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Original research
Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders
  1. Kevin Riquin1,
  2. Bertrand Isidor1,2,
  3. Sandra Mercier1,2,
  4. Mathilde Nizon1,2,
  5. Estelle Colin3,4,
  6. Dominique Bonneau3,4,
  7. Laurent Pasquier5,
  8. Sylvie Odent5,6,
  9. Xavier Maximin Le Guillou Horn7,8,
  10. Gwenaël Le Guyader7,
  11. Annick Toutain9,10,
  12. Vincent Meyer11,
  13. Jean-François Deleuze11,
  14. Olivier Pichon2,
  15. Martine Doco-Fenzy1,2,
  16. Stéphane Bézieau1,2,
  17. Benjamin Cogné1,2
  1. 1 l’institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
  2. 2 Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
  3. 3 CHU Angers, Service de Génétique médicale, Angers, France
  4. 4 UMR CNRS 6214-INSERM 1083, Université d'Angers, Angers, France
  5. 5 Service de Génétique Clinique, ERN ITHACA, Rennes, France
  6. 6 Institut de Génétique et Développement de Rennes, IGDR UMR 6290 CNRS, INSERM, IGDR Univ Rennes, Rennes, France
  7. 7 Service de génétique médicale, CHU de Poitiers, Poitiers, France
  8. 8 LabCom I3M-Dactim mis/LMA CNRS 7348, Université de Poitiers, Poitiers, France
  9. 9 UF de Génétique Médicale, Centre Hospitalier Universitaire, Tours, France
  10. 10 UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
  11. 11 Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, Evry, France
  1. Correspondence to Kevin Riquin, Nantes Université, CHU de Nantes, CNRS, INSERM, l’institut du thorax, Nantes 44007, France; kevin.riquin{at}


Background Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression.

Methods We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance.

Results We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs.

Conclusion Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols.

  • Central Nervous System Diseases
  • Clinical Laboratory Techniques
  • Genetic Research
  • Genetic Testing
  • Genomics

Data availability statement

All data relevant to the study are included in the article or uploaded as supplementary information. Additional data are available upon reasonable request.

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Data availability statement

All data relevant to the study are included in the article or uploaded as supplementary information. Additional data are available upon reasonable request.

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  • Contributors Conceptualisation, supervision of the overall project and edition of the final manuscript draft: KR, BC, SB. Validation, writing—original draft: KR, BC, SB. Data collection: BI, SM, MN, EC, DB, LP, SO, XMLGH, GG, AT, KR, OP, MD-F, BC, SB. Data analysis and interpretation: KR, OP, MD-F, BC.

    All authors revised the manuscript and approved submission of the final version. BC is guarantor for this study and accepts full responsibility for the work and the conduct of the study, had access to the data, and controlled the decision to publish.

  • Funding This work was supported by the Foundation for Rare Diseases and Groupama Foundation.

  • 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.