A

Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings

Nature Genetics, vol. 56, pp. 1644–1653

Abstract

Individuals with ultrarare disorders pose a structural challenge for healthcare systems since expert clinical knowledge is required to establish diagnoses. In TRANSLATE NAMSE, a 3-year prospective study, we evaluated a novel diagnostic concept based on multidisciplinary expertise in Germany. Here we present the systematic investigation of the phenotypic and molecular genetic data of 1,577 patients who had undergone exome sequencing and were partially analyzed with next-generation phenotyping approaches. Molecular genetic diagnoses were established in 32% of the patients totaling 370 distinct molecular genetic causes, most with prevalence below 1:50,000. During the diagnostic process, 34 novel and 23 candidate genotype-phenotype associations were identified, mainly in individuals with neurodevelopmental disorders. Sequencing data of the subcohort that consented to computer-assisted analysis of their facial images with GestaltMatcher could be prioritized more efficiently compared with approaches based solely on clinical features and molecular scores. Our study demonstrates the synergy of using next-generation sequencing and phenotyping for diagnosing ultrarare diseases in routine healthcare and discovering novel etiologies by multidisciplinary teams.

Authors 99

  1. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  2. Berlin Institute of Health at Charité - Universitätsmedizin Berlin · Charité - Universitätsmedizin Berlin

    Affiliation as printed

    BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  3. University of Tübingen

    Affiliation as printed

    Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany

  4. TUM Klinikum · Institut für Humangenetik · Technical University of Munich

    Affiliation as printed

    Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany

  5. University of Bonn · University Hospital Bonn · Institut für Medizinische Biometrie, Informatik und Epidemiologie

    Affiliation as printed

    Institut für Medizinische Biometrie, Informatik und Epidemiologie, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

    Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  6. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  7. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  8. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  9. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  10. Stellenbosch University

    Affiliation as printed

    Institute for Medical Genetics, Stellenbosch University, Cape Town, South Africa

  11. Düsseldorf University Hospital

    Affiliation as printed

    Department of Pediatrics, University Hospital Düsseldorf, Düsseldorf, Germany

  12. Berlin Institute of Health at Charité - Universitätsmedizin Berlin · Charité - Universitätsmedizin Berlin

    Affiliation as printed

    BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  13. Berlin Institute of Health at Charité - Universitätsmedizin Berlin · Charité - Universitätsmedizin Berlin

    Affiliation as printed

    BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  14. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  15. Berlin Institute of Health at Charité - Universitätsmedizin Berlin · Charité - Universitätsmedizin Berlin

    Affiliation as printed

    BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  16. Universitätsklinikum Aachen · Charité - Universitätsmedizin Berlin · RWTH Aachen University

    Affiliation as printed

    Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  17. Berlin Institute of Health at Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Core Uni Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany

    Core Uni Bioinformatics, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany

  18. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  19. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  20. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  21. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  22. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  23. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  24. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  25. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute of Cell and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatric Neurology, Charité – Universitätsmedizin Berlin, Berlin, Germany

  26. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  27. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  28. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Department of Pediatrics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  29. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  30. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  31. Charité - Universitätsmedizin Berlin

    Affiliation as printed

    Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Institute for Medical Genetics and Human Genetics, Charité – Universitätsmedizin Berlin, Berlin, Germany

  32. Ruhr University Bochum

    Affiliation as printed

    Department of Human Genetics, Ruhr University Bochum, Bochum, Germany

  33. Ruhr University Bochum

    Affiliation as printed

    Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany

  34. Ruhr University Bochum

    Affiliation as printed

    Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany

  35. Ruhr University Bochum

    Affiliation as printed

    Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany

  36. Ruhr University Bochum

    Affiliation as printed

    Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany

  37. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  38. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  39. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  40. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  41. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  42. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  43. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  44. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  45. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  46. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  47. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  48. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  49. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  50. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  51. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  52. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  53. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  54. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  55. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  56. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  57. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  58. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  59. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  60. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  61. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  62. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  63. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  64. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  65. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  66. University of Bonn · University Hospital Bonn

    Affiliation as printed

    Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany

  67. University Hospital Carl Gustav Carus

    Affiliation as printed

    Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  68. University Hospital Carl Gustav Carus

    Affiliation as printed

    Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  69. University Hospital Carl Gustav Carus

    Affiliation as printed

    Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  70. University Hospital Carl Gustav Carus

    Affiliation as printed

    Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  71. University Hospital Carl Gustav Carus

    Affiliation as printed

    Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  72. University Hospital Carl Gustav Carus

    Affiliation as printed

    Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  73. University Hospital Carl Gustav Carus

    Affiliation as printed

    Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  74. University Hospital Carl Gustav Carus

    Affiliation as printed

    Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  75. University Hospital Carl Gustav Carus

    Affiliation as printed

    Department of Neurology, University Hospital Carl Gustav Carus, Dresden, Germany

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  76. University Hospital Carl Gustav Carus

    Affiliation as printed

    University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany

  77. Essen University Hospital

    Affiliation as printed

    Institute of Human Genetics, University Hospital Essen, Essen, Germany

  78. Essen University Hospital

    Affiliation as printed

    Department of Pediatrics II, University Hospital Essen, Essen, Germany

  79. Essen University Hospital

    Affiliation as printed

    Institute of Human Genetics, University Hospital Essen, Essen, Germany

  80. Essen University Hospital

    Affiliation as printed

    Institute of Human Genetics, University Hospital Essen, Essen, Germany

  81. Essen University Hospital

    Affiliation as printed

    Department of Pediatrics II, University Hospital Essen, Essen, Germany

  82. Essen University Hospital

    Affiliation as printed

    Department of Pediatrics II, University Hospital Essen, Essen, Germany

  83. University Hospital in Halle

    Affiliation as printed

    Department of Neurology, University Hospital Halle, Halle, Germany

  84. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  85. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  86. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  87. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  88. Heidelberg University · University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Institute of Human Genetics, Heidelberg University, Heidelberg, Germany

    Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  89. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  90. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  91. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  92. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  93. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  94. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  95. University Medical Center Hamburg-Eppendorf

    Affiliation as printed

    Department of Pediatrics, University Hospital Hamburg-Eppendorf, Hamburg, Germany

  96. Heidelberg University

    Affiliation as printed

    Institute of Human Genetics, Heidelberg University, Heidelberg, Germany

  97. Heidelberg University

    Affiliation as printed

    Institute of Human Genetics, Heidelberg University, Heidelberg, Germany

  98. Heidelberg University

    Affiliation as printed

    Institute of Human Genetics, Heidelberg University, Heidelberg, Germany

  99. Heidelberg University

    Affiliation as printed

    Institute of Human Genetics, Heidelberg University, Heidelberg, Germany

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References 107