Detection of a Novel DSPP Mutation by NGS in a Population Isolate in Madagascar

Abstract

A large family from a small village in Madagascar, Antanetilava, is known to present with colored teeth. Through previous collaboration and 4 successive visits in 1994, 2004, 2005, and 2012, we provided dental care to the inhabitants and diagnosed dentinogenesis imperfecta. Recently, using whole exome sequencing we confirmed the clinical diagnosis by identifying a novel single nucleotide deletion in exon 5 of DSPP. This paper underlines the necessity of long run research, the importance of international and interpersonal collaborations as well as the major contribution of next generation sequencing tools in the genetic diagnosis of rare oro-dental anomalies. This study is registered in ClinicalTrials (https://ichgcp.net/clinical-trials-registry/NCT02397824" title="See in ClinicalTrials.gov">NCT02397824.

Keywords: NGS; dental anomalies; dentin; dentinogenesis imperfecta; human; mutations; rare disease.

Figures

Figure 1

Family pedigree. A large pedigree, spanning 5-generations with 137 individuals, of which 55 are affected, is showing a dominant inheritance pattern. Arrows point to individuals whose exomes were sequenced (affected: III.15, III.32, IV.26, IV.57, IV.65; non-affected: IV.22). Sanger sequencing was performed for the following subjects: affected (III.15, III.32, III.33, IV.25, IV.26, IV.57, IV.59, IV.64, IV.65), non-affected (III.16, III.37, IV.21, IV.22, IV.23).

Figure 2

Clinical description of the disease. (A) The remote village of Antananarivo. (B–J) Inhabitants'dentition showing the typical features of dentinogenesis imperfecta with the gray-brown discolouration of the dentin clearly visible after enamel cleavage and progressive tooth wear. (C) On the retro-alveolar radiography of the lower right premolar/molar sector of individual (B), cervical constriction, short roots and the disappearance of pulp spaces due to erratic dentin formation represent the characteristic hallmarks of dentinogenesis imperfecta. (H–J) In addition to dentin anomalies, hypoplastic enamel defects exist, with the presence of pits, striae and flattened buccal surfaces.

Figure 3

DSPP mutation analysis. DSPP mutations are indicated against the gene structure (reference sequence: NM_014208.3). (A) Schematic representation of DSPP: this gene contains 5 exons (vertical blue hatches), the position of the start codon (ATG) and the stop codon (TAG) are indicated respectively in exon 2 and exon5. The known mutations in the DSPP gene are summarized against the gene structure and associated to a literature reference. The new mutation described in this paper is boxed and written in red. For example: the most 5′ DSPP mutation, near the initiation codon (ATG) is lying in exon 2 and described as a single nucleotide variant c.16T>G leading to the following amino acid changes in the protein p.Tyr6Asp and reported in the literature in quoted reference (Rajpar et al., 2002). (B) Electrophoregrams of a part of DSPP exon 5 showing the heterozygous mutation in an affected person and the normal sequence in an unaffected individual. The deletion of 1T is indicated with an arrow, this deletion creates a shift in the reading frame in position 3676 of the cDNA reference sequence, resulting in 2 superposed sequences. On the scheme the numbering corresponds to the following references: 1. Rajpar et al. (2002); 2. Malmgren et al. (2004); 3. Xiao et al. (2001); 4. Zhang et al. (2007) and Qu et al. (2009); 5. Hart and Hart (2007); 6. Mcknight et al. (2008a); 7. Li et al. (2012) and Lee et al. (2013); 8. Wang et al. (2009); 9. Lee et al. (2008); 10. Holappa et al. (2006); 11. Kim et al. (2004); 12. Kim et al. (2005); 13. Song et al. (2006); 14. Lee et al. (2011b); 15. Kida et al. (2009); 16. Lee et al. (2009); 17. Zhang et al. (2001); 18. Wang et al. (2011); 19. Mcknight et al. (2008b); 20. Zhang et al. (2011); 21. Bai et al. (2010); 22. Nieminen et al. (2011); 23. Song et al. (2008); 24. Lee et al. (2011a); 25. Dong et al. (2005).