Preview of Association for Molecular Pathology 2017 #AMP2017

With over 2000 clinical laboratory professionals in molecular diagnostics and pathology, plenty of technology and offerings on display.

This year the Association for Molecular Pathology takes place in Salt Lake City Utah, and promises an abundance of new technology as well as the new accompanying science around diagnostic testing. Since this is a molecular pathology meeting, the focus is on cancer, then infectious disease along with inherited disorders.

This emphasis is borne out by the sheer number of posters on solid tumor and hematopathology topics: a total of 226 on these topics alone (over half of all posters or 422 that will presented). Thus if you are involved as a laboratory that does clinical oncology diagnostic testing, or work for a company that sells into this market, you will likely have some representation at the annual AMP conference.

If you’d like to take a look at the poster titles, they are available here (PDF).  And the Journal of Molecular Diagnostics, the publishing arm of AMP, has made the abstracts available here (PDF).

The highlighted presentations here will focus on clinical oncology.

Vendor Workshop Day

One unusual feature of AMP is the setting aside of an entire day of vendor-sponsored workshops. It used to be four, then five, then six parallel rooms where every hour would begin a 50-minute presentation. This year there are no less than seventeen rooms devoted to the effort; at 10 am and 4 pm there are no less than 11 concurrent workshops taking place simultaneously. A detailed description of each workshop is available here. (PDF)

Without a doubt, detection of circulating tumor DNA (also known as liquid biopsy) will be a very popular topic this year. In light of discordant results between the Guardant360 and FoundationAct ctDNA tests offered on the market it is clear to many that this is still an evolving field. (For some background, here’s a GenomeWeb piece from last December) (paywall). The JAMA Oncology paper it references is here (also behind a paywall).

Vendor Workshops of Interest Wednesday Nov 15 2017

My former employer, Thermo Fisher Scientific, has no less than five 50-minute slots, covering the waterfont of their product offerings from infectious disease, capillary electrophoresis-based sequencing, and reproductive health. At 8am they will present a session entitled “Next Generation Sequencing in NSCLC Biomarker Testing” which undoubtedly will cover their recent FDA approved Oncomine Dx Target Test as a companion diagnostic for multiple indications. (Here are the details via GenomeWeb.)

A few hours later, Roche will present the latest information about their only FDA-approved ctDNA liquid biopsy test, based on the cobas real-time PCR system. Called “Expanding the Scientific Body of Knowledge with the New BRAF/NRAS Mutation Test and KRAS Mutation Test v2 for Life Science Research (LSR)” we will see what is new about this New BRAF mutation test. An hour later, Roche will also present “A Lab’s Perspective from Evaluating the New AVENIO ctDNA Analysis Kits”. At last spring’s American Association for Cancer Research (AACR) meeting in Washington DC, there were several interesting posters from Roche and an anticipated wide availability over the summer; however given the muted marketing from Roche and no one telling me about testing this product in the clinical lab context, I gather that it may still be in an early-access phase. It will be interesting to hear about this AVENIO assay, as it is built around the CAPP-Seq technology from Stanford.

Cancer Presentations of Interest Thursday November 16 2017

The opening plenary session will be an AMP Award for Excellence in Molecular Diagnostics, where Dr. Andy Feinberg of Johns Hopkins will present on the “The Epigenetic Basis of Common Human Disease”. He has spent many years looking at epigenetics and its role in disease, from cancer to aging to neuropsychiatric illness. I first heard of his work when he started doing whole-genome microarrays to study methylation in the context of colon cancer, and this work in 2009 that first described CpG island shores. Naturally with the ocean of TCGA data with Reduced Representation Bisulfite Sequencing (RRBS) data, there will be a lot of ground to cover.

In the afternoon there is a concurrent session entitled “Bioinformatic Frontiers: Dissecting the Genetics of Cancer” and Dan Koboldt (of Massgenomics.org fame) will be speaking on “Strategies and Challenges for Somatic Mutation Detection by Next-gen Sequencing”. Given the strengths (and weaknesses) of any given approach for target enrichment, it may not be a generalizable informatic method across technologies. It’ll be worth a look nonetheless.

