The best of both worlds: Blending cutting‐edge research with clinical processes for a productive exome clinic

Author:

Sullivan Jennifer A.1,Spillmann Rebecca C.1,Schoch Kelly1,Walley Nicole1,Alkelai Anna23,Stong Nicholas24,Shea Patrick R.25,Petrovski Slavè26,Jobanputra Vaidehi7,McConkie‐Rosell Allyn1ORCID,Shashi Vandana1

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

3. Regeneron Genetics Center Regeneron Pharmaceuticals Tarrytown New York USA

4. Predictive Sciences Bristol Myers Squibb Summit New Jersey USA

5. Genomics and Bioinformatics Analysis Resource Columbia University New York New York USA

6. Department of Medicine University of Melbourne, Austin Health Melbourne Victoria Australia

7. Department of Pathology and Cell Biology Columbia University Irving Medical Center New York New York USA

Abstract

AbstractGenomic 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.

Publisher

Wiley

Subject

Genetics (clinical),Genetics

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