AMP is the leading organization in the field of molecular diagnostics, and the AMP Annual meeting is the premier gathering of molecular professionals. As technologies change and new challenges arise, members and non-members alike rely on the AMP meeting to obtain the critical information needed to ensure that their patients receive the best care and best results.

This collection contains downloadable PDF slides of many of the presentations given during the AMP 2019 Annual Meeting and Expo. See the "topics" tab for a list of all the presentations for which slides are available.


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Course Information
Course Date:
November 07, 2019
Click on a topic name to see details and purchase options.
Thursday November 7, 2019

AMP Annual Meeting 2019 - Program Book

Use of Machine Learning Algorithms to Support Clinical Microbiology Culture Interpretation

Karissa Culbreath, PhD, TriCore Reference Laboratories, Albuquerque, NM, USA

Detection of  Outbreaks and Unusual Pathogen using AI and Machine Learning

Amy Leber, PhD, Nationwide Childrens Hospital, Colubmus, OH, USA

Ultra-hypermutated Pediatric Glioblastoma of Lynch Syndrome Mimicking Constitutional Mismatch Repair Deficiency Syndrome

Chen Yang, MD, PhD, Virginia Commonwealth University, Richmond, VA, USA

A Case of T-PLL with EZH2 Mutation; EZH2 the Sword or the Shield?

Panieh Terraf, PhD, Harvard Medical School - Brigham and Women's Hospital, Boston, MA, USA

Exome Reanalysis in a Patient with a Somatic CN-LOH in 17p and TP53 Mutation, and a Germline DNAJC21 Biallelic Mutation Associated with Myelodysplastic Susceptibility

Elan Hahn, MD, University of Toronto, Toronto, Ontario, Canada

Somatic Mosaic IDH1 Mutation in a Case of Maffucci Syndrome

Diana Bryk, MD, New York Presbyterian - Columbia, New York, NY, USA

A Surprising Finding in Primary Cutaneous CD8-positive Aggressive Epidermotropic Cytotoxic T-cell Lymphoma

Mark Evans, MD, University of California, Irvine, Orange, CA, USA

“Clonal Selection Following FLT3 Tyrosine Kinase Inhibitor Treatment for Acute Myeloid Leukemia”

Adam Fisch, Brigham and Women's Hospital, Boston, MA, USA

Identification of a Cryptic ABL1 Rearrangement in a Refractory Acute Myeloid Leukemia Patient with Diploid Karyotype by Conventional Cytogenetics

Arash Ronaghy, MD, PhD, MD Anderson Cancer Center, Houston, TX, USA

Muddy Waters: A Report of Granulocytes Infusion Confounding Next-Generation Sequencing Interpretation

Tareq Qdaisat, MD, University of Nebraska Medical Center, Omaha, NE, USA


Compound EGFR and BRAF variants in NSCLC against the backdrop of suspected MEN2A

Jeremy Adler, MD, Pennsylvania Hospital, UPHS, Philadelphia, PA, USA 

Expanded Next Generation Sequencing Panel Detects A Rare EGFR Kinase Domain Duplication In A Patient with Metastatic Lung Cancer

Jong Kim, MD, Cedars-Sinai Medical Center, Los Angeles, CA, USA

Pitfalls in Identification of Mismatch Repair Deficiency: An Unusual Pulmonary Intimal Sarcoma.

Wanying Zhang, MD, New York Presbyterian Hospital, New York, NY, USA

EGFR-Mutated Lung Adenocarcinoma with Early Resistance to Osimertinib

Brennan Decker, MD, PhD, Brigham and Women's Hospital, Boston, MA, USA

Targeting Immune Signaling Checkpoints in Acute Myeloid Leukemia

Ivana Gojo, MD, Johns Hopkins, Baltimore, MD, USA

Choosing Patient Therapy with Dynamic BH3 Profiling

Anthony Letai, MD, PhD, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA USA

Diverse Mechanisms of Acquired Resistance to CAR T Cell Immunotherapy

Andrei Thomas-Tikhonenko, PhD, Children's Hospital of Philadelphia, Philadelphia, PA, USA

