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PubMed2025

Genetic-epigenetic interactions (meQTLs) in orofacial clefts etiology.

OBJECTIVES: Nonsyndromic orofacial clefts (OFCs) involve complex genetic and environmental factors, with over 60 risk loci accounting for only a minority of estimated heritability and residing in non-coding regions with unclear functional relevance. We hypothesize that some genetic variants alter orofacial cleft risk by modifying DNA methylation (DNAm) at regulatory sequences essential for craniofacial development, acting as methylation quantitative trait loci (meQTLs). METHODS: We analyzed 10 well-established OFC-associated SNPs against genome-wide DNAm profiles in 409 cases and 456 controls, identifying 23 potential meQTLs. We validated findings using 358 cleft-discordant sibling pairs analyzed with quantitative MethyLight assays. Cross-referencing with the mQTL Database assessed temporal patterns across human development. Functional annotation used GeneHancer and craniofacial enhancer databases. RESULTS: Nine meQTLs were successfully replicated, including the highly significant rs987525 (8q24) - cg16561172 (MYC) association (P = 9.610E-6). This association mapped to a mesendoderm-active enhancer upstream of MYC, providing mechanistic explanation for the longstanding 8q24 cleft locus. Additional validated associations involved MAFB-PLCG1, NOG-PPM1E, FOXE1-FRZB, and SPRY2-LGR4 interactions. Independent differential methylation analysis revealed significant differences between discordant siblings at three CpG sites. Cross-referencing confirmed concordance with population-level methylation effects, with childhood representing the critical developmental window for most associations. CONCLUSIONS: This systematic meQTL characterization in OFCs demonstrates that genetic variants influence disease risk through epigenetic mechanisms. The 8q24-MYC regulatory pathway evidence provides crucial mechanistic insight into a major OFC risk locus. These findings bridge genetic associations with functional consequences, address missing heritability challenges, and suggest potential biomarkers and therapeutic targets for OFC prevention and treatment.

Journal Article↗
PubMed2026

Comprehensive analysis of de novo variants across 2,497 orofacial cleft trios reveals novel genetic drivers of disease.

BACKGROUND: Orofacial clefts (OFCs) and other palate abnormalities (PAs) are among the most common birth defects worldwide and are characterized by the abnormal formation of the lip and/or palate. Genetic studies have traditionally classified OFC cases as either syndromic, involving OFCs alongside other congenital anomalies, or nonsyndromic, which represent the majority of cases and occur in isolation. Emerging genomic evidence indicates that genes traditionally associated with syndromic forms of OFC can also harbor variants contributing to isolated cases, challenging the notion of a strict dichotomy between these categories and supporting their integration for gene discovery. METHODS: In this study, we applied multiple analytic approaches to characterize the genetic architecture of OFC and PAs by integrating genomic data from 2,497 trios with probands diagnosed with an OFC (n=2,080) or PA (n=417). We compared these findings across OFC subtypes and syndromic status with those from 5,515 control trios to identify enriched biological pathways and mechanisms and to prioritize candidate genes using variant burden testing. RESULTS: We observed a significant enrichment of de novo protein-truncating and damaging missense variants in cases compared to controls (OR = 2.17, p = 1.21×10-32), with particularly strong signals in biologically relevant gene sets involving OFC-associated, constrained, Mendelian disorder, and mouse candidate genes. Variant burden testing identified 39 OFC risk genes at FDR ≤ 0.05, which we then integrated with 593 established OFC genes to interrogate the functional underpinnings of OFC via network analysis. This analysis revealed 309 high-order interactor genes not previously associated with OFC. Notably, this OFC network clustered into ten distinct biological pathways, with nucleosome-associated genes showing significant enrichment among cases in our cohort (OR = 14.8, p = 8.1×10-4). In a final integrative step, we combined evidence across all analyses to nominate 231 candidate genes, 32 of which contained at least two deleterious de novo variants in our cohort. CONCLUSIONS: These findings underscore the value of integrating diverse OFC and PA subtypes, syndromic status, and variant classes to elucidate the genetic architecture of these disorders, highlighting both phenotypic expansion of known disease genes and the emergence of novel gene-phenotype associations.

De Novo Variant Enrichment↗
PubMed2026

Genetic-epigenetic interactions (meQTLs) in orofacial clefts etiology.

