Program

Nirali M. Patel, MD, Tempus Labs, Durham, NC, USA
2022 Program Chair

Telomeres, Telomerase and Disease
Carol W. Greider, PhD, University of California, Santa Cruz, Santa Cruz, CA, USA

Gabriel Bien-Willner, MD, PhD, Palmetto GBA, The Woodlands, TX, USA

Marilyn Li, MD, Children's Hospital of Philadelphia, Philadelphia, PA, USA

G025 - Standardized Assessment of Oncogenicity and Clinical Significance of NTRK Fusions
Jason Saliba, PhD, Washington University School of Medicine, St. Louis, MO, USA

G026 - Comparison of PIK3CA Genetic Variation Specific to Disorders of Somatic Mosaicism (DoSM) and Variants Associated with Neoplasms
Patricia V. Hernandez, MD, Washington University School of Medicine, St. Louis, MO, USA

G028 - Loss of BRD7 Promotes Breast Cancer Lung Metastasis by Reprogramming the Tumor Immune Microenvironment
Jayanta Mondal, University of Texas MD Anderson Cancer Center, Houston, TX, USA

G048 - Validation of a Germline Genetic Testing Panel for Hematologic Malignancies Using Nail Specimens
Ozge Ceyhan-Birsoy, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

H002 - Going Beyond Karyotyping and FISH: Impact of Optical Genome Mapping (OGM) with Additional Clinically Relevant Information in 75 Hematological Malignancy Cases
Nikhil Sahajpal, PhD, Augusta University, Augusta, USA

H004 - Routine Use of cfDNA Isolated from Nail Clippings as a Source of Matched Non-tumor DNA for Genetic Studies in Hematologic Malignancies
Melissa Krystel-Whittemore, MD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

H046 - Evaluation of Incomplete DJ-Rearrangements by Next-Generation Sequencing of Immunoglobulin Genes: The Canary in the Coal Mine
Karin Miller, MD, Johns Hopkins University School of Medicine, Baltimore, MD, USA

H049 - Transcriptome Sequencing (RNA-Seq) Allows Comprehensive Genomic Characterization of Pediatric B-lymphoblastic Leukemia (B-ALL) in the Clinical Setting
Gordana Raca, MD, PhD, Children's Hospital Los Angeles, Los Angeles, CA, USA

I002 - Monitoring Specimen Molecular Identity Signatures to Capture Pre-analytic and Analytic Errors
Joy Nakitandwe, PhD, Cleveland Clinic, Cleveland, OH, USA

I004 - Application of Whole Transcriptome Sequencing to Pediatric Cancer Diagnosis and Patient Management
Alexander Gout, PhD, St Jude Children's Research Hospital, Memphis, TN, USA

I006 - Rapid Targeted Germline and Somatic Variant Detection Using the G4 Sequencing System
Timothy Looney, Singular Genomics, Austin, TX, USA

I022 - Using a Machine Learning (ML) Algorithm to Predict Quantity/quality Not Sufficient (QNS) Samples in a Clinical Massively Parallel Sequencing (MPS) Laboratory
Waqas Mahmud, MBBS, Stony Brook University Hospital, Nesconset, NY, USA

Mario Suva, MD, PhD, Massachusetts General Hospital, Broad Institute, Cambridge, MA, USA

Comprehensive assessment of germline pathogenic variant detection in tumor-only sequencing
Diana Mandelker, MD, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Points to consider for reporting of germline variation in patients undergoing tumor testing
Marilyn Li, MD, Children's Hospital of Philadelphia, Philadelphia, PA, USA

Integrating Germline Sequencing to Improve Identification of Hereditary Cancer Risk
Junne Kamihara, MD, PhD

David Rimm, MD, PhD, Yale University School of Medicine, New Haven, CT, USA

Pavitra Roychoudhury, MSc, PhD, University of Washington/Fred Hutchinson Cancer Center, Seattle, WA, USA

Overview of an Updated Clinical NGS Capture-Based Oncology Panel Workflow
Michelle Dina, MS, MB (ASCP), Mayo Clinic, Rochester, MN, USA