Rapid DNA: From Research to Field

Amanda Sozer, PhD, SNA International, Washington, DC, USA

Forensic DNA Testing at the Crossroads of Science, Law, and Policy

Frederick Bieber, PhD, Harvard Medical School, Boston, MA, USA - speaker did not provide permission to share slides

Basics of Genetic Genealogy and Its Impact on Forensic Investigation

Howard Cash, Gene Codes Corporation, Ann Arbor, MI, USA 

Getting More from your MiSeq with DASH and FLASH

Emily Crawford, PhD, Chan Zuckerberg Biohub, San Francisco, CA USA

Assessing Unintended Off-Target Mutations Caused by Cas9 and Other Gene Editing Enzymes

Vikram Pattanayak, MD, PhD, Massachusetts General Hospital, Boston, MA, USA

Clinical Implementation of Pharmacogenomics

Philip Empey, PharmD, PhD, University of Pittsburgh, UPMC, Pittsburg, PA, USA

What’s New in Pharmacogenetics?

Victoria M. Pratt. PhD, Indiana University School of Medicine, Indianapolis, IN, USA

Anthony Sireci, MD, Loxo Oncology, Stamford, CT, USA

Aaron Bossler, MD, PhD, University of Iowa, Iowa City, IA, USA

Demystifying Molecular testing coverage and policies: MolDX and Medicare

Gabriel Bien-Willner. MD, PhD, Palmetto GBA, TX, USA

Kimberle Chapin, MD, Brown Biology and Medicine, Providence, RI, USA

The Art of Navigating Molecular Infectious Disease Test Results: From Ordering To Application In the Clinical Setting

Sejal Morjaria, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Perspective on Establishing a Biorepository for Clinical and Research Use

Kristy Crooks, PhD, University of Colorado, Aurora, CO, USA

Profiling the DNA Damage Repair Capacity of High Grade Serous Ovarian Tumors using Patient-Derived Organoids

Sarah Hill, MD, PhD, Dana-Farber Cancer Institute, Boston, MA, USA

Big Data and Little Patients: Targeted Sequencing for Pediatric Brain Tumors

Sarah Leary, MD, MS, Seattle Children's Hospital, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA

Bigger is Better: More Cancer Genes in More Patients

Wendy Chung, MD, PhD, Columbia University, New York, NY, USA

Standing of Molecular within the Pathology/Lab Profession

Karen Kaul, MD, PhD, NorthShore University Health System, Evanston, IL, USA

Evolving Technologies and Automation

Karl Voelkerding, MD, University of Utah School of Medicine, Salt Lake City, UT, USA

Panel Discussion

Federico Monzon, MD, Castle Biosciences, Friendswood, TX, USA

Aaron Bossler, MD, PhD, University of Iowa, Iowa City, IA, USA

Yaolin Zhou, MD, Univ of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

Helen Fernandes, PhD, Columbia University Medical Center, New York, NY, USA

Using Polygenic Risk Scores (PRS) for Breast Cancer to Inform Screening: Model Fit, Calibration, and Utility

Peter Kraft, PhD, Harvard T.H. Chan School of Public Health, Boston, MA, USA

Friday November 8, 2019

How to Validate Rare Findings - Focus on Novel Fusions

John Iafrate, MD, PhD, Massachusetts General Hospital, Boston, MA, USA

Did I Find the Right Needle in the Haystack? Sensitivity and Specificity Challenges Revealed by Ultra-accurate NGS

Rosana Risques, PhD, UW Pathology, Seattle, WA, USA

Malachi Griffith, PhD, Washington University School of Medicine, St. Louis, MO, US

Blood Group Genotyping from High Density Arrays to Whole Genomes

Bill Lane, MD, PhD, Brigham and Women's Hospital, Boston, MA, USA

Fei Dong, MD, Brigham and Women's Hospital, Boston, MA, US

B-lymphoblastic Leukemia with ZNF384 Gene Rearrangement

Shweta Bhavsar, MBBs, MD, University of Pittsburgh Medical Center, Pittsburgh, PA, USA

