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Shen JJ, Wortmann SB, de Boer L, Kluijtmans LAJ, Huigen MCDG, Koch J, Ross S, Collins CD, van der Lee R, van Karnebeek CDM, Hegde MR. The role of clinical response to treatment in determining pathogenicity of genomic variants. Genet Med 2020; 23:581-585. [PMID: 33087887 DOI: 10.1038/s41436-020-00996-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/24/2020] [Indexed: 12/19/2022] Open
Abstract
PURPOSE The 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for the interpretation of sequence variants provide a framework to standardize terminology in the classification of variants uncovered through genetic testing. We aimed to assess the validity of utilizing clinical response to therapies specifically targeted to a suspected disease in clarifying variant pathogenicity. METHODS Five families with disparate clinical presentations and different genetic diseases evaluated and treated in multiple diagnostic settings are summarized. RESULTS Extended evaluations indicated possible genetic diagnoses and assigned candidate causal variants, but the cumulative clinical, biochemical, and molecular information in each instance was not completely consistent with the identified disease. Initiation of treatment specific to the suspected diagnoses in the affected individuals led to clinical improvement in all five families. CONCLUSION We propose that the effect of therapies that are specific and targeted to treatable genetic diseases embodies an in vivo physiological response and could be considered as additional criteria within the 2015 ACMG/AMP guidelines in determining genomic variant pathogenicity.
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Affiliation(s)
- Joseph J Shen
- Division of Genetics, Department of Pediatrics, UCSF Fresno, Fresno, CA, USA.
| | - Saskia B Wortmann
- University Children's Hospital, PMU Salzburg, Salzburg, Austria.,Radboud Centre for Mitochondrial Medicine, Department of Paediatrics, Amalia Children's Hospital, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Lonneke de Boer
- Radboud Centre for Mitochondrial Medicine, Department of Paediatrics, Amalia Children's Hospital, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Marleen C D G Huigen
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Johannes Koch
- University Children's Hospital, PMU Salzburg, Salzburg, Austria
| | | | | | - Robin van der Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Clara D M van Karnebeek
- Radboud Centre for Mitochondrial Medicine, Department of Paediatrics, Amalia Children's Hospital, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Department of Paediatrics, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Madhuri R Hegde
- PerkinElmer Genomics, Duluth, GA, USA.,Department of Applied Biology, Georgia Institute of Technology, Atlanta, GA, USA
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