Detailed Scientific Program

We are delighted to present the program of AMP Global 2019!
Please click here for download.

For details on the Pre-Congress Workshops on May 15, please see HERE.

Thursday, May 16, 2019

10:15 AM – 11:45 AM Advances of Genomic Diagnosis in Hemato-oncology & Solid Tumors
General Session
Moderators: Andrea Ferreira-Gonzalez (Richmond, USA) and Megan Lim (Philadelphia, USA)
Session Description: Genomic testing in hematologic neoplasms represents a change in the paradigm in the continuum of patient care including establishment of the diagnosis, prognosis and tailoring therapy. Recent advances in large-scale genomic analysis have led to emerging genomic signatures of most categories of lymphoid neoplasms.  High through-put sequencing of the IGH and TCR genes is a highly sensitive method for disease detection, disease monitoring in response to targeted therapies and can assess disease relapse and recurrence.  Genomic analyses also have identified pre-neoplastic conditions, mechanisms of clonal evolution and clonal heterogeneity in lymphoid neoplasms. The translation of these emerging data and concepts to the clinical setting will be an exciting area for development for the molecular pathology community and will be addressed in this session.
Session Objectives: After attending this session, participants should be able to:

  • Employ genetic data obtained by next-generation sequencing to subclassify B-cell lymphomas.
  • Apply molecular methods for monitoring of patients with B-cell lymphomas.2
  • Employ the use of molecular monitoring in therapeutic management of patients with B-cell lymphomas.
10:15 AM – 11:00 AM Genomics Advances for Diagnosis and Therapy Monitoring of B-cell Lymphoproliferative Disorders
Dan Jones (Columbus, USA)
11:00 AM – 11:45 AM Next-Generation Diagnostics for Cancer Care: Expanding the Value of NGS through Novel Algorithms and New Assays
Ahmet Zehir (New York, USA)
12:00 PM – 1:45 PM Advances in Hemato-oncology
Breakout Session
Moderators: Megan Lim (Philadelphia, USA) and Xinyan Lu (Chicago, USA)
Session Description:  T-cell lymphomas are clinically and genetically heterogenous neoplasms and many have aggressive clinical behavior. Recent application of genomic technologies has led to the identification of recurrent genetic alterations and enhanced understanding of pathogenetic mechanisms in mature T-cell neoplasms. This session will address the discovery work highlighting
novel revelations implicating recurrent alterations affecting the mutational activation of signaling pathways critical for T-cell signaling, and deregulation of immune escape in subtypes of T-cell lymphomas including adult T-cell leukemia. While some of the genetic alterations are specific to certain subtypes, others are found across multiple subtypes. The potential relevance of these
findings to diagnosis, prognosis and therapy will be discussed.
Session Objectives: After attending this session, participants should be able to:

  • Formulate a diagnosis of human T-cell leukemia/lymphoma based upon clinical findings and evidence from genetic diagnostic laboratory tests.
  • Apply the genomic findings of human T-cell leukemia/lymphoma to develop molecular methods for diagnosis.
  • Interpret clinical, laboratory and genetic alterations that may distinguish different subtypes of mature T-cell lymphoma.
  • Employ laboratory-based methods that are utilized in designing chimeric antigen receptor (CAR)-modified T cell therapy for patients with hematologic malignancies.
  • Interpret clinical and laboratory values associated with common complications associated with chimeric antigen receptor (CAR)-modified T cell therapy.
  • Apply clinical and laboratory testing methods to monitor disease in patients receiving chimeric antigen receptor (CAR)-modified T cell therapy.
12:00 AM – 12:50 AM

Genetics of Adult T-Cell Leukemia/Lymphoma
Keisuke Kataoka (Tokyo, Japan)
12:50 AM – 1:40 AM Genomic Classification of T Cell Malignancies: Opportunities for Precision Medicine
Megan Lim (Philadelphia, USA)
12:00 PM – 1:45 PM Advances in Solid Tumor
Breakout Session
Moderators: Andrea Ferreira-Gonzalez (Richmond, USA) and Robert Osamura (Tokyo, Japan)
Session Description:Current anatomic pathology practice in the era of genomic medicine goes beyond basic histologic diagnosis. Available targeted therapies, molecular diagnostic assays for molecular profiling of tumors, and morphologic-molecular correlations are part of the everyday practice. Morphologic-molecular characteristics of the tumor, information about predictors of therapy response and the patient’s prognosis, the development of targeted therapies and their link to specific genetic alterations have resulted in an unexpected revolution in our understanding of tumor responses to novel therapies. This places additional demands on pathologists who must now be aware of advances in the molecular diagnostics of solid tumors.  This session focuses on the genomic advances in diagnosis, prognosis and therapy decision for solid tumors.
Session Objectives: After attending this session, participants should be able to:

  • Be acquainted with molecular diagnostic assays of soft tissue sarcomas and with morphologic-molecular characteristics of soft tissue sarcomas
  • Be acquainted with therapeutic predictive genomic factors ofsoft tissue sarcomas
  • Be acquainted with the basic molecular testing used fordiagnosis, prognosis and therapeutic decision making ofcancers
  • To understand conventional molecular assays and neweremerging modalities.
  • Be acquainted with several tumor types to illustrate the decision-making algorithms for molecular testing.
12:00 PM – 12:50 PM Diagnostic and Therapeutic Implication of Molecular Pathology in Soft Tissue Sarcoma
Yoshinao Oda (Fukuoka, Japan)
12:50 PM – 1:40 PM Clinical and Practical Aspects of Melecular Testing in head and Neck Tumors
Jennifer L. Hunt (Little Rock, USA)
12:00 PM – 1:45 PM Predisposition to Inherited Cancers
Breakout Session
Moderators: Elaine Spector (Aurora, USA) and Alka Chaubey (Waltham, USA)
Session Description: This session will explore familial inheritance of predispositions to breast cancer with a description of variants that provide high, moderate and low risks. The session will also explore hematological malignancies with a focus on ongoing discovery of novel genes and germline sequence variants that increase the risk for both lymphoid and myeloid malignancies.
Session Objectives: After attending this session, participants should be able to:

  • Evaluate the significance of particular germ-line sequence variants in familial breast cancer.
  • Evaluated the significance of particular germ-line sequence variants in inherited haematological malignancies.
  • Identify approaches to discovering sequence variants that are related to inherited cancers.
12:00 PM – 12:50 PM
Presentation 1
High, Moderate and Low – Genetic Variation and Breast Cancer Risk
Katherine L. Nathanson (Philadelphia, USA)
12:50 PM – 1:40 PM
Presentation 2
Familial Predisposition to Haematological Malignancies: Diagnoses and Clinical Conundrums
Hamish S. Scott (Adelaide, Australia)
2:45 PM – 4:30 PM Industry Symposia
Industry Symposium
4:30 PM – 5:00 PM Coffee Break (Exhibit Hall)
Coffee Break
5:00 PM – 6:30 PM Advances of Molecular Diagnosis in Infectious Diseases.
Clinical Application of Liquid Biopsy: Current Status and Future
General Session
Moderators: David Hillyard (Salt Lake City, USA) and Andrea Ferreira-Gonzalez (Richmond, USA)
Session Description:  This session will explore two emerging areas of molecular infectious disease testing with potential for significant improvements in precision medicine. The first example is the use of the host transcriptomic response to assist with the diagnosis of infectious diseases. Most work to date on respiratory infections has analyzed human gene expression in peripheral
blood leukocytes. Analysis of human gene expression in a sample from the respiratory tract may have practical advantages. A comparison of the human transcriptomic response in nasal and
blood samples will be discussed. The second example is the use of liquid biopsies to enable tumor genome characterization by minimally invasive means for early detection of nasopharyngeal
cancer. A study aimed at early detection of nasopharyngeal cancer for a large cohort of asymptomatic healthy volunteers will be described which through the development of a sensitive test to detect cell-free Epstein-Barr virus DNA molecules in plasma achieved high sensitivity and specificity with a 10-fold increase in 3-year progression free survival among nasopharyngeal cancer cases. This portion of the session will focus on how characterizing and monitoring tumor genomes with biological fluid-base samples
Session Objectives: After attending this session, participants should be able to:

  • To understand how the use of human gene expression can
    augment the diagnosis of infectious diseases.
  • Compare characteristics of the nasal and blood
    transcriptomes for respiratory virus diagnosis.
  • Understand how to apply liquid biopsies for the advancement
    of precision medicine and evaluate the scope of clinical
    utility for liquid biopsies in cancer. Understand the current
    challenges and possible solutions for the implantation of liquid
    biopsy in cancer management.
5:00 PM – 5:45 PM Use of Human Gene Expression for the Diagnosis of Respiratory Viral Infection
Gregory Storch (St. Louis, USA)
5:45 PM – 6:30 PM Nasopharyngeal Cancer Screening Among Asymptomatic Volunteers by Circulating Tumor DNA Analysis
Rossa Chiu (Shatin, Hong Kong)
6:30 PM – 8:00 PM Get Together in Exhibit Hall
Reception

