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. 2021 Mar;23(3):581-585.
doi: 10.1038/s41436-020-00996-9. Epub 2020 Oct 22.

The role of clinical response to treatment in determining pathogenicity of genomic variants

Joseph J Shen  1 , Saskia B Wortmann  2   3 , Lonneke de Boer  3 , Leo A J Kluijtmans  4 , Marleen C D G Huigen  4 , Johannes Koch  2 , Stephanie Ross  5 , Christin D Collins  5 , Robin van der Lee  6 , Clara D M van Karnebeek #  3   6   7   8 , Madhuri R Hegde #  5   9
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Free article

The role of clinical response to treatment in determining pathogenicity of genomic variants

Joseph J Shen et al. Genet Med. 2021 Mar.
Free article

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.

Keywords: 2015 ACMG/AMP guidelines; clinical genetic testing; interpretation; treatable human conditions; variant classification.

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References

    1. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–423. - DOI
    1. Shen JJ, Davis JL, Hong X, et al. A case of lysosomal acid lipase deficiency confirmed by response to sebelipase alfa therapy. J Pediatr Gastroenterol Nutr. 2020. https://doi.org/10.1097/MPG.0000000000002870 . Online ahead of print.
    1. Chanprasert S, Wang J, Weng S, et al. Molecular and clinical characterization of the myopathic form of mitochondrial DNA depletion syndrome caused by mutations in the thymidine kinase (TK2) gene. Mol Genet Metab. 2013;110:153–161. - DOI
    1. Garone C, Garcia‐Diaz B, Emmanuele V, et al. Deoxypyrimidine monophosphate bypass therapy for thymidine kinase 2 deficiency. EMBO Mol Med. 2014;6:1016–1027. - DOI
    1. Plecko B, Paul K, Mills P, et al. Pyridoxine responsiveness in novel mutations of the PNPO gene. Neurology. 2014;82:1425–1433. - DOI

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