Molecular Diagnosis of MDS in a Non-Diagnostic Bone Marrow Specimen

Jeffrey SoRelle, MD, University of Texas Southwestern Medical Center, Dallas, TX, USA

The Role of Lymphoma Sequencing Panel in the Diagnosis of Pediatric-Type Follicular Lymphoma

Guang Yang, MD, PhD, University of Pennsylvania, Philadelphia, PA, USA

5q- in a Patient with Chronic Myelogenous Leukemia in Accelerated Phase

James Corines, DO, SUNY Upstate Medical University, Syracuse, NY, USA

Advances in Liquid Biopsy: Isolation, Analysis and Expansion of CTCs

Sunitha Nagrath, PhD, University of Michigan, Ann Arbor, MI, USA

Microfluidic Platforms for the Efficient Isolation of Circulating Leukemia Cells and Circulating Plasma Cells

Steven A. Soper, PhD, The University of Kansas, Lawrence, KS, USA

The Limitations and Consequences of Ethnicity-specific Guidelines for Carrier Screening

Dale Muzzey, PhD, Myriad Women's Health, Inc., San Francisco, CA, USA

Current Complexities and Future Directions of Expanded Carrier Screening

Nicole Faulkner, PhD, FACMGG, Invitae Corporation, San Francsico, CA, USA

Technological Advances and Detections Rates: Demystifying the Influence of Ethnicity on Carrier Detection and Residual Risk

Lisa Edelmann, PhD, Sema4, New York, NY, USA

Patterns of Complex Structural Variation across Thousands of Cancer Whole Genomes

Marcin Imielinski, MD, PhD, Weill Cornell Medical College, New York, NY, USA

Identification and Characterization of Cryptic Structural Variation in Human Genomes

Ryan Mills, PhD, University of Michigan, Ann Arbor, MI, USA

Do-It-Yourself Molecular LIMS

Long P. Le, MD, PhD, Massachusetts General Hospital, Charlestown, MA, USA

Factors to Consider When Purchasing a LIMS Platform

Kristina Cusmano-Ozog, MD, Children’s National, Palo Alto, CA, USA

Development of a Laboratory Information System to Support Clinical NGS Testing

Michael Kluk, MD, PhD, Weill Cornell Medicine, New York, NY, USA

Mark Routbort, MD, PhD, University of Texas MD Anderson Cancer Center, Houston, TX, US

Nanopore Sequencing Comes of Age

Miten Jain, PhD, University of California Santa Cruz, Santa Cruz, CA, USA

Extreme Molecular Diagnostics

Carl Wittwer, MD, PhD, University of Utah, Salt Lake City, UT, USA

ESP Molecular Pathology WG: Diagnosis and Clinical Research Reproducibility

Giorgio Stanta, MD, PhD, University of Trieste, Duino-Aurisina, Italy

Quality Assessment Experience in Brazil

Roberta Sitnik, MSc, PhD, Departamento de Patologia Clínica e Anatomia Patológica, São Paulo, Brazil

Non-invasive Prenatal Sequencing for Multiple Mendelian Monogenic Disorders using Circulating Cell-free Fetal DNA

Shashikant Kulkarni, PhD, FACMG, Baylor College of Medicine, Houston, TX, USA

Prenatal Diagnosis: The Next Generation

Mark Evans, MD, Comprehensive Genetics, New York, NY, USA

Centralized Testing in Molecular Pathology via Lean Laboratory Design

John Longshore, PhD, Carolinas Pathology Group, Charlotte, NC, USA

Molecular Laboratory Organization: the University of Washington Experience

Daniel E. Sabath, MD, PhD, University of Washington School of Medicine, Seattle, WA, USA

