A targeted next-generation sequencing assay for the molecular diagnosis of genetic disorders with orodental involvement

Megana K Prasad, Véronique Geoffroy, Serge Vicaire, Bernard Jost, Michael Dumas, Stéphanie Le Gras, Marzena Switala, Barbara Gasse, Virginie Laugel-Haushalter, Marie Paschaki, Bruno Leheup, Dominique Droz, Amelie Dalstein, Adeline Loing, Bruno Grollemund, Michèle Muller-Bolla, Séréna Lopez-Cazaux, Maryline Minoux, Sophie Jung, Frédéric Obry, Vincent Vogt, Jean-Luc Davideau, Tiphaine Davit-Beal, Anne-Sophie Kaiser, Ute Moog, Béatrice Richard, Jean-Jacques Morrier, Jean-Pierre Duprez, Sylvie Odent, Isabelle Bailleul-Forestier, Monique Marie Rousset, Laure Merametdijan, Annick Toutain, Clara Joseph, Fabienne Giuliano, Jean-Christophe Dahlet, Aymeric Courval, Mustapha El Alloussi, Samir Laouina, Sylvie Soskin, Nathalie Guffon, Anne Dieux, Bérénice Doray, Stephanie Feierabend, Emmanuelle Ginglinger, Benjamin Fournier, Muriel de la Dure Molla, Yves Alembik, Corinne Tardieu, François Clauss, Ariane Berdal, Corinne Stoetzel, Marie Cécile Manière, Hélène Dollfus, Agnès Bloch-Zupan, Megana K Prasad, Véronique Geoffroy, Serge Vicaire, Bernard Jost, Michael Dumas, Stéphanie Le Gras, Marzena Switala, Barbara Gasse, Virginie Laugel-Haushalter, Marie Paschaki, Bruno Leheup, Dominique Droz, Amelie Dalstein, Adeline Loing, Bruno Grollemund, Michèle Muller-Bolla, Séréna Lopez-Cazaux, Maryline Minoux, Sophie Jung, Frédéric Obry, Vincent Vogt, Jean-Luc Davideau, Tiphaine Davit-Beal, Anne-Sophie Kaiser, Ute Moog, Béatrice Richard, Jean-Jacques Morrier, Jean-Pierre Duprez, Sylvie Odent, Isabelle Bailleul-Forestier, Monique Marie Rousset, Laure Merametdijan, Annick Toutain, Clara Joseph, Fabienne Giuliano, Jean-Christophe Dahlet, Aymeric Courval, Mustapha El Alloussi, Samir Laouina, Sylvie Soskin, Nathalie Guffon, Anne Dieux, Bérénice Doray, Stephanie Feierabend, Emmanuelle Ginglinger, Benjamin Fournier, Muriel de la Dure Molla, Yves Alembik, Corinne Tardieu, François Clauss, Ariane Berdal, Corinne Stoetzel, Marie Cécile Manière, Hélène Dollfus, Agnès Bloch-Zupan

Abstract

Background: Orodental diseases include several clinically and genetically heterogeneous disorders that can present in isolation or as part of a genetic syndrome. Due to the vast number of genes implicated in these disorders, establishing a molecular diagnosis can be challenging. We aimed to develop a targeted next-generation sequencing (NGS) assay to diagnose mutations and potentially identify novel genes mutated in this group of disorders.

Methods: We designed an NGS gene panel that targets 585 known and candidate genes in orodental disease. We screened a cohort of 101 unrelated patients without a molecular diagnosis referred to the Reference Centre for Oro-Dental Manifestations of Rare Diseases, Strasbourg, France, for a variety of orodental disorders including isolated and syndromic amelogenesis imperfecta (AI), isolated and syndromic selective tooth agenesis (STHAG), isolated and syndromic dentinogenesis imperfecta, isolated dentin dysplasia, otodental dysplasia and primary failure of tooth eruption.

Results: We discovered 21 novel pathogenic variants and identified the causative mutation in 39 unrelated patients in known genes (overall diagnostic rate: 39%). Among the largest subcohorts of patients with isolated AI (50 unrelated patients) and isolated STHAG (21 unrelated patients), we had a definitive diagnosis in 14 (27%) and 15 cases (71%), respectively. Surprisingly, COL17A1 mutations accounted for the majority of autosomal-dominant AI cases.

Conclusions: We have developed a novel targeted NGS assay for the efficient molecular diagnosis of a wide variety of orodental diseases. Furthermore, our panel will contribute to better understanding the contribution of these genes to orodental disease.

Trial registration numbers: NCT01746121 and NCT02397824.

Keywords: Diagnostics tests; Genetic screening/counselling; Genetics; Genome-wide; Molecular genetics.

Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Figures

Figure 1
Figure 1
Distribution of pathogenic variants identified by disease category. The genes in which pathogenic mutations were identified are shown with respect to the disease in which they were identified. In parentheses next to each gene is the number of independent patients in whom mutations were identified in the gene. This figure includes results from patients V1.09–V1.16 and V2.01–V2.95. DD dentin dysplasia; DGI, dentinogenesis imperfecta; STHAG selective tooth agenesis.
Figure 2
Figure 2
COL17A1 mutations show a characteristic enamel phenotype in autosomal-dominant amelogenesis imperfecta. (A–H) Photos of the enamel phenotypes of individuals with COL17A1 mutations. (A, B) Patient V2.82. (C, D) Mother of patient V2.82. (E, F) Patient V2.09. (G, H) Patient V2.48. Arrows mark pits in the enamel that are characteristic of COL17A1 mutations. Extrinsic colouration makes these pits more visible in (B), (E) and (H). (I) Seemingly digenic inheritance of amelogenesis imperfecta in patient V2.82. Asterisks on the sequence chromatograms mark the mutated nucleotides.
Figure 3
Figure 3
The variety of isolated amelogenesis imperfecta phenotypes seen in this cohort. Representative images of the enamel phenotype associated with mutations in different genes. The mutated gene and patient number are indicated in each panel.

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