Clinical NGS Assays

Molecular diagnostics, particularly next-generation sequencing (NGS), have become an integral component of disease diagnosis. Still, there is work to be done to establish these tools as the standard of care. The Third Annual Clinical NGS Assays event will address NGS assay validation, establishing NGS standards, and determining clinical relevance. The pros and cons of various techniques such as gene panels, whole exome, and whole genome sequencing will also be debated with regards to depth of coverage, clinical utility, and reimbursement. Overall, this event will address the needs of both researchers and clinicians while exploring strategies to increase collaboration for improved patient outcomes.


7:30 am Main Conference Registration & Morning Coffee


8:30 Chairperson’s Opening Remarks

Kent Lohman, Ph.D., MRIGlobal

8:40 Best Practices for Using Genome in a Bottle Reference Materials to Benchmark Variant Calls

Justin_ZookJustin Zook, National Institute of Standards and Technology

NIST has hosted the Genome in a Bottle Consortium to develop well-characterized human genomes to enable benchmarking of variant calls. We also are working with the Global Alliance for Genomics and Health Benchmarking Team to develop tools to calculate standardized performance metrics when comparing variant calls to our benchmark samples. I will discuss our well-characterized genomes and how to use them to benchmark variant call accuracy, and important considerations for clinical laboratories.

9:10 NGS in Clinical Diagnosis: Aspects of Quality Management

Pinar Bayrak-Toydemir, M.D., Ph.D., FACMG, Associate Professor, Pathology, University of Utah; Medical Director, Molecular Genetics and Genomics, ARUP Laboratories

Next-generation sequencing (NGS) technologies continue to be improved in clinical laboratories, enabling rapid transformations in genomic medicine. NGS could be an extensive process both at the wet bench and bioinformatics levels. Quality assurance steps including how to detect sample switch, alignment and variant calling algorithms for in-dels, and necessity for Sanger sequencing confirmation will be discussed using interesting clinical cases.

9:40 Thorough Validation and Implementation of Preimplantation Genetic Screening for Aneuploidy by NGS

Rebekah_ZimmermanRebekah Zimmerman, Ph.D., Laboratory Director, Clinical Genetics, Foundation for Embryonic Competence

We have developed and validated a targeted NGS assay for whole chromosome aneuploidy that has comparable accuracy to qPCR, while improving cost and throughput limitations. Also of critical interest, we have explored limits of detection for mosaicism and segmental aneuploidy, which are two areas of major concern among the IVF community.

10:10 Coffee Break in the Exhibit Hall with Poster Viewing


10:55 Chairperson’s Remarks

Avni B. Santani, Ph.D.,The Children’s Hospital of Philadelphia

11:00 Are We There Yet? The Odyssey of Exome Analysis and Interpretation

Avni_SantaniAvni B. Santani, Ph.D., Director, Genomic Diagnostics, Pathology and Lab Medicine, The Children’s Hospital of Philadelphia

The comprehensive analysis of complex genomic data such as exome sequencing presents several challenges to a clinical laboratory. Factors including phenotyping, use of public and internal databases and balancing sensitivity with a rapid return of results are critical. Using several cases as examples, the critical areas during the exome interpretation process will be highlighted.

11:30 Challenges in Exome Interpretation: Intronic Variants

Rong_MaoRong Mao, M.D., Associate Professor, Pathology, University of Utah; Medical Director, Molecular Genetics and Genomics, ARUP Laboratories

Exome sequencing, the targeted sequencing of the subset of the human genome that is protein coding, is a powerful and cost-effective new tool for dissecting the genetic basis of diseases and provide a diagnostic odyssey for undiagnostic rare and complex conditions. Interpretations of variants detected by exome sequencing, determination of the pathogenicity and clinical significant of the variants are big challenge. Hereby I present the intonic variants detection and interpretation by exome sequencing

12:00 pm Exome Sequencing: Case Studies of Diagnostic and Ethical Challenges

Lora_BeanLora J. H. Bean, Ph.D., Assistant Professor, Human Genetics, Emory University

Exome sequencing in the age of variant databases and data sharing is a powerful tool in genetic diagnostics; however, analysis of variants across the entire exome presents interpretative and ethical challenges. Cases will be presented demonstrating the challenge of diagnosing a newly described syndrome and making a dual diagnosis, as well as cases exemplifying the challenges of technical limitations, specifically the inability to detect deletions or sequence genes with pseudogenes.

12:30 Sponsored Presentation (Opportunity Available)

1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:30 Refreshment and Cookie Break in the Exhibit Hall with Poster Viewing


2:00 Chairperson’s Remarks

Karl V. Voelkerding, M.D., ARUP Laboratories

2:05 Assessing the Feasibility of Establishing Performance Standards for Next Generation Sequencing Based Genetic Testing

Karl_VoelkerdingKarl V. Voelkerding, M.D., Professor, Pathology, University of Utah; Medical Director for Genomics and Bioinformatics, ARUP Laboratories

In this presentation, the concepts of validation and establishment of performance characteristics for NGS tests will be discussed in relation to CAP accreditation requirements. Results from the CAP methods based proficiency testing program for detection of germline variants launched in 2015 will be presented in the context of a discussion of the feasibility of establishing performance standards for germline NGS testing.