Frederick Nolte, PhD, Medical Univ of South Carolina, Charleston, SC, USA

Nathan Ledeboer, PhD, Medical College of Wisconsin, Milwaukee, WI, USA

Advances in Multiple Myeloma Genomics

Brian A. Walker, BSc, PhD, University of Arkansas for Medical Sciences, Little Rock, AR

Molecular Monitoring of Myeloma

Nikhil Munshi, MD, Dana-Farber Cancer Institute, Boston, MA, USA

Arturo Casadevall, MD, PhD, Johns Hopkins, Baltimore, MD, USA

Saturday November 9, 2019

The Skeletal Dysplasias; the Long and Short of It

Deborah Krakow, FACMG, UCLA School of Medicine, Los Angeles, CA USA

Barriers to Integrating Genomics More Fully into the EHR

Brian Shirts, MD, PhD, University of Washington, Seattle, WA, USA

DNA Methylation and Machine Learning in Molecular Pathology for Diagnosis and Clinical Management

Matija Snuderl, MD, NYU Langone Medical Center, New York, NY, USA

Oncogene Activation by Pan-Cancer DNA Hypermethylation

Wei Li, PhD, Baylor College of Medicine, Houston, TX, USA

speaker did not provide permission to share slides

Opportunities and Challenges of Fungal Cell-Free DNA Testing for Diagnosis of Invasive Fungal Infection

Niaz Banaei, MD, Stanford University, Stanford, CA, USA

Detecting HPV Circulating Tumor DNA by Liquid Biopsy

Daniel Higginson, MD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

An Interesting Case Involving a CIC-NUTM1 Rearranged Epitheliod Tumor

Latrice Landry, PhD, MMSc, MS, Dana Farber Cancer Institute/ Brigham and Women's Hospital, Boston, MA, USA

Detection of Rare Fusion using Foundation One and Oncomine Tests: A Male in his 20’s with an Aggressive Orbital Tumor

Terri Jones, MD, University of Pittsburgh Medical Center, Pittsburgh, PA, USA

A Case of Cutaneous Lymphoma with PCM1-JAK2 Rearrangement

Talent Theparee, MD, Stanford Healthcare, Stanford, CA, USA

Microsatellites: Instability in an Apparently Stable World

Patrick Leach, BS, TriCore Reference Laboratories, Albuquerque, NM, USA

RNA-seq for the Detection of Gene Fusions and Other Alterations in Cancer

Kevin Halling, MD, PhD, Mayo Clinic, Rochester, MN, USA

Applications of RNA-Seq in Cancer

Olena Vaske, PhD, FCCMG, University of California, Santa Cruz, CA, USA

Genotypic Antiretroviral Resistance Testing

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

speaker did not provide permission to share slides

Bacteriome and Mycobiome Imbalance and Design of Precision Medicine and Nutrition

Mahmoud A. Ghannoum, PhD, EMBA, FIDSA,FAAM, University Hospitals Cleveland Medical

Approaches to Returning Germline Results in an Era of Agnostic Cancer Predisposition Testing

Michael F. Walsh, MD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

speaker did not provide permission to share slides

The Evolving Landscape of Clinical Genomic Testing: Elective Genome Sequencing

Birgit Funke, Dr, Veritas Genetics, Newton, MA, USA

What to Expect When You Find the Unexpected: Pregnancy and Incidental Findings in Noninvasive Prenatal Screening

Susan Hancock, MS, Myriad Women's Health, Salt Lake City, UT, USA

Real-time Clinical Applications for Whole Genome Sequencing of Bacteria

Brad Cookson,MD, PhD, University of Washington, Seattle, WA, USA

Bacterial Strain Typing in the Age of Whole Genome Sequencing: Promises and Pitfalls

