Infectious Diseases

Thursday, November 7, 2019


7:00am - 8:00am


Artificial Intelligence and Diagnostics Microbiology: Friend or Foe?

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

Case Studies in Genetics

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

10:00am - 11:30am


CRISPR-CAS: Applications for Diagnostics & Therapeutics of Human Diseases

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

12:45pm - 2:00pm


Diagnostic Stewardship for Molecular Testing

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

3:45pm - 4:30pm


AMP CPC’s ID Multiplex Working Group: Update & Open Comment Forum

Michael Lewinski, PhD, Roche Molecular Systems, Inc, Pleasanton, CA, USA

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


Friday, November 8, 2019


10:45am - 12:15pm


Metagenomics in Prime Time

Panel Discussion

Robert Schlaberg, MD, MPH, IDbyDNA, Salt Lake City, UT, USA

Charles Chiu, MD, PhD, University of California, San Francisco, CA, USA

Erin Graf, PhD, Mayo Clinic Hospital, Arizona, Phoenix, AZ, USA

Patricia Simner, MSc, PhD, Johns Hopkins University School of Medicine, Baltimore, MD, USA

1:30pm - 2:45pm


Point Counterpoint: Who Owns Molecular Infectious Disease Testing?

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

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

4:00pm - 5:00pm


Climate Change & Global Surveillance

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



Saturday, November 9, 2019


7:00am - 8:00am


Liquid Biopsy in Infection & Cancer

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


8:15am - 9:45am


Precision Medicine in Infectious Disease

Genotypic Antiretroviral Resistance Testing

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

Bacteriome and Mycobiome Imbalance and Design of Precision Medicine and Nutrition

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


10:45am - 12:15pm


Whole Genome Sequencing for Bacterial Strain Typing & Genomic Surveillance

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

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


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

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 Infectious Diseases Abstracts

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

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