 Genotyping Allele Selection: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists”

Hosted by: AMP Clinical Practice Committee 

Authors: Victoria M. Pratt, Larisa H. Cavallari, Andria L. Del Tredici, Houda Hachad, Yuan Ji, Ann M. Moyer, Stuart A. Scott, Michelle Whirl-Carrillo, and Karen E. Weck

The Association of Molecular Pathology in collaboration with Clinical Pharmacogenetics Implementation Consortium and College of American Pathologists has developed and published a manuscript defining key attributes of CYP2C9 alleles and describes a recommended minimum set of variants that should be included in clinical pharmacogenomic genotyping assays. This manuscript appears in the September 2019 edition of JMD. Don’t miss a great opportunity to talk to the authors and ask questions.

Q&A with the AMP VITAL Somatic Working Group

Are you participating in the AMP VITAL Somatic Challenges? This is your opportunity to meet the working group members and ask questions regarding the VITAL Somatic Challenge sets.

Enabling Comprehensive Genomic Profiling from FFPE & liquid biopsy samples on a
single high-throughput Sequencing platform

Hosted by: Illumina

Speakers: Brandon Kocher, Ph.D, Senior Product Manager, Oncology, Illumina; Brandon Selby, Senior Product Manager, Oncology, Illumina

Dr. Kocher will provide an overview of how Illumina plans to enable comprehensive genomic profiling from circulating tumor DNA.
Mr. Selby will discuss how Illumina will enable high-throughput comprehensive genomic profiling.

Clinical Variant Analysis: Applying the AMP & ACMG Guidelines in the Clinical Practice

Hosted by: Golden Helix

VSClinical enables the interpretation of both somatic and germline variants following the AMP & ACMG Guidelines, respectively. By incorporating new algorithms and annotation sources, detailed variant scoring, classification, and interpretation can occur right within VarSeq without the need for additional, external tools or resources. These capabilities are designed to improved throughput while allowing the lab to maintain consistent quality.
Join Golden Helix President & CEO, Andreas Scherer, Ph.D., and VP of Product & Engineering, Gabe Rudy, in this spotlight to learn more about these powerful capabilities:
• Streamline germline variant interpretation using the ACMG scoring guidelines with automatic criteria recommendations and incorporated historical data
• Quickly determine the oncogenicity of somatic mutations using our automated oncogenicity scoring system
• Apply the AMP Tiers to the available clinical evidence for Drug Sensitivity, Drug Response, Prognostics and Diagnostics
• Develop a lab-specific knowledgebase of interpretations that allow maximum re-use of interpretations and descriptions from one patient to the next
• Leverage the built-in Golden Helix CancerKB interpretation knowledgebase that covers many common genes and biomarkers
• Finalize your interpretation for a sample and compose the clinical report with the classified variants and their interpretation

The AMP Educational Needs Survey: A Summation and Discussion

Hosted by: AMP Training and Education Committee

Speaker: Cecilia Yeung, MD, Chair, AMP Training & Education Committee

The AMP Training and Education Committee surveys AMP Membership every two years regarding their needs and preferences for the design and delivery of new educational content. Join the Chair of the AMP Training & Education Committee as she presents the results of the 2018 Educational Needs Survey. We also hope that you will join in on a discussion of your educational goals and ways that AMP Education and the Training and Education Committee can help you meet them.