Automation of The Taqpath Covid-19 Combo Assay using the Epmotion 5075c and the Qiagility
Krupa Jani, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Next Generation Sequencing Changing a Preliminary Diagnosis of Lung Lesion, Case Series
Tarneem Darwish, MD, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH, USA

Case Study of a Patient with Multiple Vascular Malformations and Three Variants in the TEK Gene
Fernando Zazueta Leon-Quintero, MD, Washington University in Saint Louis, St. Louis, MO, USA

CMA Pattern in Recognition of Derived Inversion—a Lesson Learned from a Fetal Demise Potentially Caused by Parental Chromosomal Inversion
Reza Ghasemi, PhD, Washington University in Saint Louis, St. Louis, MO, USA

Deceptively Bland: Viral Meningitis Associate with Normal CSF Findings
Patricia Hernandez, MD, Washington University in Saint Louis, St. Louis, MO, USA

The Dangers of Single Modality Testing in a Case of Undifferentiated Pleomorphic Sarcoma with Low Level Involvement by Chronic Lymphocytic Leukemia/Small Cell Lymphoma
Kelly Craven, MD, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

AML Relapse After Stem Cell Transplant from a Presumed Carrier of MyD88 Deficiency
Cansu Karakas, MD, University of Rochester Medical Center, Rochester, NY, USA

Relapsed Post-transplant Acute Myeloid Leukemia with Testicular Involvement and Concurrent Bone Marrow Donor-derived Pathogenic Variants
Dorottya Laczko, MD, PhD, Hospital of the University of Pennsylvania, Philadelphia, PA, USA

Vexed by VEXAS Syndrome: UBA1 mutation—Agent for Autoinflammatory Marrow Destruction or Driver for Myelodysplasia?
Lisa Robinson, MD, University of Nebraska Medical Center, Omaha, NE, USA

Incidental IDH2 Variant in Low Grade Glioneuronal Tumor: A Tale of a Hematopoietic Clone
Fei Chen, MD, PhD, NYU Langone Health, New York, NY, USA

PTCHing Together a Diagnosis: Molecular Resolution of a Challenging Case
Amy Guimaraes-Young, MD, PhD, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

Molecular Lineage Tracing Reveals Cancer Diagnosis
David Basta, MD, PhD, Brigham and Women’s Hospital, Boston, MA, USA

Novel BRAF Activating Mutation in a Case of Hyalinizing Trabecular Tumor of the Thyroid
Christopher Zarbock, MD, University of Minnesota, Minneapolis, MN, USA

Pelvic Mass with Unique FGFR1-TACC Fusion
Jack Reid, MD, University of California Irvine Medical Center, Orange, CA, USA

SHH-Activated Medulloblastoma With or Without TP53 Mutation? Tumor Heterogeneity Causes a Diagnostic Dilemma with Profound Clinical Implications
Vanessa Smith, MD, Duke University Medical Center, Durham, NC, USA

Homozygous SMARCA4 Deletion in SMARCA4 Deficient Undifferentiated Tumor
Kenneth Ofori, MD, MHS, Columbia University Irving Medical Center, New York, NY, USA

Origin of a Cancer of Unknown Primary Traced to Donor Kidney by Short Tandem Repeat Testing
Bryan Iorgulescu, MD, MPH, MD Anderson Cancer Center, Houston, TX, USA

Elin Grundberg, PhD, Children's Mercy Kansas City, Kansas City, MO, USA

Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency
Adrian Levine, MD, The Hospital for Sick Children, Toronto, Ontario, Canada

A Genome-First Approach to Characterize Prevalence, Penetrance, and Phenotype for Pathogenic Variants in DICER1 and Other Tumor-Predisposition Genes
Douglas Stewart, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA

Moving Cancer Genomics into the Clinic: The Genomes for Kids (G4K) Research Study
Kim Nichols, MD, St. Jude Children's Research Hospital, Memphis, TN, USA

Donna Wolk, MHA, PhD, Geisinger, Danville, PA, USA

Matt Charles, MPH, Northshore University HealthSystem, Chicago, IL, USA

Standardization of Gene Product Nomenclature for Variant Reporting and Collaborative Databases
Shuji Ogino , MD, PhD, MS, Dept. of Pathology, Brigham & Women's Hospital, Boston, MA, USA