Understanding how genetic variants influence disease risk through molecular mechanisms remains a central challenge in complex disease genetics. Nonsyndromic orofacial clefts (OFCs) exemplify this challenge, with most risk loci residing in non-coding regions. We hypothesized that common genetic variants influence OFC risk by modulating DNA methylation at regulatory elements through methylation quantitative trait loci (meQTLs). We analyzed 10 OFC-associated SNPs against genome-wide DNA methylation profiles in 409 cases and 456 controls, identifying 23 potential meQTLs. Findings were validated using 358 cleft-discordant sibling pairs with MethyLight assays. We performed formal mediation analysis, genotype-tissue interaction and cross-referenced with the mQTL Database to assess developmental timing. Nine meQTLs were validated, including rs987525 (8q24)-cg16561172 (MYC) (P = 9.6 × 10⁻⁶), which mapped to a mesendoderm-active enhancer upstream of MYC. Genotype × tissue interaction confirmed tissue-specificity (P = 1.00 × 10- 3), with stronger effects in oral-derived tissue (saliva). Additional validated SNP-CpG associations involved MAFB-PLCG1, NOG-PPM1E, FOXE1-FRZB, and SPRY2-LGR4. While effect sizes correlated between tissues (r = 0.81), formal mediation analysis indicated individual CpG sites do not fully mediate SNP-phenotype relationships, suggesting coordinated epigenetic mechanisms. Most associations showed peak effects during childhood, while 8q24 showed unique adult-specific patterns. We identified genetic variants influencing methylation at craniofacial regulatory elements, and provided a mechanistic link for a major risk locus, 8q24, with tissue-specific effects in saliva. While individual CpG sites did not fully mediate the genetic risk, our findings identified specific regulatory regions where coordinated epigenetic changes may contribute to OFC susceptibility.

Humans↗
PubMed2026

Orofacial Cleft Disparities in American Indian and Alaska Native Populations: A Systematic Review and Meta-Analysis.

ObjectiveTo evaluate the prevalence, access to care, and health outcomes of orofacial clefts (OFCs) among American Indian and Alaska Native (AI/AN) populations through a systematic review and meta-analysis.DesignSystematic review and meta-analysis performed in accordance with PRISMA 2020 guidelines and registered with PROSPERO (CRD420251035364).SettingUS-based population registries, hospital databases, and institutional or community-level retrospective studies involving AI/AN populations.Patients and ParticipantsAI/AN individuals with OFCs compared with non-Hispanic White patients.InterventionsPrimary cleft lip and palate repair, secondary cleft-related procedures, and multidisciplinary cleft care.Main Outcome Measure(s)Prevalence of OFCs, timing of cleft surgery, discharge disposition, access to specialists, and qualitative determinants of disparities.ResultsEighteen studies including more than 1985 AI/AN patients were identified. Meta-analysis of 5 studies estimated a pooled OFC prevalence of 15 per 10 000 live births (95% confidence interval: 5-49), with substantial heterogeneity (I2 = 99.8%). Individual studies reported significantly higher OFC prevalence in AI/AN populations compared to non-Hispanic Whites (odds ratio range: 1.44-2.68). Geographic maldistribution of craniofacial-trained surgeons, increased odds of nonhome discharge, and delayed cleft palate repair were consistently observed barriers. Qualitative analyses highlighted structural inequities, perceived racism, and lack of culturally responsive care as major contributors to disparities.ConclusionsAI/AN populations face a disproportionately high burden of OFCs alongside structural barriers to timely, culturally competent care. Addressing these disparities requires community-engaged, multidisciplinary interventions that improve geographic access and integrate culturally responsive approaches to care.

Humans↗
PubMed1978

Upper extremity deformities associated with the orofacial clefts.

A material of 89 cases of upper extremity deformities, among the 3225 cleft patients born during the period 1950-75, and treated in the Finnish Red Cross Cleft Centre is presented. About two-thirds of the patients had an isolated cleft palate--half of the male and nearly all of the female patients. The percentage of upper extremity deformities appearing with the different types of the orofacial clefts was, for clefts of the primary palate 2.0: specifically for cleft lip 0.8, cleft lip--palate 2.6, and cleft lip and palate 3.6; and for clefts of the secondary palate 3.5: specifically for cleft palate 3.7, submucous cleft palate 1.6; and for the branchial arch syndrome (lateral cleft) 5.2; the total average being 2.8 percent. About one-third of the patients were dwarfs, most of them diastrophic dwarfs. Syndactyly was somewhat more common among cleft patients, 0.3%, than in the average population. Polydactyly, 0.1% was about as common as the average. Ectrodactyly was more common among cleft patients, 0.4%, than either syndactyly or polydactyly that are considered the most common hand deformities among the general population. The syndactyly cases were more complicated than the average, among them 4 cases of Apert syndrome were noted. About three-fourths of the 89 patients had multiple deformities.

Abnormalities, Multiple↗
PubMed1992

[Prenatal virus infections and orofacial clefts].

