Shugo Haga

Association of common PAX9 variants with permanent tooth size variation in non-syndromic East Asian populations

Studies on the heredity of dental characteristics in humans have indicated that the variance in many dental traits results from genetic variation. However, the genetic factors that influence commonly occurring dental variants are poorly understood. Paired domain box 9 (PAX9) codes a transcription factor that is important in tooth development. We investigated whether PAX9 polymorphisms are associated with normal variations in tooth agenesis and morphology. The study subjects were 273 Japanese and 223 Korean adults. Single-nucleotide polymorphisms (SNPs) in PAX9 (rs2295222, rs4904155, rs2073244, rs12881240 and rs4904210) were genotyped, and third molar agenesis and mesiodistal and buccolingual diameters were measured. We found that four of the five SNPs were significantly associated with the crown size. However, no SNP was associated with third molar agenesis. In additional analyses on non-metric dental traits, we found significant associations of PAX9 SNPs with shoveling of upper first incisors. In summary, common variants in PAX9 contributed to morphological variation in permanent teeth in humans.

A genome-wide association study of third molar agenesis in Japanese and Korean populations

Tooth agenesis is the most common developmental anomaly of human dentition, occurring most often in the third molar (wisdom tooth). It is affected by genetic variation, so this study aimed to identify susceptibility genes associated with third molar agenesis. Examination of panoramic radiographs and medical history about third molar extraction were used to diagnose third molar agenesis. We then conducted a genome-wide association study of 149 cases with at least one-third molar agenesis and 338 controls from Japan and Korea using the Illumina HumanOmniExpress BeadChip. After rigorous quality-control filtering, approximately 550 000 single-nucleotide polymorphisms (SNPs) were analyzed in association tests with the status. We identified three SNPs showing evidence of association at P<1 × 10−5 and 69 SNPs showing evidence of association at P<1 × 10−4. SNP rs1469622, which maps to an intron of THSD7B (thrombospondin, type I, domain containing 7B) on chromosome 2, showed the strongest association (combined odds ratio=1.88, 95% confidence interval=1.43–2.47, P=7.5 × 10−6). The identified SNPs may be considered candidates for future replication studies in independent samples.

Genome-wide association study of degenerative bony changes of the temporomandibular joint

OBJECTIVES To identify susceptibility genes underlying degenerative bony changes of the temporomandibular joint (TMJ). MATERIALS AND METHODS Bony changes of the TMJ condylar head were diagnosed by examination of panoramic radiographs and/or magnetic resonance images and/or computed tomography images. We conducted a genome-wide association study (GWAS) of 146 cases with TMJ degeneration and 374 controls from East Asian populations using an Illumina HumanOmniExpress BeadChip. After rigorous quality-control filtering, approximately 550,000 single nucleotide polymorphisms (SNPs) were used for tests of associations with disease status. RESULTS Forty-one SNPs at 22 independent loci showed association signals at P < 1 × 10(-4). The SNP rs878962, which maps on an intron of TSPAN9 on chromosome 12, showed the strongest association (combined OR = 1.89, 95% confidence interval = 1.43-2.50, P = 8.1 × 10(-6)). According to in silico predictions of the 41 SNPs, two intronic SNPs of APOL3 (rs80575) and MRC2 (rs2460300) may fall within regulatory elements and affect DNA-protein interactions. We could not replicate SNPs located on genes that have been reported to be associated with temporomandibular disorder or temporomandibular osteoarthritis in previous studies at P < 1 × 10(-4). CONCLUSIONS Our GWAS identified 22 independent loci showing suggestive association signals with degenerative bony changes of the TMJ. These loci provide good candidates for future follow-up studies.

Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing

Tooth agenesis is described as the absence of one or more teeth. It is caused by a failure in tooth development and is one of the most common human developmental anomalies. We herein report genomic analyses of selective mandibular incisor agenesis (SMIA) using exome sequencing. Two Japanese families with SMIA were subjected to exome sequencing, and family with sequence similarity 65 member A (FAM65), nuclear factor of activated T-cells 3 (NFATC3) and cadherin-related 23 gene (CDH23) were detected. In the follow-up study, 51 Japanese and 32 Korean sporadic patients with SMIA were subjected to exome analyses, and 18 reported variants in PAX9, AXIN2, EDA, EDAR, WNT10A, BMP2 and GREM2 and 27 variants of FAM65, NFATC3 and CDH23 were found in 38 patients. Our comprehensive genetic study of SMIA will pave the way for a full understanding of the genetic etiology of SMIA and provide targets for treatment.

The role of polymorphisms associated with early tooth eruption in dental and occlusal traits in East Asian populations

Objective A recent study suggested that rs6504340, a polymorphism within the homeobox B (HOXB) gene cluster, is associated with the susceptibility for malocclusions in Europeans. The resulting malocclusions require orthodontic treatment. The aim of this study was to investigate the association of rs6504340 and other dentition-implicated polymorphisms with dental and occlusal traits in Korean and Japanese populations. Methods The study participants included 223 unrelated Koreans from the Busan area and 256 unrelated Japanese individuals from the Tokyo metropolitan area. DNA samples were extracted from saliva specimens. Genotyping for rs6504340 and four single nucleotide polymorphisms (SNPs) that have been shown to be associated with the timing of first tooth eruption and the number of teeth at 1 year of age (rs10506525, rs1956529, rs9674544, and rs8079702) was performed using TaqMan assays. The Index of Orthodontic Treatment Need (IOTN), overjet, overbite, arch length discrepancy, crown sizes, and length and width of the dental arches were measured. Spearmans correlation coefficients were calculated to evaluate relationships between rs6504340 and these dental/occlusal traits. Results We evaluated the aesthetic components and dental health components of the IOTN in the Korean and Japanese populations and found that neither rs6504340 nor the other four SNPs showed any association with dental and occlusal traits in these East Asian populations. Conclusions These negative results suggest that further research is needed to identify the genetic determinants of malocclusions in order to reach a consensus.

Evaluation of mandibular volume using cone-beam computed tomography and correlation with cephalometric values

OBJECTIVE To investigate the association between maxillofacial morphology and mandibular bone volume in patients with skeletal malocclusion. MATERIALS AND METHODS Subjects were 118 adult Japanese (58 males and 60 females). Skeletal malocclusion was classified, based on cephalometric analysis, into skeletal Classes I (-1° ≤ ANB < 4°), II (ANB ≥ 4°), and III (ANB < -1°). Using cone-beam computed tomography and three-dimensional image analysis software, the dental crowns and mandible were separated, with only the mandible extracted. This was then reconstructed as a three-dimensional model, from which the mandibular volume was measured. RESULTS No significant difference in mandibular volume was noted among skeletal Classes I, II, and III, nor was there any significant correlation between mandibular volume and the ANB, SNB, or mandibular plane angles. There was occasional and limited correlation between mandible volume and gonial angle and certain cephalometric distance parameters. CONCLUSION We conclude that proper understanding of the three-dimensional maxillofacial morphology requires not only cephalometric radiographic tracings but also high-resolution analysis of the mandibular area, width, and volume.

Whole-exome sequencing analysis of supernumerary teeth occurrence in Japanese individuals

A common disorder of human dentition is the existence of supernumerary teeth. Impacted supernumerary teeth occur most frequently in the maxillary incisor area and are termed mesiodens. We conducted whole-exome sequencing of non-syndromic Japanese individuals possessing supernumerary teeth to identify genes and/or loci involved in the pathogenesis of the condition.