Richard Goering, PhD, Creighton University School of Medicine, Omaha, NE, USA

Tumor Mutational Burden (TMB): Harmonization and Future Application

Jeff Allen, PhD, Friends of Cancer Research, Washington, DC, USA

TMB: The Case for Understanding and Harmonizing Complex Biomarkers

Albrecht Stenzinger, MD, University Hospital Heidelberg, Heidelberg, Germany

James Versalovic, MD, PhD, Texas Children's Hospital, Houston, TX, USA

Kevin Halling, MD, PhD, Mayo Clinic, Rochester, MN, USA

Stephen Lincoln, Invitae, San Francisco, CA, USA

Jeremy Segal, MD, PhD, University of Chicago, IL, USA

Ahmet Zehir, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

G008 - Germline RAD51B loss-of-function variants confer susceptibility to hereditary breast and ovarian cancers and result in homologous recombination deficient tumors

Diana Mandelker, MD, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

G014 - A framework of critical considerations in interpretation of NGS based tests for germline disorders - On Behalf of CLSI Document Development Committee (DDC) on Nucleic Acid Sequencing (MM09)

Avni Santani, PhD, Children's Hospital of Philadelphia, Philadelphia, PA, USA

G023 - Integrated Germline and Somatic Analysis Identifies Actionable Cancer Predisposing Germline Mutations in 9,734 Patients with Advanced Cancers

Liying Zhang, MD, PhD, Memorial Slone Kettering Cancer Center, New York, NY, USA

G036 - Significance Associated with Phenotype (SAP) Score – A Method for Ranking Genes and Genomic Regions Based on Sample Phenotype

Jianling Ji, MD, MS, Children's Hospital of Los Angeles, South Pasadena, CA, USA

G010 - A Method to Missense Madness: Improving Clinical Variant Interpretation with a Pathway-Focused Functional Assay

Sarah Brnich, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

H034 - Identification of Neoplastic Clonal T-cell Sequences in Unrelated Healthy Individuals: Limitations of High Throughput TRG Sequencing for Minimal Residual Disease (MRD) Analysis

Siddhartha Sen, MD, PhD, Duke University Medical Center, Durham, NC, USA

H039 - Measurable Residual Disease Monitoring for Patients with Acute Myeloid Leukemia Following Hematopoietic Cell Transplantation Using Error Corrected Hybrid Capture Next Generation Sequencing

Vidya Balagopal, PhD, University of Chicago, Chicago, IL, USA

H021 - IGH locus assessment using hybrid-capture, a proof-of-concept study

Etienne Mahe, MD, MSc, FRCPC, FCAP, University of Calgary, Calgary, Alberta, Canada

H027 - Convergence on Genomic Abrogation of the DNA Damage Response Pathway in CLL is Observed in Patients with Loss of18p

Waihay Wong, Brigham and Women's Hospital and Harvard Medical School

H020 - IDH1 p.S280F mutation is potentially a novel mechanism of resistance to Ivosidenib therapy in an IDH1 positive acute myeloid leukemia

Zoltan Oltvai, MD, University of Pittsburgh, Pittsburgh, PA, USA

ID019 - Mycoplasma genitalium assay results from high and low risk populations: implications for sexually transmitted infection panel menu

Kimberle Chapin, MD, Brown Biology and Medicine, Providence, RI, USA

ID018 - Cell-free RNA is More Sensitive than DNA for the Detection of Pediatric Bacterial Sepsis via Shotgun Metagenomic Sequencing

Caitlin Dougherty, The Children's Hospital of Philadelphia, Philadelphia, PA, USA

ID020 - Clinical and Histologic Features of Patients Tested Using the BioFire FilmArray Gastrointestinal Panel

Jonathan Mowers, MD, PhD, Michigan Medicine, Ann Arbor, MI, USA

ID043 - Investigation of amplicon sequencing technology in diagnosis of drug resistant tuberculosis by testing FFPE specimens

Nanying Che, PhD, Departement of Pathology, Beijing Chest Hospitial, Medical Capital University, Beijing, China

ID003 - Microbial Cell-free DNA Sequencing for Multiplexed Detection and Quantitation of Cytomegalovirus, Epstein-Barr Virus, and BK Virus

Timothy Blauwkamp, Karius, Inc., Iowa City, CA, USA

I031 - Platform-agnostic deployment of bioinformatics pipelines for clinical NGS assays using containers, infrastructure orchestration, and workflow manager

Sabah Kadri, PhD, Lurie Children's Hospital of Chicago, Chicago, IL, USA

I013 - Benchmarks for Difficult-to-Sequence Genes and Structural Variants

Justin Zook, PhD, National Inst of Standards & Tech, Gaithersburg, MD, USA

I040 - Machine Learning Applications for Patient Testing: Computational Assessment of MSI by NGS in the Clinical Laboratory

Gregory Omerza, PhD, The Jackson Laboratory, Farmington, CT, USA

I020 - Mixed Reality for a Precision Medicine Laboratory: the Future is Now!