A potential teratogenic activity of virus infections caused by the viruses of rubella, influenza, parotitis, hepatitis B, cytomegalovirus and the Epstein-Barr virus was investigated. Specific antibodies against these viruses were examined serologically in children with orofacial clefts and in their mothers and the results were compared with those obtained in control children and their mothers. Different micromethods were used in performing the examinations (ELISA, RIA, NIR, KFR, HIT). Evaluation of the results and their statistical processing supports the assumption that prenatal infection may have occurred in the series studied induced by the viruses of influenza, rubella, cytomegalovirus, and possibly also by the Epstein-Barr virus. No association with the viruses of parotitis and hepatitis B was established. (Tab. 5, Ref. 36.)

Antibodies, Viral↗
PubMed1979

A study of relationships between judgments of speech and appearance of patients with orofacial clefts.

A series of six studies was designed to examine the effects of subjects' appearance on listeners' judgments of nasal speech and to examine the effects of nasal speech on viewers' judgments of attractiveness. In three studies, pictures of male and female subjects with varying degrees of orofacial clefts were paired with tape-recorded speech samples with varying degrees of nasality, and judges rated speech acceptability. Results of two-way analysis of variance failed to support the idea that appearance has an effect on ratings of nasality. In three other studies, the same stimuli were used to examine the effects of nasal speech on judges' ratings of appearance. Results of a two-way analysis of variance indicated that nasality had an effect on ratings of appearance. As the severity of nasality increased, ratings of attractiveness decreased. Results imply that a decrease in nasality may enhance the way persons with cleft lips are perceived cosmetically.

Cleft Lip↗
PubMed2026

Trio-based GWAS reveals loci associated with different forms of isolated cleft lip.

Orofacial clefts (OFCs) are the most common craniofacial birth defect and comprise a diverse group of traits with complex and heterogeneous etiologies. Genetic studies of OFCs typically approach this diversity by stratifying cases into broad diagnostic classes, including cleft lip (CL), cleft palate (CP), and cleft lip with palate (CLP). Although this strategy has yielded important insights into OFC risk, it ignores the phenotypic heterogeneity within each subtype. CL exhibits marked phenotypic variability, involving differences in alveolar involvement, laterality, and sidedness that may reflect distinct etiologies. Given this phenotypic diversity within CL, we assembled a multi-ancestry cohort of 837 nonsyndromic CL case-parent trios with whole-genome sequencing and detailed phenotyping. We performed genome-wide association scans (GWAS) via transmission disequilibrium tests for CL overall and for 14 CL subtypes defined by involvement of the alveolus (with and without), laterality (uni- and bilateral), and sidedness (left and right). We identified four genome-wide significant loci. Two loci, IRF6 and 8q24.21, were both detected in the overall CL GWAS. PLCB1/PLCB4 and MAFB were detected in GWASs of alveolar cleft involvement and CL left sidedness, respectively. These subtype-specific associations were followed by case-only comparisons that reflect the presence or absence of alveolus cleft or left-sided bias of CL to confirm the specificity of the association signal to the particular subtype. Our results provide evidence of within-class CL subtype-specific genetic links for loci previously discussed in the context of primary OFC classes and demonstrate the value of granular OFC subtype characterization to capture trait-specific associations.

Alveolus Cleft↗
PubMed1992

Association of autosomal dominant cleft lip and palate and translocation 6p23;9q22.3.

Orofacial clefting (OFC) is genetically complex in that no single gene defect is responsible for all forms. We have identified a family who exhibit autosomal dominant orofacial clefting together with some features of ectodermal dysplasia. In this family there is concordance between these features and an apparently balanced translocation t(6;9)(p23;q22.3) which raises the possibility that a locus for one form of orofacial clefting may be located at one of the translocation breakpoints. Fluorescent in situ hybridization has shown that a candidate gene for OFC, which maps to distal 6p, is located on the derived chromosome 9 in affected individuals from this family. Further characterization of the translocation breakpoints and of their relationship with the candidate gene will determine whether a gene important for normal facial and/or ectodermal development is disrupted in this family.

Adult↗
PubMed1978

Syndromes with cleft lip and cleft palate.

A series of tables is presented as a diagnostic aid for the clinician when he confronts a patient who has a cleft lip and/or palate, together with associated anomalies. The tables provide a rapid way of sorting through the recognized syndromes with orofacial clefting in search of a possible overall diagnosis. Today, 154 such syndromes are recognized. This is more than twice as many as were known in 1971. Undoubtedly, many new syndromes with orofacial clefting will be delineated in the future.

Abnormalities, Multiple↗
PubMed1992

Confirmation of an association between RFLPs at the transforming growth factor-alpha locus and non-syndromic cleft lip and palate.

Three RFLPs at the TGFA locus were studied in 60 unrelated British Caucasian subjects with non-syndromic cleft lip/palate and 60 controls. A highly significant association between the TaqI RFLP and the occurrence of clefting was found (chi 2 = 15.04, p = less than 0.001). No significant association was found with the two other RFLPs studied (BamHI and RsaI). Haplotypes derived from the three RFLPs at the TGFA locus also showed an over-representation of the C2A2B2 haplotype in cases compared to controls. Analyses of genotypes according to type of cleft and the presence or absence of a family history of clefting were also carried out. These results provide further support for the role of TGFA as a gene of major effect in the development of orofacial clefts in humans.

