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Translational Diagnostics

An In-House Pipeline to Validate Genetic Variants in Children with Undiagnosed and Rare Diseases
  • Jordi Pijuan
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • María Rodríguez-Sanz
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • Daniel Natera-de Benito
    Affiliations
    Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
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  • Carlos Ortez
    Affiliations
    Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
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  • Arola Altimir
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • Mireia Osuna-López
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • Montserrat Roura
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • Maddi Ugalde
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • Liedewei Van de Vondel
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • Judith Reina-Castillón
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
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  • Carme Fons
    Affiliations
    Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain

    Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
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  • Raúl Benítez
    Affiliations
    Automatic Control Department and Biomedical Engineering Research Center, Universitat Politècnica de Catalunya, Barcelona, Spain
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  • Andrés Nascimento
    Affiliations
    Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu, Barcelona, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
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  • Janet Hoenicka
    Correspondence
    Janet Hoenicka, Ph.D., Laboratory of Neurogenetics and Molecular Medicine, Institut de Recerca Sant Joan de Déu, C/ Santa Rosa 39-57, 08950, Esplugues de Llobregat, Barcelona, Spain.
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
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  • Francesc Palau
    Correspondence
    Address reprint requests to Francesc Palau, M.D., Ph.D., Department of Genetic Medicine, Hospital Sant Joan de Déu, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain.
    Affiliations
    Laboratory of Neurogenetics and Molecular Medicine–Pediatric Institute of Rare Diseases, Institut de Recerca Sant Joan de Déu, Barcelona, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain

    Department of Genetic Medicine–IPER, Hospital Sant Joan de Déu, Barcelona, Spain

    Clinic Institute of Medicine and Dermatology, Hospital Clínic, Barcelona, Spain

    Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
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Published:October 23, 2020DOI:https://doi.org/10.1016/j.jmoldx.2020.10.006
      Diagnosis is essential for the management and treatment of patients with rare diseases. In a group of patients, the genetic study identifies variants of uncertain significance or inconsistent with the phenotype; therefore, it is urgent to develop novel strategies to reach the definitive diagnosis. Herein, we develop the in-house Translational Diagnostics Program (TDP) to validate genetic variants as part of the diagnostic process with the close collaboration of physicians, clinical scientists, and research scientists. The first 7 of 33 consecutive patients for whom exome-based tests were not diagnostic were investigated. The TDP pipeline includes four steps: (i) phenotype assessment, (ii) literature review and prediction of in silico pathogenicity, (iii) experimental functional studies, and (iv) diagnostic decision-making. Re-evaluation of the phenotype and re-analysis of the exome allowed the diagnosis in one patient. In the remaining patients, the studies included either cDNA cloning or PCR-amplified genomic DNA, or the use of patients' fibroblasts. A comparative computational analysis of confocal microscopy images and studies related to the protein function was performed. In five of these six patients, evidence of pathogenicity of the genetic variant was found, which was validated by physicians. The current research demonstrates the feasibility of the TDP to support and resolve intramural medical problems when the clinical significance of the patient variant is unknown or inconsistent with the phenotype.
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