SC3: NGS Assay Selection, Validation and Compliance
Room Location:  154

Avni Santani, PhD, Director, Genomic Diagnostics, Children’s Hospital of Philadelphia (AMP Member)

Birgit Funke, PhD, FACMG, Vice President, Clinical Affairs, Veritas Genetics; Associate Professor of Pathology, Harvard Medical School (AMP Genetics Subdivision Chair and Representative to the AMP 2018 Board of Directors; Member)

Karl Voelkerding, MD, Professor of Pathology, University of Utah School of Medicine (AMP Member)

Course Description:

Clinical NGS is going mainstream – technical, operational and regulatory perspectives. This course will cover the state-of-the-art exome sequencing as a first line clinical test, designing NGS assays for disorders with clinical and genetic heterogeneity and the current and future regulatory landscape for NGS diagnostics

Detailed agenda:

2:00 - 2:05 Chairperson’s Remark

Birgit Funke, PhD, FACMG, Vice President, Clinical Affairs, Veritas Genetics; Associate Professor of Pathology, Harvard Medical School (AMP Genetics Subdivision Chair and Representative to the AMP 2018 Board of Directors; Member)

2:05 - 2:55 State-of the Art Clinical NGS – Moving Towards Exome Sequencing as a First Line Test

Avni Santani, PhD, Director, Genomic Diagnostics, Children’s Hospital of Philadelphia (AMP Member)

A decade after clinical NGs made its debut, exome sequencing is on the verge of becoming the predominant genetic test. This presentation will provide a comprehensive overview on the key considerations for implementation of clinical exome sequencing including resource allocation, assay validation, data management, analysis and interpretation of data and re-analysis of exome data.

2:55 - 3:45 Designing NGS Assays for Inherited Disorders with Genetic and Clinical Heterogeneity

Birgit Funke, PhD, FACMG, Vice President, Clinical Affairs, Veritas Genetics; Associate Professor of Pathology, Harvard Medical School (AMP Genetics Subdivision Chair and Representative to the AMP 2018 Board of Directors; Member)

NGS based assays are optimal for disorders with clinical and genetic heterogeneity but the ability to interrogate unlimited numbers of genes requires careful consideration when designing the test to ensure optimal technical and clinical validity. This applies to large gene panels as well as exome based diagnostic testing. This presentation focuses on important considerations for content selection and test design. Topics covered include the evaluation of the clinical validity of gene-disease associations, how to deal with clinically important genes that are difficult to sequence by NGS and the development of standards for clinical NGS.

3:45 – 3:55 Coffee Break

3:55 - 4:45 Current and Future Regulatory Landscape for NGS Diagnostics

Karl Voelkerding, MD, Professor of Pathology, University of Utah School of Medicine (AMP Member)

Recently published guidelines for validation of next generation sequencing diagnostic assays have provided clinical laboratories with expert driven recommendations for both germline and somatic variant testing. Inclusive in these recommendations are guidance on numbers and types of samples for validation, test design, statistical approaches for data evaluation, and recommended quality metrics to implement and monitor. Continued interest and activity in the regulatory oversight of NGS diagnostic assays at the federal level is anticipated based on current legislative initiatives and FDA commentary. This presentation will focus on two areas of growing interest in the regulatory oversight of NGS diagnostic assays. These include the use of design control principles in the total analytical test lifecycle, and the feasibility of establishing performance thresholds for germline and somatic variant testing. Concepts and challenges for implementation will be discussed.

4:45 - 5:00 Q & A

Meet the instructors:

Santani_AvniAvni Santani, PhD, Director, Genomic Diagnostics, Children’s Hospital of Philadelphia (AMP Member)

Avni Santani, PhD, is the scientific director and has over seven years of experience in molecular diagnostic testing. She obtained her PhD at Texas A&M University and her clinical laboratory training in genetics at The Children’s hospital of Philadelphia. Dr. Santani holds specialty board certifications in Clinical Molecular Genetics and Clinical Cytogenetics. Her primary focus is on new test development and adoption of next generation sequencing technologies for diagnostic testing. Dr. Santani has experience in developing diagnostic tests for over 100 disease genes implicated in disorders such as hearing loss, epilepsy, Noonan syndrome, Rett syndrome, paraganglioma, neuroblastoma and others. Her training and experience make her an expert in a wide variety of genetic disorders, molecular biology applications and genomics.

Funke_BirgitBirgit Funke, Ph.D., FACMG, Vice President, Clinical Affairs, Veritas Genetics; Associate Professor of Pathology (part-time), Harvard Medical School (AMP Genetics Subdivision Chair and Representative to the AMP 2018 Board of Directors; Member)

Birgit Funke, Vice President of Clinical Affairs, a board-certified clinical molecular geneticist, and also an Associate Professor of Pathology at Harvard Medical School. Dr. Funke focuses on genetic testing with emphasis on genetically heterogeneous inherited diseases, with further specialization in cardiomyopathies, myopathies, and congenital cardiovascular malformations. Her main goals are to pave the way for implementing clinical exome sequencing as a universal first-line test, to improve curation of genetic knowledge, and to work towards automation of knowledge-driven decision support for interpreting and reporting genetic test results. In addition, she is interested in facilitating clinical genome-wide reporting for common, complex disorders and pharmacogenetic traits.

Voelkerding_KarlKarl Voelkerding, MD, Professor of Pathology, University of Utah School of Medicine (AMP Member)

Dr. Voelkerding is a professor of pathology at the University of Utah School of Medicine and past president of the Association for Molecular Pathology. He is the former chair of the College of American Pathologists’ Next-Generation Sequencing Project Team, which has developed laboratory accreditation requirements and proficiency testing programs for clinical next-generation sequencing. Dr. Voelkerding is currently chair of the newly formed College of American Pathologists’ Genomic Medicine Resource Committee. Dr. Voelkerding received his MD from the University of Cincinnati College of Medicine and is board certified in clinical pathology and molecular genetic pathology. His applied research focuses on the translation of genomics technologies into clinical diagnostics. During the past few years, his basic research has centered on the utilization of genomic approaches to elucidate the genetic basis of primary immune deficiencies, which has resulted in the discovery of two new genes being associated with common variable immunodeficiency.


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