Friday, May 17, 2019

8:30 AM – 10:00 AM The ACMG/AMP Standards & Guidelines for Germline Variant Interpretation & Updates
Clinical Implementation of the AMP/ASCO/CAP Standards and Guidelines for Somatic Variant Interpretation and Reporting
General Session
Moderators: Elaine Spector (Aurora, USA) and Victoria Pratt (Indianapolis, USA)
Session Description: In 2015 and 2017, AMP partnered with other stakeholders to develop and publish the Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology and Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, respectively. This session will discussion the evidence used for classification, interpretation, and reporting of germline and somatic variants, and provide practical examples of how to implement the guidelines for laboratories both currently performing germline and somatic NGS testing and those considering bringing the technology into their laboratories.
Session Objectives: After this session, participants will be able to:

  • Evaluate the difference between strong and weak evidence regarding the pathogenicity of a germ-line sequence variant.
  • Identify the difference between interpretation of germ-line and somatic sequence variants.
  • Apply information contained in various databases e.g., ClinVar/ClinGen.
8:30 AM – 9:15 AM Establishing Standards and Resources for Interpreting Cardiomyopathy Variants
Birgit Funke (Danvers, Boston)
9:15 AM – 10:00 AM Clinical Implementation of AMP/ASCO/CAP Guidelines for Somatic Variant Interpretation and Reporting in Cancer NGS Testing
Marilyn M. Li (Philadelphia, USA)
10:00 AM – 10:45 AM Coffee Break & Poster Visits (Odd Poster Numbers)
Coffee Break
10:45 AM – 11:45 AM Abstract Session: Cancer Genomics (Solid Tumor)
Abstract Session
Moderators: Andrea Ferreira-Gonzalez (Richmond, USA) and Yuan Ji (Salt Lake City, USA)
Session Description: Oral Presentations from Abstracts
Session Objectives: After this session, participants will be able to:

  • Analyze presentations of abstracts highlighted by the
    Organizing Committee as particularly significant.
  • Evaluate the scientific merit and significance of these selected
    studies through further discussion with the authors.
10:45 AM – 11:00 AM Clinical Implication of ctDNA Analysis in Advanced Lung Carcinoma Patients Using Different Technologies: Real-Time PCR and MALDI-TOF
Pierre-Jean Lamy (Montpellier, France)
11:00 AM – 11:15 AM Adjusting for Variation in Tumor Mutation Burden Using a Cancer-Specific Threshold in Whole Exome Sequencing
Wei Song (New York, USA)
11:15 AM – 11:30 AM Integrated Genomic Profiling of 289 Pediatric Brain Tumors Uncovers Genomic Signatures Significantly Impacting Patient Care
Fumin Lin (Philadelphia, USA)
11:30 AM – 11:45 AM Biomarker Analysis on Limited Biopsy Lung Cancer Samples in Tertiary Care Cancer Centre in South India Basavatarakam Indo American Cancer Hospital, Hyderabad, India
Surisetti Sudha Murthy (Hyderabad, India)
10:45 AM – 11:45 AM Abstract Session: Cancer Genomics (Hemato-oncology) 
Abstract Session
Moderators: Megan Lim (Philadelphia, USA) and Weiqiang (John) Zhao (Columbus, USA)
Session Description: Oral Presentations from Abstracts
Session Objectives: After this session, participants will be able to

  •  Analyze presentations of abstracts highlighted by the Organizing Committee as particularly significant.
  • Evaluate the scientific merit and significance of these selected studies through further discussion with the authors.
10:45 AM – 11:00 AM
Validation of Immunohistochemistry by a Monoclonal Antibody CAL2 on Trephine Biopsy for CALR Mutation Detection in Myeloproliferative Neoplasms
Man Kin Ng (Hong Kong)
11:00 AM – 11:15 A Comparison of a 640-Gene Next Generation Sequencing Panel to a Virtual 41-Gene Panel for the Diagnostic Utility in Unexplained Cytopenia
Gang Zheng (Baltimore, USA)
11:15 AM – 11:30 A T-Cell Clonality Testing by Next Generation Sequencing Facilitates the Initial Diagnosis and Disease Monitoring of Cutaneous T-Cell Lymphomas
Jinjuan Yao (New York, USA)
11:30 AM – 11:45 AM
Clinical Implications of Cytogenetic Heterogeneity in BCR-ABL1 Fusion Positive Adult B Cell Acute Lymphoblastic Leukemia
Xinyan Lu (Chicago, USA)
10:45 AM – 11:45 AM Abstract Session: Constitutional Genetics
Abstract Session
Moderators: Marilyn M. Li (Philadelphia, USA) and John Maris (Philadelphia, USA)
Session Description: Oral Presentations from Abstracts
Session Objectives: After this session, participants will be able to:

  • Analyze presentations of abstracts highlighted by the Organizing Committee as particularly significant.
  • Evaluate the scientific merit and significance of these selected studies through further discussion with the authors.
10:45 AM – 11:00 AM Prospective Study to Determine the Spectrum of Mutations among Patients with Multiple Endocrine Neoplasia 1 (MEN-1) and to Identify “At Risk”, First-Degree Relatives
Rekha Pai (Vellore, India)
11:00 AM – 11:15 AM
Five Year Experience of Clinical Next-Generation Sequencing for Somatic Overgrowth and Related Syndromes: Non-PIK3CA Cumulative Findings
Yang Cao (St. Louis, USA)
11:15 AM – 11:30 AM
An International Interlaboratory Study of Complex Variant Detection by NGS
Stephen Lincoln (San Francisco, USA)
11:30 AM – 11:45 AM
High-Risk Cytogenetics in Multiple Myeloma: Further Scrutiny of Deletions within the IGH Gene Region Enhances Risk Stratification
Jennifer N. Sanmann (Omaha, USA)
12:00 PM – 12:45 PM Industry Symposia
Industry Symposia
12:45 PM – 1:45 PM Lunch in the Industrial Exhibition
Lunch Break
1:45 PM – 3:15 PM New Discoveries from Genome-scale Sequencing
General Session
Moderators: Marilyn Li (Philadelphia, USA) and Elaine Spector (Aurora, USA)
Session Description: Copy number variations (CNVs) in  the human genome comprise a significant proportion of the variants.  CNVs and structural changes are one of the most common causes of human diseases. New approaches are being developed for the detection of CNVs and can be implemented for clinical use to improve diagnostic yield and facilitate new discoveries. Disease-causing germ line variants, including SNVs/indels and CNVs account for a significant portion of human cancer. These variants can be detected through tumor or tumor/normal paired analysis. Interpretation of these variants and ultimately delivery of the results are new challenges for both laboratory and clinical professionals.
Session Objectives: After this session, participants will be able to:

  • Understand the pros and cons of traditional and new methods of CNV detection
  • Understand the clinical significance of CNVs and SVs
  • Describe germline mutations associated with human cancer
  • Understand the challenges in interpretation of variant of uncertain significance
1:45 PM – 2:30 PM Genome-wide, Comprehensive Structural Variation Detection Using Multiple Technologies
Charles Lee (Farmington, USA)
2:30 PM – 3:15 PM Results on Incorparating Genome-Scale Sequencing into Care of Childhood Cancer Patients
Sharon E. Plon (Houston, USA)
3:15 PM – 3:45 PM Coffee Break (Exhibit Hall)
Coffee Break
3:45 PM – 4:45 PM Advances in Infectious Disease
Breakout Session
Moderators: David Hillyard (Salt Lake City, USA) and Robert Osamura (Tokyo, Japan)
Session Description: This session will first address the value of Co-testing of HPV with cytology which is recommended as the most accurate method as compared with cytology or HPV alone. The results from a study of 2495 co-tested cytology cases with biopsy follow-up of 404 cases to study infection rate, typing, the sensitivity and specificity and quality control will be discussed as well as a comparison to published data from China and abroad. The session will also include a presentation of issues for Next-generation sequencingbased metagenomic testing for pathogens and commensals.
This presentation will highlight the use of metagenomics-based testing for infectious syndromes and summarize benefits of metagenomic testing, remaining challenges, and examples of successful implementation.
Session Objectives: After this session, participants will be able to:

  • Identify unmet needs in pathogen syndromic testing and describe technical advances that will likely contribute to improved multiplex testing.
  • Evaluate the emerging potential for improved patient management based on examination of host response biomarkers
  • Understand new developments in Next Generation sequencing and informatic technologies with high potential for improving patient care
3:45 PM – 4:15 PM Co-Test of HR-HPV with Cytology in Cervical Smear of Liquid Base Cytology: Experiences in a Beijing Hospital
Lan Chen (Beijing, China)
4:15 PM – 4:45 PM Metagenomics-Based Testing in Routine Practice, Are We Ready?
Robert Schlaberg (Salt Lake City, USA)
3:45 PM – 4:45 PM Advances in Constitutional Genetics
Breakout Session
Moderators: Elaine Spector (Aurora, USA) and Alka Chaubey (Duluth, USA)
Session Description: Population screening for inherited disorders has been in place for many years. Screening includes newborns, children and adults.  The results of screening individuals (children and adults) for thalassemias in Southern China and implementation of treatment will be discussed. Nextgeneration sequencing adds a new layer of testing for babies with abnormal newborn screening results. Carriers for pathogenic variants will be able to be distinguished from affected babies with two pathogenic variants in a gene.  Implementation of nextgeneration sequencing technologies is allowing for carriers of these disorders and individuals with two variants in a gene to be distinguished.
Session Objectives: After this session, participants will be able to:

  • Identify the differences between population screening for a disorder and testing affected individuals.
  • Identify the components of accurate clinical and molecular diagnosis of hemoglobinopathies in southern China.
  • Identify the advances in newborn screening provided by whole genome sequencing including mitochondria that can identify sequence variants as well as copy number variants.
3:45 PM – 4:15 PM Mutation Characterization and Precise Molecular Diagnosis of Inherited Disorders of Hemoglobin
Xiangmin Xu (Guangzhou, China)
4:15 PM – 4:45 PM Newborn Screening to Whole Genome Sequencing
Madhuri Hegde (Waltham, USA)
3:45 PM – 4:45 PM Liquid Biopsy: Clinical Validity and Clinical Utility
Breakout Session
Moderators: Rami Mahfouz (Beirut, Lebanon) and Chris Wong (Hong Kong)
Session Description: The session will discuss the importance of the use of circulating tumor DNA in many different types of cancer where ctDNA was found to be useful for diagnosis and treatment monitoring as well. The latter is best achieved through sequential testing of ctDNA. This session will also discuss the use of circulating DNA in monitoring response to therapy upon the use of, Lorlatinib, a novel inhibitor across ALK variants. The effect of such medications is now being proposed to be monitored through circulating tumor DNA. Response to treatment and prediction of early relapse may be followed through testing for ctDNA at different stages of treatment.
Session Objectives: After this session, participants will be able to:

  • Understand the importance of circulating tumor DNA in assessing minimal residual disease and response to therapy.
  • Realize the presence of multiple testing modalities for ctDNA.
  • Recognize the essential use of sequential testing for ctDNA for adequate patient care and management.
  • Describe the use of circulating DNA in disease diagnosis and prognosis.
  • Understand the importance of ctDNA in assessing response to treatment.
  • Estimate the use of ctDNA in following ALK alterations to monitor for resistance.
3:45 PM – 4:15 PM Use of Circulation Tumor DNA in Patient Management: Data from Lung, Colorectal, Bladder and Breast Cancer
Alexey Aleshin (San Carlos, USA)
4:15 PM – 4:45 PM Longitudinal Liquid Biopsy in the Lorlatinib Trial for Patients with Refractory/Resistant Aslk-driven Neuroblastoma
Yael P. Mosse (Philadelphia, USA)
5:00 PM – 6:00 PM Roundtable Discussion: Molecular Diagnosis of Infectious Diseases
Roundtable Discussion
Moderators: David Hillyard (Salt Lake City, USA) and Benedict Yan (Singapore)
Session Description: Traditional approaches to pathogen detection and characterization are rapidly being complemented or eclipsed by technologies allowing multiplex detection, advanced sequencing and interrogation of host response. Across this spectrum, testing is becoming more rapid and decentralized allowing for easy access and quick resulting for improved management of acutely
infected patients. This session will examine new developments in syndromic pathogen testing, next generation sequencing, and host response interrogation and their potential impact on patient care.
Session Objectives: After attending this session, participants should be able to:

  • Identify unmet needs in pathogen syndromic testing and
    describe technical advances that will likely contribute to
    improved multiplex testing.
  • Evaluate the emerging potential for improved patient
    management based on examination of host response
    biomarkers
  • Understand new developments in Next Generation sequencing
    and informatic technologies with high potential for improving
    patient care.
5:00 PM – 6:00 PM Roundtable Discussion: Next Generation Molecular Infectious Disease Testing
David R. Hillyard, MD (Salt Lake City, USA)
5:00 PM – 6:00 PM Roundtable Discussion: Molecular Diagnosis in Underserved Areas
Roundtable Discussion
Moderators: Megan Lim (Philadelphia, USA) and Federico Monzon (Houston, USA)
Session Description: The entire spectrum of knowledge acquisition to application to molecular diagnostic laboratory testing to clinical implementation is rapidly evolving. Thus, the utilization of molecular diagnostics is dependent on resources for lab implementation, clinical implementation and availability of targeted therapies.  These factors contribute to variable utilization in underserved areas. This roundtable session will focus on barriers, potential solutions and opportunities for collaborations to address the discrepancies in the utilization of molecular diagnosis in resource-scarce regions.
Session Objectives: After this session, participants will be able to:

  • Formulate an approach to identify disparities in implementation of molecular testing in different countries.
  • Interpret regulatory and reimbursement policies that impact molecular genetic testing.
  • Employ methods to implement sharing of educational resources related to molecular testing.
5:00 PM – 6:00 PM Roundtable Discussion: Molecular Diagnosis in Underserved Areas
Megan S. Lim (Philadelphia, USA)
5:00 PM – 6:00 PM Roundtable Discussion: Implementation of the Germline and Somatic Guidelines
Roundtable Discussion
Moderators: Elaine Spector (Aurora, USA), Andrea Ferreira-Gonzalez (Richmond, USA), Marilyn Li (Philadelphia, USA), and Birgit Funke (Boston, USA), Alka Chaubey (Waltham, USA) and
Madhuri Hedge (Waltham, USA)
Session Description: Guidelines for the interpretation of sequence variants in germ line and somatic cells have been issued by AMP and ACMG since 2015.  Examples of difficult to interpret variants will be presented.
Session Objectives: After this session, participants will be able to:

  • Analyze difficult germ-line sequence variants.
  • Analyze difficult somatic sequence variants.
  • Delineate the differences between analyzing germ-line and somatic variants.
5:00 PM – 6:00 PM Roundtable Discussion: Implementation of the Germline and Somatic Guidelines
Elaine B. Spector (Aurora, USA)

Saturday, May 18, 2019

8:00 AM – 9:00 AM Abstract Session: Infectious Diseases
Abstract Session
Moderators: David Hillyard (Salt Lake City, USA)
Session Description: Oral Presentations from Abstracts
Session Objectives: After this session, participants will be able to:

  • Analyze presentations of abstracts highlighted by the Organizing Committee as particularly significant.
  • Evaluate the scientific merit and significance of these selected studies through further discussion with the authors.
08:00 AM – 08:15 AM
Comparative Whole-Genome Analysis between Pregnant Women-Colonizing and Neonate-Infecting Group B Streptococcus Isolates
Lijuan Wu (Shenzhen, China)
08:15 AM – 08:30 AM
Suppressor of Cytokine Signaling (SOCS)-3 Downregulation Is Associated with Increased Proinflammatory Responses in Diabetic Individuals with M. Tuberculosis Infection
Kiran Iqbal (Karachi, Pakistan)
08:30 AM – 08:45 AM
High Prevalence of NDM-1-Producing Enterobacter Cloacae from Three Tertiary Hospitals in China
Bin Huang (Grangzhou, China)
08:45 AM – 09:00 AM
Incidental Detection of Malignancies in Metagenomics Cell-Free DNA Testing
Wei Gu (Menlo Park, United States)
8:00 AM – 9:00 AM Abstract Session: Bioinformatics
Abstract Session
Moderators: Elaine Gee (Windsor, USA) and Annette Meredith Leon (Elmwood Park, USA)
Session Description: Oral Presentations from Abstracts
Session Objectives: After this session, participants will be able to:

  • Analyze presentations of abstracts highlighted by the Organizing Committee as particularly significant.
  • Evaluate the scientific merit and significance of these selected studies through further discussion with the authors.
08:00 AM – 08:15 AM
Identifying True Somatic Variants in Cancer Using Machine Learning
Chao Wu (Philadelphia, USA)
08:15 AM – 08:30 AM
Development and Clinical Validation of a Bioinformatics Pipeline for CNV Detection on Cancer NGS Panels
Kajia Cao (Philadelphia, USA)
08:30 AM – 08:45 AM
Pan-Cancer Repository of Validated Natural and Cryptic mRNA Splicing Mutations
Peter Rogan (London, Canada)
08:45 AM – 09:00 AM
Error Rate Normalization to Establish Position-Specific Limits of Detection in Next Generation Sequencing Assays
Julian D’Angelo (San Diego, USA)
8:00 AM – 9:00 AM Abstract Session: Technology and Education
Abstract Session
Moderators: Elaine Spector (Denver, USA) and Alka Chaubey (Waltham, USA)
Session Description: Oral Presentations from Abstracts
Session Objectives: After this session, participants will be able to:

  • Analyze presentations of abstracts highlighted by the Organizing Committee as particularly significant.
  • Evaluate the scientific merit and significance of these selected studies through further discussion with the authors.
08:00 AM – 08:15 AM
The Clinical Utility of Tumour Mutational Signatures for Identifying Hereditary Colorectal Cancer and Polyposis Syndromes
Daniel Buchanan (Melbourne, Australia)
08:15 AM – 08:30 A
A Noise-Cancelling Method Based on Information Theory for ctDNA Variant Calling
Hao Chen (Shenzhen, China)
08:30 AM – 08:45 AM
Performance Evaluation of the BioFire FilmArray® Respiratory Panel 2 Plus (RP2plus) for the Detection of Respiratory Viruses in Swab Specimens
Benedict Yan (Singapore)
08:45 AM – 09:00 AM
Oncologists’ Review of ctDNA EGFR Mutation Testing Reports
Zandra Deans (Edinburgh, United Kingdom)
9:00 AM – 10:00 AM Practical Clinical Bioinformatics: From Automation to Validation 
Breakout Session
Moderators: Elaine Gee (Windsor, USA) and Kajia Cao
Session Description: This session will discuss the implementation of bioinformatics tools and pipelines for clinical testing. This session will highlight a method for automating analysis by applying deep learning to interpret digital histopathological images and the construction of a bioinformatics pipeline to process Illumina-based NGS assay. A case study for the validation of an NGS-based assay for a myeloid neoplasm test in accordance with AMP/CAP bioinformatics validation published guidelines will be presented.
Session Objectives: After attending this session, participants should be able to:

  • Identify how machine learning methods can be applied to automate large scale digital histopathological image retrieval
  • Interpret the recommendations for NGS bioinformatics pipeline validation published by AMP/CAP/AMIA
  • Outline how to apply the NGS bioinformatics pipeline validation recommendations to clinical practice
9:00 AM – 9:30 AM Developing Large Scale Histopathological Image Retrieval System Using Deep Texture Representations
Shumpei Ishikawa (Tokyo, Japan)
9:30 AM – 10:00 AM Best Practices for Bioinformatics Pipeline Validation: The AMP/CAP Guidelines With A Clinical Implementation Example
Somak Roy (Pittsburgh, USA)
9:00 AM – 10:00 AM Tumor Mutational Burden
Breakout Session
Moderators: Marilyn Li (Philadelphia, USA) and Yajuan Li (Seattle, USA)
Session Description: Tumor Mutational Burden (TMB) has emerged recently as a new predictive biomarker for immunotherapy response in some cancer types for identification of patients that will benefit from immunotherapy. TMB was initially assessed using whole exome sequencing, however, it can also be efficiently assessed using targeted sequencing panels to reduce the turnaround time and costs. TMB still suffers from specific limitations, such as absence of standardization, and these challenges will need to be addressed before broader use in different tumor types. A systematic harmonization process will be required for optimal utility and alignment across all platforms.
Session Objectives: After this session, participants will be able to:

  • Understand what is TMB and its clinical significance.
  • Understand factors that may affect TMB.
  • Understand challenges in determining TMB
9:00 AM – 9:30 AM Timing and Signatures of Hypermutant Cancer
Adam Shlien (Toronto, Ontario)
9:30 AM – 10:00 AM Genomic and Molecular Landscape of DNA Damage Repair Deficiency
David Wheeler (Houston, USA)
9:00 AM – 10:00 AM Continuing Education for Pathologists and Clinical Molecular Geneticists
Breakout Session
Moderators: Elaine Spector (Aurora, USA) and Robert Osamura (Tokyo, Japan)
Session Description: NGS has become a routinely used technology in molecular diagnostics. Despite its ubiquity of use, its implementation can still be a challenge and validating laboratory developed tests (LDTs) using this technology is complex. Results from an external quality assessment (EQA) scheme for NGS will be presented.  The study  demonstrates a global perspective on the quality of NGG testing process, and demonstrates a role for this type of activity in helping laboratories to benchmark and improve their NGS testing.  Components of an educational program in Japan for genomic pathology, especially directed to treatment of clinical samples in the pre-analytical phase will be presented.
Session Objectives: After this session, participants will be able to:

  • Define the need for quality assurance programs for clinical NGS testing.
  • Know the need for continuing education programs for pathologists and clinical molecular diagnostic laboratory directors.
  • Implement an appropriate quality assurance program in their laboratory.
9:00 AM – 9:30 AM Educational Program for Genomic Pathology at JSP
Eiichi Morii (Osaka, Japan)
9:30 AM – 10:00 AM Quality Assurance in Molecular Testing: Evidencing the Global Quality to Next Generation Sequencing
Simon Patton (Manchester, United Kingdom)
10:00 AM – 10:45 AM Visit Posters and Exhibit (Even-numbered Posters Attended)
Coffee Break
10:45 AM – 11:30 AM Industry Symposia
Industry Symposia
11:45 AM – 1:15 PM Artificial Intelligence Powered Informatics Integration
New Technologies: CRISPR
General Session
Moderators: Elaine Gee (Windsor, USA) and Andrea Ferreira-Gonzalez (Richmond, USA)
Session Description: RNA plays important and diverse roles in biology, but molecular tools to manipulate and measure RNA are limited. RNA- targeting CRISPR effector Cas13 can be engineered for mammalian cell RNA knockdown, binding, and RNA editing. Cas13a with isothermal amplification can be established as a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity. In this session the use of this Cas13a-based molecular detection platform, termed SHERLOCK, will be described and future
clinical applications discussed. This session will also highlight the informatics behind creating a centralized data portal in the cloud for serving data from distributed research centers with the goal
of advancing treatment of pediatric disease. Precision medicine is supported by large scale integrated data analysis of various data sources, including genomic and clinical phenotype data. Progress in understanding genomic alterations relevant to rare disease is limited by data silos that isolate data and limit its utility. Consolidation of genomic data from the broader community could leverage the statistical power associated with large scale analysis to enable new insights.
Session Objectives: After attending this session, participants should be able to:

  • Identify the benefits of investing in building centralized data resources for genomic data.
  • Understand the informatics requirements for creating a cloudbased data resource that aggregates and serves genomic and phenotype data from distributed data sources.
  • Describe how CRISPR technology can be modified to target RNA and understand how CRSIPR technology could be used in the clinical laboratory.
  • Identify challenges for adoption of CRISPR technology for the clinical laboratory.
11:45 AM – 12:30 PM Informatics Ecosystem Behind Data Consolidation for the Gabrielle Miller Kid’s First Pediatric Data Resource Program
 Adam Resnick (Philadelphia, USA)
12:30 PM – 1:15 PM Nucleic Acid Detection with CRISPR-Cas13
Omar Abudayyeh (Cambridge, USA)
1:15 PM – 1:30 PM Poster Awards Acknowledgements / Closing Remarks
Moderators: Marilyn Li (Philadelphia, USA)
1:30 PM – 2:30 PM Lunch in the Industrial Exhibition
Lunch Break
2:30 PM – 3:00 PM Storing & Sharing Big Data, Precision Medicine Knowledgebase, New Technology & Population genetics
Breakout Session
Storing & Sharing Big Data, Precision Medicine Knowledgebase
Moderators:Elaine Gee (Windsor, USA), Annette Meredith Leon (Elmwood Park, USA), Chris Wong (Hong Kong) and Sainan Wei (Lexingto, USA)
Description: Genetic variations identified from a bioinformatics pipeline require annotation to provide context into the clinical implications of the variants identified. This session will highlight data aggregation and visualization methods of somatic variants and their curated annotations on open precision medicine knowledgebase platforms that aid in clinical decision support.
This session will dive into the standardization of somatic genetic alterations and associated biological, clinical, and therapeutic supporting evidence for presentation on the precision oncology knowledgebase platform OncoKB and describe its integration with larger datasets on cBioPortal.
Objectives: After attending this session, participants should be able to:

  • Identify the complexity behind aggregating and standardizing variant annotations from distributed sources
  • Describe the methods for accessing data in OncoKB, from website portals to programmatic APIs
  • Outline the hierarchy for data organization to link genes, genetic alterations, indications, and levels of evidence
Harnessing Genomic Big Data for Evidence-Based Precision Medicine: A Case Study using OncoKB and cBioPortal
Debyani Chakravarty (New York, USA)
New Technology
Description:Rapid accurate diagnosis of emerging infectious diseases is important for treatment, monitoring and infection control during outbreak. However, the development of a comprehensive and sensitive diagnostic assay is challenging. This session describes how new technology “NGS” could be applied to supplement routine diagnostic test in clinical diagnostic laboratory.
Objectives: After this session, participants will be able to:

  • Understand the application of NGS for multiplex serological detection of viral infections.
  • Understand the laboratory validation of new diagnostic platform.
Epitobe-Based High Resolution Multiplex Serology fpr Infectious Disease Investigation
Linfa (Lin-Fa) Wang (Singapore)
Population Genetics
Description: Population database is important for variant curation. Different populations may carry different frequencies for both polymorphic alleles and disease-causing alleles. Genome aggregation database for different populations can help not only population specific variant analysis, but also contribute to the global database and improve the resources for different populations.
Objectives: After this session, participants will be able to:

  • Describe the utility and importance of population-specific mutation database
  • Understand the application of gene mutation database in disease diagnosis.
Chinese Gene Mutation Database (CNGMD) from 30K Chinese Genomes and Exomes for Disease Diagnostics to Eastern Asian Population
Jonathan Liu (Pennsylvania, USA & Beijing, China)