Cancer Presentations of Interest Friday November 17 2017

The early bird ‘meet-the-expert’ sessions start at 7am and are always worthwhile, and one session that intrigues me is called “New Tools for Detecting Low Frequency Variants Applications in Hematopoietic Neoplasms”, where Todd Druley of Washington University (St. Louis MO) will present “Single Molecule Quantification of Rare DNA and RNA Variants in Heterogeneous Samples”. Single molecule quantification is hard, given the statistical laws of a Poisson distribution; yet given the importance of tumor heterogeneity in cancer treatment resistance, cancer recurrence and metastasis this is an important topic.

Later in the morning’s informatics plenary session, “Molecular Informatics at Scale for Genomics-based Personalized Cancer Care”, Dr. Nikolaus Schultz of Memorial Sloan-Kettering Cancer Center (New York, NY) will present “Interpreting the Cancer Genome: Identifying Driver Alterations and Therapeutic Options”.

In the early afternoon during the Oncology/Cancer Plenary Session, Dr. John Iafrede (Massachusetts General Hospital MA) will speak on “Solid Tumor Genotyping: Technical and Clinical Validation with a Focus on Fusions”. While a co-founder of the company ArcherDx and their single-primer Anchored Multiplex PCR technology, we will certainly hear about the latest in clinically-relevant fusion transcripts and their relevance for diagnostics.

Cancer Presentations of Interest Saturday November 18 2017

One section of the aforementioned posters is the “Technical Topics” section, and an early-bird session entitled “Platform Presentations of Selected Technical Topics Abstracts” should prove interesting. One is on RNA extraction from archived bone marrow, another uses single-color digital PCR for mutation detection in circulating DNA, and a third engineers cell lines using CRISPR/Cas9 for low variant frequency mutations in FFPE cell blocks (similar to how Horizon Discovery produces their reference standards). The last one, “Screening Circulating Nucleic Acids of Pancreatic Ductal Adenocarcinoma Using a Plasmonic Nanosensor”, where Dr. Amogha Tadimety (Dartmouth College NH) will present on technology coming out of Dr. John Zhang’s group at Dartmouth.

Lastly an interesting concurrent session on Saturday morning will be “Review and Implementation of New AMP Guidelines on NGS Somatic Variant Test Validation, Interpretation, and Reporting”, a set of three presentations sponsored by the clinical practice committee. Dr. Lawrence Jennings (Chicago Children’s Hospital, IL) will present “AMP/CAP Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels”; Dr. Marylin Li (Children’s Hospital of Philadelphia, PA) will present “AMP/ASCO/CAP Standards and Guidelines of Somatic Variant Interpretation and Reporting”; and Dr. Marina Nikiforova (University of Pittsburgh Medical Center, PA) will present “Implementation of NGS Somatic Variant Guidelines into Clinical Practice”.

Visit Pillar Biosciences at Association for Molecular Pathology 2017

If you plan to attend AMP do swing by the Pillar Biosciences’ booth 1724 and say hello! We’ll have data on three new products we’re launching, the ONCO/Reveal Solid Tumor Lung/Colon panel, the ONCO/Reveal Solid Tumor Pan-Cancer panel, and the germline ONCO/Reveal BRCA Panel.

Also take a look at Dr. Greg Tsongalis’ poster presented by Dr. Fran de Abreu in the Solid Tumor section, ST131, entitled “Evaluation of the Pillar NGS SLIMamp Cancer Hotspot Panel”. He will be doing a side-by-side analysis and comparison of the Pillar technology with over 100 samples with another well-characterized assay.

Lastly, we’ll have some data on an upcoming assay for circulating tumor DNA which is currently in development. Come by and ask about it. Hope to see you in Salt Lake!