Gene Product Nomenclature: Advances in Standardization
Alex H. Wagner, PhD, Nationwide Children's Hospital, Dublin, OH, USA

Using Variant Nomenclature to Communicate Genetic Results
Laura Conlin, PhD, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA

Panel Discussion
Ian S. Hagemann, MD, PhD, Washington Univ School of Medicine, St. Louis, MO, USA
Valentina Nardi, MD, Massachusetts General Hospital, Boston, MA, USA
Nikoletta Sidiropoulos, Doctor of Medicine, University of Vermont Medical Center, Burlington, VT, USA
Joel Moncur, MD, PhD, The Joint Pathology Center, Silver Spring, MD, USA

Automated Disease Classification Using Whole Genome Sequencing (WGS) and Whole Transcriptome Sequencing (WTS) Data with Transparent Artificial Intelligence (AI)
Torsten Haferlach, MD, Munich Leukemia Laboratory, Munich, Germany

Digital Pathology-based AI for Classification of Solid Tumors
Faisal Mahmood, PhD, Harvard Medical School, Boston, MA, USA

Ting Wang, PhD, Washington University, St. Louis, MO, USA

Eimear Kenny, PhD, Institute for Genomic Heath/Icahn School of Medicine at Mount Sinai, New York, NY, USA

Victoria Pratt, PhD, Optum Genomics, Zionsville, IN, USA

Genomic Answers for Children: Dynamic Analyses of >1000 Pediatric Rare Disease Genomes
Tomi Pastinen, MD, PhD, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA

Assessing the utility of RNA sequencing in the diagnosis of rare Mendelian diseases
Stephen Montgomery, PhD, Stanford University, Stanford, CA, USA

Clinical Applications of Long-read Genome Sequencing
Danny Miller, MD, PhD, University of Washington, Seattle, WA, USA

Whole Genome Sequencing for Next Generation Cytogenetics
Eric Duncavage, MD, Washington University School of Medicine, St. Louis, MO, USA

Implementation of Long read sequencing and optical genome sequencing in the cytogenetic laboratory
Adam Smith, MSc, PhD, FCCMG, FACMG, erCLG, University Health Network, Toronto, Ontario, Canada

Panel Discussion
Eric Duncavage, MD, Washington University School of Medicine, St. Louis, MO, USA
Adam Smith, MSc, PhD, FCCMG, FACMG, erCLG, University Health Network, Toronto, Ontario, Canada
Yassmine Akkari, PhD, Nationwide Children's Hospital, Portland, OR, USA
Robert Hasserjian, MD, Massachusetts General Hospital, Boston, MA, USA

Evan Eichler, PhD, University of Washington & HHMI, Seattle, WA, USA

The World Health Organization classification of myeloid malignancies: updates in the 5th edition
Joseph Khoury, MD, University of Nebraska, Omaha, NE, USA

The International Consensus Classification of myeloid malignancies:  points of divergence from the WHO
Robert Hasserjian, MD, Massachusetts General Hospital, Boston, MA, USA

NGS Test Development
Birgit Funke, PhD, Icahn School of Medicine at Mount Sinai, Newton, MA, USA

The Bioinformatics Pipeline: Principles and Practice Recommendations
Dan Jones, MD, PhD, The Ohio State University, Columbus, OH, USA

Metagenomic Medicine and the Human Microbiome
James Versalovic, MD, PhD, Baylor College of Medicine / Texas Children's Hospital, Houston, TX, USA

Microbiome in Health and Disease
Michael Woodworth, MD MSc, Emory University School of Medicine, Cape Elizabeth, ME, USA

Microbiome in Health and Disease
Xin V. Li, PhD, Weill Cornell Medicine, New York, NY, USA

Kenneth Aldape

Laura Tafe, MD, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA

Marjorie P. David, MD, MSc, UT Health San Antonio, San Antonio, TX, USA

ID001 - Clinical Evaluation of the Accelerate Arc™ Module and BC Kit for Isolation of Microorganisms from Positive Blood Culture Broths and Suitability for Maldi-tof Analysis
Blake Buchan, PhD, The Medical College of Wisconsin, Children's Wisconsin, Brookfield, WI, USA

