Thursday, November 7, 2019


3:45pm - 4:30pm


AMP CPC’s In Silico Reference Materials Working Group: Update & Open Comment Forum

Eric Duncavage, MD, Washington University, Saint Louis, MO, USA

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


4:45pm - 5:45pm


Polygenic Risk Scores: Translating Research Advances into the Clinical Domain

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


7:00am - 8:00am


Behind the Curtain: Developing Clinical Knowledgebase Systems

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


8:15am - 9:45am


Structural Variation Detection in Human Disease

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

10:45am - 12:15pm


Picking a LIMS System

Do-It-Yourself Molecular LIMS

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


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

Hands-on Workshop: Variant Interpretation & Classification

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



Saturday, November 9, 2019


7:00am - 8:00am


Integrating Genomics into the EHR

Barriers to Integrating Genomics More Fully into the EHR

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


10:45am - 12:15pm


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

Hands-on Workshop: Informatic Tools in Metagenomics

Alexander L. Greninger, MD, PhD, MS, MPhil, University of Washington, Seattle, WA, USA

Samia Naccache, PhD, LabCorp, Seattle, WA, USA

Pipeline Showcase

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 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