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The best of both worlds: Blending cutting-edge research with clinical processes for a productive exome clinic |
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| Authors: | Jennifer A. Sullivan Rebecca C. Spillmann Kelly Schoch Nicole Walley Anna Alkelai Nicholas Stong Patrick R. Shea Slavè Petrovski Vaidehi Jobanputra Allyn McConkie-Rosell Vandana Shashi |
| Affiliation: | 1. Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA;2. Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA;3. Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, USA;4. Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA Genomics and Bioinformatics Analysis Resource, Columbia University, New York, New York, USA;5. Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia;6. Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA |
| Abstract: | Genomic medicine has been transformed by next-generation sequencing (NGS), inclusive of exome sequencing (ES) and genome sequencing (GS). Currently, ES is offered widely in clinical settings, with a less prevalent alternative model consisting of hybrid programs that incorporate research ES along with clinical patient workflows. We were among the earliest to implement a hybrid ES clinic, have provided diagnoses to 45% of probands, and have identified several novel candidate genes. Our program is enabled by a cost-effective investment by the health system and is unique in encompassing all the processes that have been variably included in other hybrid/clinical programs. These include careful patient selection, utilization of a phenotype-agnostic bioinformatics pipeline followed by manual curation of variants and phenotype integration by clinicians, close collaborations between the clinicians and the bioinformatician, pursuit of interesting variants, communication of results to patients in categories that are predicated upon the certainty of a diagnosis, and tracking changes in results over time and the underlying mechanisms for such changes. Due to its effectiveness, scalability to GS and its resource efficiency, specific elements of our paradigm can be incorporated into existing clinical settings, or the entire hybrid model can be implemented within health systems that have genomic medicine programs, to provide NGS in a scientifically rigorous, yet pragmatic setting. |
| Keywords: | exome sequencing genome sequencing Mendelian disorders next-generation sequencing rare disorders ultra-rare disorders undiagnosed diseases |