Thursday, November 7, 2019


7:00am - 8:00am


Case Studies in Hematopathology

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

Case Studies in Solid Tumors

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

10:00am - 11:30am


Genetics of Sensitivity & Resistance to Non-Chemo Agents

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

12:45pm - 2:00pm


State of Pharmacogenetics

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

Biobanking and 3D-Organoid Technology

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

Is Bigger Always Better? Targeted Versus Genome Oncology Tests

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

3:45pm - 4:30pm


AMP CPC’s Tumor Mutational Burden Working Group: Update & Open Comment Forum

Larissa Furtado, MD, St. Jude Children's Research Hospital, Memphis, TN, USA

AMP CPC’s T & B Cell Clonality Working Group : Update & Open Comment Forum

David S. Viswanatha, MD, Mayo Clinic and Foundation, Rochester, MN,  USA

The First 25 Years of AMP: Our Society’s Groundbreaking Past and Future Opportunities

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


Friday, November 8, 2019


7:00am - 8:00am


How to Validate Rare Findings

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

Novel Mechanisms of Acquired Resistance to Targeted Therapies in Cancer

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

Case Studies in Hematopathology

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

8:15am - 9:45am


Emerging Technology for Circulating Tumor Cells, Beyond Counting/ctDNA Alternative Fluids

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


1:30pm - 2:45pm


Updates in Myeloma Genomics

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



Saturday, November 9, 2019


7:00am - 8:00am


Genetics & Immunity In Bone Marrow Failure Syndromes

Genetic Pathways of Myeloid Transformation in Bone Marrow Failure Syndromes

Coleman Lindsley, MD, PhD, Dana-Farber Cancer Institute, Boston, MA, USA

Case Studies in Solid Tumors

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

8:15am - 9:45am


Standards and Applications of RNA-seq in Cancer

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

Incidental Findings from Somatic Testing/Cancer Predispositions

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

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

10:45am - 12:15pm


Tumor Mutation Burden, Clinical Utility/Efficacy and Harmonization Project

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

Featured Selections from the Journal of Molecular Diagnostics in 2019

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

1:30pm - 2:45pm


Platform Presentations of Selected Abstracts

Abstracts are selected by the Program Committee

Platform Presentations of Selected Genetics Abstracts

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

Platform Presentations of Selected Hematopathology Abstracts

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

Platform Presentations of Selected Informatics Abstracts

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

Platform Presentations of Selected Solid Tumors Abstracts

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

Platform Presentations of Selected Technical Topics Abstracts

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

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 

The Future of the AMP v. Myriad Decision: Exploring Potential Impacts on Multigene Panel Testing and Patient Care

(Sponsored by the AMP Professional Relations Committee)

Panel Discussion

Charles Duan, JD, The R Street Institute, Washington, DC, USA
Robert Nussbaum, MD, Invitae, San Francisco, CA, USA
Sandra Park, JD, American Civil Liberties Union, New York, NY, USA
Hans Sauer, JD, Biotechnology Innovation Organization, Washington, DC, USA

4:00pm - 5:00pm


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

MRD in AML - Promises, Problems and Perspectives

Christian Thiede, MD, University of Technics, Dresden, Germany