Next-Generation Sequencing as a Clinical Test Banner

May 16

8:00 am Symposia Registration and Morning Coffee

9:00 Part 1: Primer: NGS as a Clinical Test

Next-Generation Sequencing (NGS) is used widely in clinical research for the discovery of disease-associated genes, and the clinical community is beginning to embrace this technology for diagnostic testing. The rapid evolution of NGS technologies presents significant opportunities and challenges for researchers and clinicians for improving health outcomes, particularly with respect to an increased emphasis on personalized and preventive medicine. Adoption of NGS in the clinical laboratory setting requires the adoption of many processes and procedures, such as the analytic and clinical validation of the test, CLIA certification/CAP accreditation, standards for reference materials, availability for proficiency testing, and questions regarding reimbursement and informed consent. The success of NGS as a viable diagnostic modality depends on many branches of the health care community working together. This session will be informative and practical for the researcher and laboratorians who are considering launching NGS as a clinical test.


Seth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

Avni Santani, Ph.D., Assistant Professor, Clinical Pathology, Perelman School of Medicine, University of Pennsylvania

12:00 pm Enjoy Lunch on Your Own

Part 2: Clinical NGS Assay Development and Validation

12:55 Chairperson’s Opening Remarks

David I. Smith, Ph.D., Professor, Laboratory Medicine & Pathology, Mayo Clinic

1:00 Next-Generation Sequencing Technologies and Their Clinical Adoption

David I. Smith, Ph.D., Professor, Laboratory Medicine & Pathology, Mayo Clinic

NGS has transformed how we can look at our DNA. There are many applications of NGS technologies including whole genome sequencing, exome sequencing, small gene panel sequencing and even transcriptome sequencing. I will describe the various applications of NGS and how they will quickly develop into powerful and viable clinical tools that will transform how we care for patients.

1:30 Developing NGS as a Clinical Assay: Strategies for Design, Implementation and Validation

Matthew Lebo, Ph.D., Director, Bioinformatics, and Instructor, Pathology, Brigham & Woman’s Hospital, Harvard Medical School

This talk will focus on the necessary components to launch an NGS testing platform in a clinical laboratory. This includes comparison of targeted panels, exome and genome sequencing. Specific focus will be paid to implementing the bioinformatics infrastructure needed to process NGS data, including important points of consideration. Strategies for dealing with validation, quality control and completeness will also be reviewed.

2:00 Talk Title to be Announced

Saumya Pant, Ph.D., Senior Research Investigator & Head, Sequencing Technologies, Bristol-Myers Squibb

2:30 Validation Approach for Developing a Pediatric Cancer Genomic Test

Nazneen Aziz, Ph.D., Chief Research Officer & Senior Vice President, Phoenix Children’s Hospital

Treatment for childhood cancer with chemotherapy, radiation and/or hematopoietic cell transplant can result in long-term comorbidities that may not become evident for many years. Unlike the rapid adoption of genomic analysis of adult cancers, pediatric cancer genomic analysis for clinical management has been surprisingly slow. Dr. Aziz will describe the validation approach for a test that analyzes the malignant exome, normal exome and RNA analysis being developed at Phoenix Children’s Hospital (PCH). Genomic analysis is critical for understanding pediatric cancer mechanisms that will lead to development of new therapeutics as the need is acute. Virtually no new therapy has been introduced in the past two decades. Treatment for relapsed patients is lower than in adults yet a large number of childhood cancer patients will relapse. In stark contrast to the rapid introduction of targeted therapies in adults, more effective therapies are unavailable in pediatric cancer.

3:00 Networking Refreshment Break

3:30 Platform Comparison for Circulating Tumor DNA as a Biomarker in Clinical Laboratory

Rajyalakshmi Luthra, Ph.D., Professor, Pathology and Laboratory Medicine, Director, Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center

4:00 Clinical Utility of a Next-Generation Sequencing Oncology Panel Designed for Low Input DNA

Midhat Farooqi, M.D., Ph.D., Molecular Genetic Pathology Fellow, Pathology & Laboratory Medicine, Hospital of the University of Pennsylvania

One drawback to next-generation sequencing (NGS)-based clinical oncologic testing is high DNA input requirements, which may not be met when only scant tumor material is available or in samples with low DNA quality. Given the importance of testing as many clinical specimens as possible, we developed a focused NGS panel of 20 cancer-associated genes that captured hotspot amplicons and tumor suppressor exons, while requiring < 10ng input DNA. The clinical utility for this panel lies in the ability to detect clinically significant variants (i.e. those involved in solid tumor prognostication and/or therapy selection) for specimens unable to be tested by larger, more conventional, panels.

Part 3: ThinkTank: Next-Generation Sequencing in Clinical Diagnostics

4:30 Moderated Discussion

Moderator: Elaine Lyon, Ph.D., Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Associate Professor, University of Utah School of Medicine; Past President, Association for Molecular Pathology


Kojo SJ Elenitoba-Johnson, M.D., Peter C. Nowell, M.D., Professor, University of Pennsylvania Perelman School of Medicine; Director, Center for Personalized Diagnostics; Director, Division of Precision and Computational Diagnostics

Jennifer J.D. Morrissette, Ph.D., Assistant Professor, Clinical Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania

Avni Santani, Ph.D., Assistant Professor, Clinical Pathology, Perelman School of Medicine, University of Pennsylvania

5:30 Close of Symposium