Homozygosity Mapping and Candidate Prioritization Identify Mutations, Missed by Whole-Exome Sequencing, in SMOC2, Causing Major Dental Developmental Defects

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Homozygosity Mapping and Candidate Prioritization Identify Mutations, Missed by Whole-Exome Sequencing, in SMOC2, Causing Major Dental Developmental Defects Agnès Bloch-Zupan, Xavier Jamet, Christelle Etard, Virginie Laugel, Jean Muller, Véronique Geoffroy, Jean-Pierre Strauss, Valérie Pelletier, Vincent Marion, Olivier Poch, Uwe Strahle, Corinne Stoetzel, Hélène Dollfus The American Journal of Human Genetics Volume 89, Issue 6, Pages 773-781 (December 2011) DOI: 10.1016/j.ajhg.2011.11.002 Copyright © 2011 The American Society of Human Genetics Terms and Conditions

Figure 1 Clinical Description of the Affected Family Members A clinical description of individuals III.3 (A, B, and C) and III.4 (D, E, and F) shows major dental developmental abnormalities in tooth number, size, shape, structure, eruption, and resorption, as seen in the intraoral photographs (A, B, D, and E) and the panoramic radiographs (C and F). (A and B) (A) shows an intraoral view of III.3 (10 years old). Beside the microdont primary and permanent teeth, which show spaced dentition, double tooth formation (notched and macrodont) is visible on permanent central incisors 21 and 31; 21 shows a vestibular abnormal relief. These anomalies are clearly seen on (B) in an enlargement of the left incisor region. (C) A panoramic radiograph shows III.3, who is missing the following permanent teeth: 18, 15, 24, 25, 28, 48, 45, 44, 43, 32, 33, 34, 35, and 38. The primary and permanent molars are taurodont. The roots are extremely short and are slightly more developed in the permanent dentition but are, however, conical with sharp endings. The pulp has a flame-like shape. The enamel is very thin and has limited contrast compared to the dentin in the X-Ray. Teeth 64, 65, 74, and 75 are reincluded. (D) Intraoral view of III.4 (9.5 years old). Double tooth formation (notched and macrodont) is visible on the permanent central-upper-left incisor (21). The lower arch seems interrupted in the area of missing teeth (45, 43, 42, 32, 33, 34, and 35). Teeth 85 and 75 are reincluded, indicating ankylosis in the alveolar bone. (E) A close-up on macrodont tooth 46 (lower-right permanent first molar) shows extra cusps and an elongated crown on its mesiodistal axis. (F) A panoramic radiograph of III.4 at 5 years old shows oligodontia—13 permanent teeth are missing (18, 15, 25, 28, 48, 45, 43, 42, 32, 33, 34, 35, and 38)—and extreme microdontia of all the primary teeth. Note the short and sharp roots and the hypodeveloped alveolar bone. The American Journal of Human Genetics 2011 89, 773-781DOI: (10.1016/j.ajhg.2011.11.002) Copyright © 2011 The American Society of Human Genetics Terms and Conditions

Figure 2 Homozygosity Mapping and Mutation Detection (A) A simplified pedigree of the family, underlined by corresponding schematic representation of the homozygosity mapping results, shows the chromosome 6 homozygous region that is common in affected individuals: Gray shading indicates homozygous SNPs and white zones indicate heterozygous alleles. (B) Electropherograms of a part of the SMOC2 exon1-intron1 boundary show (a) a homozygous c.84+1G>T mutation in an affected child; (b) a heterozygous c.84+1G>T mutation in a nonaffected sibling; and (c) a healthy control individual. The American Journal of Human Genetics 2011 89, 773-781DOI: (10.1016/j.ajhg.2011.11.002) Copyright © 2011 The American Society of Human Genetics Terms and Conditions

Figure 3 Dentition in smoc2 Morphants The heads of the control (A) and the smoc2-2 morphants (B–D) stained with alizarin red at 5 dpf show different degrees of reduction of pharyngeal tooth size (arrows in B and C) and the complete absence of pharyngeal teeth (black stars in D) in the morphants. Control (E) and morphant (F and G) teeth are shown at higher magnification. Note the misorientation and the difference in the shape of the teeth in (F) compared to the control. Compared to the control (H and J), the morphants (J and K) show no additional emerging teeth. The white stars represent the transparent second tooth. The scale bars represent the following measurements: (A–D): 50 μm; (E–G): 25 μm; and (H–K): 12 μm. The following terms are abbreviated: branchiostegal ray (br); ceratobranchial 5 (cb5); parasphenoid (ps); ceratohyal (cl); notochord (nc); and opercle (op). All embryos are presented in ventral view, anterior up. The American Journal of Human Genetics 2011 89, 773-781DOI: (10.1016/j.ajhg.2011.11.002) Copyright © 2011 The American Society of Human Genetics Terms and Conditions

Figure 4 smoc2 Morphants Exhibit Tooth-Germ Defects (A–I) In situ hybridization of both dlx2b (A–D; probe obtained from D.W. Stock, Colorado, USA), bmp2a (E and F; probe obtained from M. Hammerschmidt, Cologne, Germany) and pitx2 (G–I, pitx2 full-length cDNA was cloned into the Flc3 plasmid [Riken]) on wild-type (A, E, and G), smoc2-2 (B, F, and H), smoc2-1 (D and I), and smoc2-1cont morphants (C) shows a loss of dlx2b and bmp2 expression in smoc2 morphants (B, F, and D) and reduced and fused expression of pitx2 (H and I). The smoc2-1cont morphants do not show any defects. The arrows represent teeth germs; the arrow heads represent missing dlx2b or bmp2a expression. The black star represents a gap within pitx2 expression, the white star represents fused pitx2 expression. Abbreviations are as follows: pf, pectoral fin; tg, teeth germs; fb, forebrain; and pp, pharyngeal pouches. Lateral (C and D) and ventral (A, B, E–I) views of embryos, 56 hpf. The scale bar represents 100 μm. The American Journal of Human Genetics 2011 89, 773-781DOI: (10.1016/j.ajhg.2011.11.002) Copyright © 2011 The American Society of Human Genetics Terms and Conditions