Interferon regulatory factor 6 variants affect nasolabial morphology in East Asian populations

OBJECTIVE The interferon regulatory factor 6 gene (IRF6) is one of the most conspicuous genes among a large number of candidate risk genes for non-syndromic cleft lip with or without cleft palate, which is considered to be a multifactorial defect. Variants of IRF6 are also suggested to affect normal craniofacial variations, especially in the area of the nose and the upper lip. In the present study, we used lateral cephalograms to establish the relationship between IRF6 and sagittal nasolabial morphology in healthy East Asian subjects. DESIGN Genomic DNA was extracted from 215 Japanese and 226 Korean individuals, and genotyped for five IRF6 single nucleotide polymorphisms (SNPs): rs17389541, rs642961, rs2013162, rs2235371, and rs7802. These SNPs were tested by multiple regression analyses for their association with craniofacial measurements obtained from lateral cephalometrics. RESULTS We detected a significant association between the derived variants, rs2013162 and rs2235371 and the distances between a facial bone plane indicated by distance from Nasion and Point A (NA plane) to soft tissue landmarks; the Subalare (NA-Sbal) and the Subnasale (NA-Sn) in the sagittal plane. CONCLUSION Our results indicate that IRF6 variants play an important role in the normal range of variation in nasolabial soft-tissue morphology.

Contribution of FGFR1 Variants to Craniofacial Variations in East Asians

FGFR1 plays an important role in the development of the nervous system as well as the regulation of the skeletal development and bone homeostasis. Mutations in FGFR1 genes affect skull development, specifically suture and synchondrosis, resulting in craniosynostosis and facial abnormalities. We examined subjects with normal skull morphology for genetic polymorphisms that might be associated with normal craniofacial variations. Genomic DNA was obtained from 216 Japanese and 227 Korean subjects. Four FGFR1 SNPs, namely, rs881301, rs6996321, rs4647905, and rs13317, were genotyped. These SNPs were tested for association with craniofacial measurements obtained from lateral and posteroanterior cephalometries, in which principle component analysis was performed to compress the data of the craniofacial measurements. We observed that SNPs rs13317 and rs6996321 were correlated with the overall head size and midfacial development, indicating that FGFR1 SNPs played crucial roles in the normal variation of human craniofacial morphology. Subjects with the derived alleles of SNPs rs13317 and rs6996321 had a small face and a facial pattern associated with a retruded midface and relatively wide-set eyes. These facial features were similar to but were milder than those of individuals with Pfeiffer syndrome, which is caused by a dysfunctional mutation in FGFR1.

Association between the FGFR1 rs13317 single nucleotide polymorphism and orbitale-nasion depth based on cephalometric images

The fibroblast growth factor receptor 1 (FGFR1) gene plays an important role in craniofacial morphogenesis. In our previous study, an association between FGFR1 single nucleotide polymorphisms (SNPs) and craniofacial morphology was demonstrated in Japanese and Korean subjects. The present study aimed to evaluate the relationship between a common FGFR1 SNP (rs13317) with craniofacial morphology, increasing the number of measurements and examining Egyptian subjects (n = 191) in addition to the Japanese (n = 211) and Korean (n = 226) subjects. Genotyping for rs13317 was performed using the TaqMan assay, and its associations with 81 craniofacial measurements derived from lateral and posteroanterior cephalograms were analyzed by multiple regression analysis controlling sex and facial size. The results from each of the populations were then statistically combined. In the Egyptian subjects, rs13317 was significantly associated with the nasion-orbitale depth (P = 0.00040), and a suggestive association was also observed in the Japanese (P = 0.037) and Korean subjects (P = 0.045). The combined analysis revealed that only the nasion-orbitale depth showed a significant association (P = 0.000062) and that several measurements showed a suggestive association. Our results strongly indicate that rs13317 is associated with a smaller depth between the nasion and orbitale, representing a relative protrusion of the cheekbones and retrusion of the nasal root. A similar characteristic is also observed in individuals with Pfeiffer syndrome, which is caused by a dysfunctional FGFR1 mutation.