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Neurogenetics
Original research
High efficiency and clinical relevance of exome sequencing in the daily practice of neurogenetics
  1. Quentin Thomas1,2,3,
  2. Antonio Vitobello1,4,
  3. Frederic Tran Mau-Them1,4,
  4. Yannis Duffourd1,4,
  5. Agnès Fromont3,
  6. Maurice Giroud3,5,
  7. Benoit Daubail6,
  8. Agnès Jacquin-Piques6,
  9. Marie Hervieu-Begue3,
  10. Thibault Moreau3,
  11. Guy-Victor Osseby3,
  12. Philippine Garret1,4,
  13. Sophie Nambot1,2,
  14. Julian Delanne1,2,
  15. Ange-Line Bruel1,4,
  16. Arthur Sorlin1,4,
  17. Patrick Callier4,
  18. Anne-Sophie Denomme-Pichon1,4,
  19. Laurence Faivre2,
  20. Yannick Béjot3,5,
  21. Christophe Philippe4,
  22. Christel Thauvin-Robinet2,4,
  23. Sébastien Moutton1,2
  1. 1 Inserm UMR1231 team GAD, University of Burgundy and Franche-Comté, Dijon, France
  2. 2 Genetics Center, FHU-TRANSLAD, Dijon University Hospital, Dijon, Burgundy, France
  3. 3 Neurology Department, Dijon University Hospital, Dijon, Burgundy, France
  4. 4 Functional Unity of innovative diagnosis for rare diseases, Dijon Bourgogne University Hospital, Dijon, Burgundy, France
  5. 5 Dijon Stroke Registry, EA7460, Pathophysiology and Epidemiology of Cerebro-Cardiovascular Diseases (PEC2), University of Burgundy and Franche-Comté, Dijon, Burgundy, France
  6. 6 Department of Adult Neurophysiology, Dijon University Hospital, Dijon, Burgundy, France
  1. Correspondence to Quentin Thomas, Inserm UMR1231 team GAD, University of Burgundy, Dijon 21000, France; quentin.thomas{at}chu-dijon.fr

Abstract

Objective To assess the efficiency and relevance of clinical exome sequencing (cES) as a first-tier or second-tier test for the diagnosis of progressive neurological disorders in the daily practice of Neurology and Genetic Departments.

Methods Sixty-seven probands with various progressive neurological disorders (cerebellar ataxias, neuromuscular disorders, spastic paraplegias, movement disorders and individuals with complex phenotypes labelled ‘other’) were recruited over a 4-year period regardless of their age, gender, familial history and clinical framework. Individuals could have had prior genetic tests as long as it was not cES. cES was performed in a proband-only (60/67) or trio (7/67) strategy depending on available samples and was analysed with an in-house pipeline including software for CNV and mitochondrial-DNA variant detection.

Results In 29/67 individuals, cES identified clearly pathogenic variants leading to a 43% positive yield. When performed as a first-tier test, cES identified pathogenic variants for 53% of individuals (10/19). Difficult cases were solved including double diagnoses within a kindred or identification of a neurodegeneration with brain iron accumulation in a patient with encephalopathy of suspected mitochondrial origin.

Conclusion This study shows that cES is a powerful tool for the daily practice of neurogenetics offering an efficient (43%) and appropriate approach for clinically and genetically complex and heterogeneous disorders.

  • neurodegenerative diseases
  • molecular diagnostic techniques
  • clinical laboratory techniques
  • neurology

Data availability statement

All data relevant to the study are included in the article or uploaded as online supplemental information.

https://doi.org/10.1136/jmedgenet-2020-107369

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    Data availability statement

    All data relevant to the study are included in the article or uploaded as online supplemental information.

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    Footnotes

    • Contributors QT collected and analysed data and wrote the manuscript. AV collected and analysed the data. FTM-T collected and analysed the data. AF collected and analysed the data. MG collected and analysed the data. BD collected and analysed the data. AJ-P collected and analysed the data. MH-B collected and analysed the data. TM collected and analysed the data. G-VO collected and analysed the data. SN collected and analysed the data. A-LB collected and analysed the data. AS collected and analysed the data. PC collected and analysed the data. A-SD-P collected and analysed the data. LF collected and analysed the data. YB collected and analysed the data. CP collected and analysed the data. CT-R designed the study, collected and analysed the data, and wrote the manuscript. SM collected and analysed the data and wrote the manuscript. The last two authors co-directed the works (CT-R, SM).

    • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

    • Disclaimer The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

    • Competing interests None declared.

    • Provenance and peer review Not commissioned; externally peer reviewed.

    • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.