Reference : A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals commo...
Scientific journals : Article
Life sciences : Genetics & genetic processes
Human health sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/54941
A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing
English
Denommé-Pichon, Anne-Sophie [> >]
Matalonga, Leslie [> >]
de Boer, Elke [> >]
Jackson, Adam [> >]
Benetti, Elisa [> >]
Banka, Siddharth [> >]
Bruel, Ange-Line [> >]
Ciolfi, Andrea [> >]
Clayton-Smith, Jill [> >]
Dallapiccola, Bruno [> >]
Duffourd, Yannis [> >]
Ellwanger, Kornelia [> >]
Fallerini, Chiara [> >]
Gilissen, Christian [> >]
Graessner, Holm [> >]
Haack, Tobias B. [> >]
Havlovicova, Marketa [> >]
Hoischen, Alexander [> >]
Jean-Marçais, Nolwenn [> >]
Kleefstra, Tjitske [> >]
López-Martín, Estrella [> >]
Macek, Milan [> >]
Mencarelli, Maria Antonietta [> >]
Moutton, Sébastien [> >]
Pfundt, Rolph [> >]
Pizzi, Simone [> >]
Posada, Manuel [> >]
Radio, Francesca Clementina [> >]
Renieri, Alessandra [> >]
Rooryck, Caroline [> >]
Ryba, Lukas [> >]
Safraou, Hana [> >]
Schwarz, Martin [> >]
Tartaglia, Marco [> >]
Thauvin-Robinet, Christel [> >]
Thevenon, Julien [> >]
Tran Mau-Them, Frédéric [> >]
Trimouille, Aurélien [> >]
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Zurek, Birte [> >]
Verloes, Alain [> >]
Philippe, Christophe [> >]
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Macek Jr., Milan [> >]
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Morleo, Manuela [> >]
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Pinelli, Michele [> >]
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Pauly, Martje [> >]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core]
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Afenjar, Alexandra [> >]
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Gilbert-Dussardier, Brigitte [> >]
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Paul, Carle [> >]
Vincent-Delorme, Catherine [> >]
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Poirsier, Céline [> >]
Quélin, Chloé [> >]
Chiaverini, Christine [> >]
Coubes, Christine [> >]
Francannet, Christine [> >]
Colson, Cindy [> >]
Desplantes, Claire [> >]
Wells, Constance [> >]
Goizet, Cyril [> >]
Sanlaville, Damien [> >]
Amram, Daniel [> >]
Lehalle, Daphné [> >]
Geneviève, David [> >]
Gaillard, Dominique [> >]
Zivi, Einat [> >]
Sarrazin, Elisabeth [> >]
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Schaefer, Élise [> >]
Lacaze, Elodie [> >]
Jacquemin, Emmanuel [> >]
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Kilic, Esra [> >]
Colin, Estelle [> >]
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Prieur, Fabienne [> >]
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Pinson, Lucile [> >]
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Bonnet-Dupeyron, Marie Noëlle [> >]
Vincent, Marie [> >]
Jacquemont, Marie-Line [> >]
Cordier-Alex, Marie-Pierre [> >]
Gérard-Blanluet, Marion [> >]
Willems, Marjolaine [> >]
Spodenkiewicz, Marta [> >]
Doco-Fenzy, Martine [> >]
Rossi, Massimiliano [> >]
Renaud, Mathilde [> >]
Fradin, Mélanie [> >]
Mathieu, Michèle [> >]
Holder-Espinasse, Muriel H. [> >]
Houcinat, Nada [> >]
Hanna, Nadine [> >]
Leperrier, Nathalie [> >]
Chassaing, Nicolas [> >]
Philip, Nicole [> >]
Boute, Odile [> >]
Van Kien, Philippe Khau [> >]
Parent, Philippe [> >]
Bitoun, Pierre [> >]
Sarda, Pierre [> >]
Vabres, Pierre [> >]
Jouk, Pierre-Simon [> >]
Touraine, Renaud [> >]
El Chehadeh, Salima [> >]
Whalen, Sandra [> >]
Marlin, Sandrine [> >]
Passemard, Sandrine [> >]
Grotto, Sarah [> >]
Bellanger, Séverine Audebert [> >]
Blesson, Sophie [> >]
Nambot, Sophie [> >]
Naudion, Sophie [> >]
Lyonnet, Stanislas [> >]
Odent, Sylvie [> >]
Attie-Bitach, Tania [> >]
Busa, Tiffany [> >]
Drouin-Garraud, Valérie [> >]
Layet, Valérie [> >]
Bizaoui, Varoona [> >]
Cusin, Véronica [> >]
Capri, Yline [> >]
Alembik, Yves [> >]
19-Jan-2023
Genetics in Medicine
Lippincott Williams & Wilkins
25
4
100018
Yes
International
1098-3600
1530-0366
United States
[en] ClinVar ; Developmental disorder ; Rare diseases ; Exome reanalysis
[en] Purpose
Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned.
Methods
Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted.
Results
We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency).
Conclusion
The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock.
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Solve-RD
Researchers ; Professionals
http://hdl.handle.net/10993/54941
10.1016/j.gim.2023.100018
https://doi.org/10.1016/j.gim.2023.100018

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