Andrea Sboner, PhD, Weill Cornell Medicine, New York, NY, USA

I004 - Impact of Next Generation Sequencing Panel Composition on Tumor Mutation Burden Calculation – In Silico Comparison of Frequently Utilized Panels

Nicholas Bevins, MD, PhD, University of California at San Diego, San Diego, CA, USA

ST132 - The Impact of Clinical Molecular Testing and Precision Medicine in Thyroid Cancer

Dora Dias-Santagata, PhD, FACMG, Massachusetts General Hospital - Harvard Medical School, Boston, MA, USA

ST009 - Improved Detection of MET Exon 14 Skipping Mutations in Lung Adenocarcinoma with Combined DNA/RNA Testing and Refined Analysis Methods

David Manthei, MD, PhD, University of Michigan, Department of Pathology, Ann Arbor, MI, USA

ST010 - Detection of Point Mutations in Paediatric Low Grade Glioma (PLGG) and Diffuse Intrinsic Pontine Glioma (DIPG) Patients: Validation of a Novel Liquid Biopsy Assay

Monique Johnson, MSc, The Hospital for Sick Children, Toronto, Ontario, Canada

ST015 - Clonal hematopoiesis mutations in plasma cfDNA RAS/BRAF genotyping of metastatic colorectal cancer

Fei Huang, Zhongshan Hospital, Fudan University, Shanghai, China

ST094 - STK11 Loss of Function Variants Mediate Immune Evasion in NSCLC via Dysregulation of the FAK/Hippo Signaling Axis and Subsequent Alterations in Tumor-Intrinsic Cytokine Expression

Liam Donnelly, MD, University of Vermont Medical Center, Burlington, VT, USA

TT011 - A Comprehensive Assessment of onco-panel sequencing across multiple laboratories and technologies

Joshua Xu

TT066 - Variants Reported by Tumor-Only Clinical Oncology NGS Testing Are Frequently Found in the Germline of Pediatric Patients

Azhar Saeed, MD, MSc, University of Kansas Medical Center, Kansas City, KS, USA

TT071 - EXaCT-2: Augmented Whole Exome Sequencing Optimized for Clinical Testing in Oncology

Duane Hassane, PhD, Weill Cornell Medicine, New York, NY, USA

TT072 - Dissimilarity score (DisScore): identifying potential discordance between anatomic pathology and mutation landscape in the evaluation of clinical sequencing as part of a molecular tumor board

Grzegorz Gurda, MD, PhD, Gundersen Health System, La Crosse, WI, USA

speaker did not provide permission to share slides

TT055 - Digital Methylation Specific Multiplex Ligation-Dependent Probe Amplification: A novel MLPA based technique for assessing promoter methylation status in cancer

Jan Smout, MSc, MRC Holland, Amsterdam, Netherlands 

AMP Hematopathology Subdivision Open Forum

Annette S. Kim, MD PhD & Maria Arcila, MD

AMP Solid Tumors Subdivision Open Forum

Roger D. Klein, MD JD

AMP Infectious Disease Subdivision Open Forum

Frederick Nolte, PhD

AMP Informatics Subdivision Open Forum

Somak Roy, MD

AMP Genetics Subdivision Open Forum

Thomas Prior, PhD & Elaine Spector, PhD



Liquid Biopsies for MRD/Opportunities & Pitfalls in Monitoring AML Patients

Eric Duncavage, MD, Washington University in St. Louis

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