Next generation phenotyping for diagnosis and phenotype-genotype correlations in Kabuki syndrome.

Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
28 Jan 2024
Historique:
received: 20 12 2023
accepted: 22 01 2024
medline: 29 1 2024
pubmed: 29 1 2024
entrez: 28 1 2024
Statut: epublish

Résumé

The field of dysmorphology has been changed by the use Artificial Intelligence (AI) and the development of Next Generation Phenotyping (NGP). The aim of this study was to propose a new NGP model for predicting KS (Kabuki Syndrome) on 2D facial photographs and distinguish KS1 (KS type 1, KMT2D-related) from KS2 (KS type 2, KDM6A-related). We included retrospectively and prospectively, from 1998 to 2023, all frontal and lateral pictures of patients with a molecular confirmation of KS. After automatic preprocessing, we extracted geometric and textural features. After incorporation of age, gender, and ethnicity, we used XGboost (eXtreme Gradient Boosting), a supervised machine learning classifier. The model was tested on an independent validation set. Finally, we compared the performances of our model with DeepGestalt (Face2Gene). The study included 1448 frontal and lateral facial photographs from 6 centers, corresponding to 634 patients (527 controls, 107 KS); 82 (78%) of KS patients had a variation in the KMT2D gene (KS1) and 23 (22%) in the KDM6A gene (KS2). We were able to distinguish KS from controls in the independent validation group with an accuracy of 95.8% (78.9-99.9%, p < 0.001) and distinguish KS1 from KS2 with an empirical Area Under the Curve (AUC) of 0.805 (0.729-0.880, p < 0.001). We report an automatic detection model for KS with high performances (AUC 0.993 and accuracy 95.8%). We were able to distinguish patients with KS1 from KS2, with an AUC of 0.805. These results outperform the current commercial AI-based solutions and expert clinicians.

Identifiants

DOI: 10.1038/s41598-024-52691-3 PMID: 38282012
pubmed: 38282012
doi: 10.1038/s41598-024-52691-3
pii: 10.1038/s41598-024-52691-3
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

2330

Subventions

Organisme : Agence Nationale de la Recherche
ID : ANR-10-IAHU-01
Organisme : Thailand Science Research and Innovation
ID : N42A650229

Informations de copyright

© 2024. The Author(s).

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Auteurs

Quentin Hennocq (Q)

Imagine Institute, INSERM UMR1163, 75015, Paris, France. quentin.hennocq@aphp.fr.
Service de chirurgie maxillo-faciale et chirurgie plastique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France. quentin.hennocq@aphp.fr.
Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Paris, France. quentin.hennocq@aphp.fr.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France. quentin.hennocq@aphp.fr.
Laboratoire 'Forme et Croissance du Crâne', Faculté de Médecine, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France. quentin.hennocq@aphp.fr.
Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015, Paris, France. quentin.hennocq@aphp.fr.
ORCID: 0000-0001-7882-8287

Marjolaine Willems (M)

Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier University, Montpellier, France.

Jeanne Amiel (J)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.
Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.

Stéphanie Arpin (S)

Service de Génétique, CHU Tours, UMR 1253, iBrain, Université de Tours, Inserm, Tours, France.

Tania Attie-Bitach (T)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.
Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.

Thomas Bongibault (T)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Laboratoire 'Forme et Croissance du Crâne', Faculté de Médecine, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France.

Thomas Bouygues (T)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Laboratoire 'Forme et Croissance du Crâne', Faculté de Médecine, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France.

Valérie Cormier-Daire (V)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.
Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.

Pierre Corre (P)

Nantes Université, CHU Nantes, Service de chirurgie maxillo-faciale et stomatologie, 44000, Nantes, France.
Nantes Université, Oniris, UnivAngers, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR 1229, 44000, Nantes, France.

Klaus Dieterich (K)

Univ. Grenoble Alpes, Inserm, U1209, IAB, CHU Grenoble Alpes, 38000, Grenoble, France.

Maxime Douillet (M)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.

Jean Feydy (J)

HeKA team, INRIA, 75012, Paris, France.

Eva Galliani (E)

Service de chirurgie maxillo-faciale et chirurgie plastique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.
Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.

Fabienne Giuliano (F)

MEDISYN Genetics, Lausanne, Switzerland.

Stanislas Lyonnet (S)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.
Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.

Arnaud Picard (A)

Service de chirurgie maxillo-faciale et chirurgie plastique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.
Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.

Thantrira Porntaveetus (T)

Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.

Marlène Rio (M)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.
Service de médecine génomique des maladies rares, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.

Flavien Rouxel (F)

Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier University, Montpellier, France.

Vorasuk Shotelersuk (V)

Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.

Annick Toutain (A)

Service de Génétique, CHU Tours, UMR 1253, iBrain, Université de Tours, Inserm, Tours, France.

Kevin Yauy (K)

Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier University, Montpellier, France.

David Geneviève (D)

Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Génétique clinique, CHU Montpellier, Centre de référence anomalies du développement SOOR, INSERM U1183, Montpellier University, Montpellier, France.

Roman H Khonsari (RH)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.
Service de chirurgie maxillo-faciale et chirurgie plastique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.
Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Paris, France.
Faculté de Médecine, Université de Paris Cité, 75015, Paris, France.
Laboratoire 'Forme et Croissance du Crâne', Faculté de Médecine, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France.

Nicolas Garcelon (N)

Imagine Institute, INSERM UMR1163, 75015, Paris, France.

Classifications MeSH