ID014 - Balancing Act in the Face of Variants: Testing Strategies to Minimize Infections and Maximize In-person Learning in Schools
Teddie Proctor, MSN, RN, ThermoFisher Scientific, South San Francisco, CA, USA

ID016 - SARS-CoV-2 Variant Identification in Long Term Viral Shedding and Re-infection Cases at a Tertiary Cancer Center
Krupa Jani, MS, ASCP(iMB), Memorial Sloan Kettering Cancer Center, Jersey City, NJ, USA

ID048 - Detection and Quantification of EBV Transcript in Whole Blood, Plasma and Paraffin Embedded Tissue Samples from Organ Transplant Recipients with Post-transplant Lymphoproliferative Disorder (PTLD)
Ryan Martinez, MD, PhD, University of Minnesota, Minneapolis, USA

ST052 - The Clinical Utility of DNA Methylation Profiling in Pediatric CNS Tumors: Comparison of Methylation Classification and Integrated Diagnosis in a Cohort of 184 Pediatric CNS Tumors
Luca Pagliaroli, Children's Hospital of Philadelphia, Philadelphia, USA

ST077 - Assessing Variability Across HRD Assays: Findings from the Friends’ HRD Harmonization Project
Hillary Stires, PhD, Friends of Cancer Research, Washington, DC, USA

ST081 - Rescuing Low Tumor Cell Content Carcinoma Samples from Formalin-fixed Paraffin-embedded Biopsies for Clinical Next-generation Sequencing by Dielectrophoretic (DEP) Array Sorting
Matija Snuderl, MD, NYU Langone Health, New York, NY, USA

ST084 - Reversal of Idh-dependent Global Hypermethylation and Enrichment of TP53 and TERT Mutations Distinguish Dedifferentiated Chondrosarcoma from Conventional Chondrosarcoma on Integrated Genomic Profiling
Josephine K. Dermawan, MD, PhD, Memorial Sloan Kettering Cancer Center, Mentor, OH, USA

TT002 - Gene-specific Validation of Copy Number Gains from a Massively Parallel Sequencing Assay
James Corines, DO, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, NY, USA

TT004 - Treatment with DNA Repair Enzyme Removes NGS Variant Call Artifacts in Archival FFPE Tissues
Lisa M. Haley, MS, MB ASCP(CM), Johns Hopkins, Forest Hill, MD, USA

TT006 - Neurodegenerative Disease Differences in Luminex and Lumipulse ATN Categories
Lavanya Jain, PhD, Cleveland Clinic Foundation, Cleveland, OH, USA

TT008 - Are We Using the Right Tools to Calculate Homologous Recombination Deficiency (HRD) Scores?
Nikhil Sahajpal, PhD, Augusta University, Augusta, USA

VITAL Inherited Overview
Madhuri Hegde, PhD, PerkinElmer, Duluth, GA, USA
VITAL Somatic Overview
Marilyn Li, MD, Children's Hospital of Philadelphia, Philadelphia, PA, USA

Eric Duncavage, MD, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
Justin Zook, PhD, NIST, Gaithersburg, MD USA

The World Health Organization classification of lymphoid malignancies: updates in the 5th edition
Daphne de Jong, MD, PhD, Amsterdam UMC, Haarlem, Noord-Holland, Netherlands
The International Consensus Classification of lymphoid malignancies: points of divergence from the WHO
James Cook, MD

Multi-cancer Early Detection Through Multiple Analyte Liquid Biopsy Testing
Frank Diehl, PhD, Exact Sciences, Cambridge, MA, USA
Multi-cancer Early Detection
Daniel Duncan, MD, GRAIL, Exact Sciences, Cambridge, MA, USA
Genome-wide cfDNA Fragmentation in Patients with Cancer
Timothy McDaniel, PhD, Delfi Diagnostics, Palo Alto, CA, USA

Karen Miga, PhD, University of California, Santa Cruz. CA, USA

Nirali M. Patel, MD, Tempus Labs
2022 Program Chair
Yassmine Akkari, PhD
2023 Program Chair