Family-based GWAS for dental class I malocclusion and clefts

• Published in: BMC oral health Vol. 24; no. 1; pp. 665 - 5
• Main Authors: Bezamat, Mariana, Carver, Chelsea E, Vieira, Alexandre R
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 07-06-2024; BioMed Central; BMC
• Subjects: Adolescent; Adult; Analysis; Child; Class I malocclusion; Cleft lip; Cleft Lip - genetics; Cleft lip/palate; Cleft palate; Cleft Palate - genetics; Cohort Studies; Craniofacial growth; Dental caries; Dental occlusion; Diagnosis; Family; Female; Females; Genes; Genetic aspects; Genetic Markers; Genetic variation; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Genotype; Genotype & phenotype; Genotyping; GWAS; Humans; Hypoplasia; Linkage Disequilibrium - genetics; Male; Malocclusion; Malocclusion, Angle Class I - genetics; Methods; Multifactorial Inheritance - genetics; Orofacial clefts; Phenotype; Phenotypes; Polygenic inheritance; Polymorphism, Single Nucleotide; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Young Adult; Philippines; Cleft palate; Class I malocclusion; Cleft lip; GWAS; Genetic variation
• DOI: 10.1186/s12903-024-04444-x
• EISSN: 1472-6831

Individuals born with cleft lip and/or palate who receive corrective surgery regularly have abnormal growth in the midface region such that they exhibit premaxillary hypoplasia. However, there are also genetic contributions to craniofacial morphology in the midface region, so although these individuals appear to have Class III skeletal discrepancy, their molar relationship may be Class I. Past genome-wide association studies (GWASs) on skeletal Class II and III malocclusion suggested that multiple genetic markers contribute to these phenotypes via a multifactorial inheritance model, but research has yet to examine the genetic markers associated with dental Class I malocclusion. Thus, our goal was to conduct a family based GWAS to identify genes across the genome that are associated with Class I malocclusion, as defined by molar relations, in humans with and without clefts.
Our cohort consisted of 739 individuals from 47 Filipino families originally recruited in 2006 to investigate the genetic basis of orofacial clefts. All individuals supplied blood samples for DNA extraction and genotyping, and a 5,766 single nucleotide polymorphism (SNP) custom panel was used for the analyses. We performed a transmission disequilibrium test for participants with and without clefts to identify genetic contributors potentially involved with Class I malocclusion.
In the total cohort, 13 SNPs had associations that reached the genomic control threshold (p < 0.005), while five SNPs were associated with Class I in the cohort of participants without clefts, including four associations that were identified in the total cohort. The associations for the SNPs ABCA4 rs952499, SOX1-OT rs726455, and RORA rs877228 are of particular interest, as past research found associations between these genes and various craniofacial phenotypes, including cleft lip and/or palate.
These findings support the multifactorial inheritance model for dental Class I malocclusion and suggest a common genetic basis for different aspects of craniofacial development.