2:35 Clinical Cancer Genomics-Driving Precision Medicine

Shashi Kulkarni, MS, Ph.D., Vice Chairman, Research, Molecular and Human Genetics, Baylor College of Medicine Houston Texas; Chief Scientific Officer, Baylor Miraca Genetics Laboratory

Next-generation DNA sequencing technology is revolutionizing clinical cancer genomic diagnostics by enabling precision cancer medicine by directing molecularly targeted therapies. Adoption of NGS brings unprecedented challenges in incorporating this technology in the clinical setting. This presentation will provide a comprehensive overview on the key considerations for implementation of clinical next-generation sequencing including resource allocation, assay development, compliance, bioinformatics, data management, analysis and interpretation of data in a CAP/CLIA environment.

3:05 NGS Harmonization Manifold: From Data to Ontologies, from Computations to Knowledge

Vahan_SimonyanVahan Simonyan, Ph.D., Lead Scientist, Director, Bioinformatics; Principal Investigator, HIVE, Food and Drug Administration (FDA)

Multiple aspects of data and computation standardizations will be discussed from research and regulatory perspectives. Brief description of FDA’s NGS harmonization efforts in the form of High-performance Integrated Virtual Environment (HIVE) will be outlined and biocompute object database for harmonized computational protocols will be described.

3:35 An NGS Inter-Laboratory Study to Assess Performance and QC

Andrea Ferreira-Gonzalez, Ph.D., Chair, Molecular Diagnostics Division, Pathology, Virginia Commonwealth University Medical School

Trevor Brown, MSc, Vice President, Precision Medicine, SeraCare Life Sciences

NGS assays that accurately detect somatic mutations in tumor tissue are crucial to precision medicine. Laboratory-developed test procedures need to be accurate, precise, clinically relevant, and monitored for continued quality performance. However, the technical performance between laboratories has been difficult to assess because there are no widely accepted standards. This presentation describes an inter-laboratory study using Seraseq™ biosynthetic reference materials to assess different platforms, assays, and pipelines for routine QC use.

4:05 Refreshment Break in the Exhibit Hall with Poster Viewing

4:50 PANEL DISCUSSION: Whole Exome vs.Whole Genome

Moderator: Kent Lohman, Ph.D., MRIGlobal

Panelists: Avni B. Santani, Ph.D., Director, Genomic Diagnostics, Pathology and Lab Medicine, The Children’s Hospital of Philadelphia

Justin Zook, National Institute of Standards and Technology

  • Depth of coverage
  • Increasing speed
  • Impediments to WGS and WES becoming routine practice
  • What do clinicians want?
  • Reimbursement and coding

Slone Partners5:50 Wine & Cheese Pairing Welcome Reception in the Exhibit Hall with Poster Viewing

6:50 Close of Day


7:15 am Registration

7:30 Problem-Solving Breakout Discussions with Continental Breakfast

Clinical NGS Data for Translational Studies

Moderator: Helen Fernandes, Ph.D., Pathology & Laboratory Medicine, Weill Cornell Medical College


8:25 Chairperson’s Opening Remarks

Helen Fernandes, Ph.D., Weill Cornell Medical College

8:30 Applications of Clinical NGS Data for Translational Studies

Helen_FernandesHelen Fernandes, Ph.D., Pathology & Laboratory Medicine, Weill Cornell Medical College

This presentation will discuss how clinical NGS data obtained from formalin fixed paraffin embedded (FFPE) and Fine Needle Aspirate (FNA) derived tumor DNA is used for translational studies.

9:00 NGS-Based Tests: Understanding Performance, Sharing Data, and Providing Transparency

Živana Težak, Ph.D., Associate Director, Science and Technology, Office of In Vitro Diagnostics and Radiological Health (OIR), CDRH/FDA

As a part of the White House’s Precision Medicine Initiative, FDA was tasked with optimizing regulatory framework for NGS based clinical tests. This presentation will describe FDA’s current thinking on the content and possible use of standards in design and performance evaluation of NGS-based tests, crowdsourcing efforts to share and improve bioinformatics tools, and the use of public human genetic variant databases to help assessing clinical relevance of test results. Ultimately, the goal is to accelerate the clinical adoption of precision medicine while ensuring that the tests used are safe and effective.

9:30 Genetic Counseling in the Era of Genomic Medicine

Sarah_ScollonSarah Scollon, MS, C.G.C., Instructor, Pediatrics-Oncology, Baylor College of Medicine

As NGS has been incorporated into clinical care, genetic counselors have played critical roles in translating this new technology to patients. This presentation will share genetic counseling experiences from the NHGRI/NCI supported Clinical Sequencing Exploratory Research Consortium including the BASIC3 study at Baylor College of Medicine. Topics will include lessons learned consenting patients and communicating genomic test results and future challenges and opportunities in the era of genomic medicine.

Integrated DNA Technologies (IDT)10:00 Accurate Detection of Low Frequency Variants Using Novel, Molecular Tagged Adapters

Mirna Jarosz, Director, NGS Scientific Applications, Research & Development, Integrated DNA Technologies, Inc.

10:30 Coffee Break in Exhibit Hall with Poster Viewing

11:15 PLENARY KEYNOTE SESSION: Click here for details

12:50 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:20 Close of Clinical NGS Assays

1:25 Ice Cream and Cookie Break in the Exhibit Hall with Poster Viewing