Alleles↗
PubMed2025

Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.

As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud-based research continue to expand. Besides the potential for accelerated and diverse biomedical discovery that comes from a harmonized data ecosystem, the cloud also presents a shift away from the standard practice of duplicating data to computational clusters or local computers for analysis. However, despite these benefits, researcher migration to the cloud has lagged, in part due to insufficient educational resources to train biomedical scientists on cloud infrastructure. There exists a conceptual lack especially around the crafting of custom analytic pipelines that require software not pre-installed by cloud analysis platforms. We here present three fundamental concepts necessary for custom pipeline creation in the cloud. These overarching concepts are workflow and cloud provider agnostic, extending the utility of this education to serve as a foundation for any computational analysis running any dataset in any biomedical cloud platform. We illustrate these concepts using one of our own custom analyses, a study using the case-parent trio design to detect sex-specific genetic effects on orofacial cleft (OFC) risk, which we crafted in the biomedical cloud analysis platform CAVATICA.

Cloud Computing↗
PubMed2025

Novel Protein-Altering Variants in Cleft Genes Transmitted in Families With NSCL±P.

BACKGROUND: Pathogenic protein-altering variants play a role in the etiology of nonsyndromic cleft lip with or without palate (nsCL±P), one of the most common craniofacial anomalies. However, the genetic basis of many cases remains unclear, complicating risk prediction for affected families. PURPOSE: This study utilized whole-genome sequencing (WGS) of 150 case-families with nsCL±P from sub-Saharan Africa to identify pathogenic risk variants. STUDY DESIGN, SETTING, SAMPLE: This study utilized whole-genome sequencing (WGS) of 150 case-families with nsCL±P from sub-Saharan Africa to identify risk variants. PREDICTOR/EXPOSURE/INDEPENDENT VARIABLE: Genetic variants. MAIN OUTCOME VARIABLES: Nonsyndromic cleft lip with or without palate (nsCL±P). ANALYSES: Genomes were sequenced at a mean ×30 coverage, and variants were prioritized using CADD (≥20), REVEL (≥0.5), and ACMG/AMP clinical significance criteria. RESULTS: We identified pathogenic protein-altering variants in CHD7 (p.Arg1345His), LRP2 (p.Asp3245Asn), RYR1 (p.Arg2163Leu, p.Pro2903Thr), SHH (p.Met114Val), and WNT3 (p.Ser112Pro) highlighting the role of hedgehog signaling pathway (FDR=5.32e-12) in nsCL±P. These variants were inherited from unaffected parents suggesting an incomplete penetrance of the variant effect. Although mouse data showed that knockout of these genes produces cleft phenotypes, in vivo studies will help us better understand how the consequences of these variants differ from benign mutations. The presence of these protein-altering variants in unaffected parents-incomplete penetrance, provides additional evidence supporting the trait complexity. CONCLUSIONS AND RELEVANCE: This study identified rare, pathogenic protein-altering variants in genes involved in key developmental pathways in African families affected by nsCL±P. These findings highlight the critical role of the hedgehog signaling pathway and related networks in the etiology of nsCL±P. These findings underscore the importance of whole-genome sequencing in genetically diverse populations to uncover novel risk variants. These findings enhance our understanding of the genetic etiology of nsCL±P, particularly in under-represented African populations and support the multifactorial inheritance and the involvement of developmental pathways, such as hedgehog signaling in the etiology of clefting.

Humans↗
PubMedDate not supplied

Genetic aspects of some orofacial anomalies.

The increased importance of congenital anomalies in childhood disease is stressed. It is suggested that treatment and research in congential craniofacial anomalies would benefit from centralized registration. Their clinical management should be delegated to centres with a multidisciplinary team. Some problems related to genetic counselling and identification of microforms are illustrated by cleft lip and palate. An account is given of some orofacial anomalies.

Abnormalities, Multiple↗
PubMed1976

Studies of malformation syndromes of man XXXXI B: nosologic studies in the Hanhart and the Möbius syndrome.

We reviewed etiologic and phenotypic aspects of those orofacial and limb anomalies usually diagnosed as Hanhart syndrome and Mobius syndrome but also those described, among others, under names such as aglossia-adactylia syndrome, gloss-palatine ankylosis, ankyloglossia superior, peromelia and micrognathia, cleft palate/lateral synechiae syndrome, and the Charlie M. syndrome. By coding the degree of severity of the limb defects it was possible to compare these cases quantitatively and to determine the nosologic significance of associated cranial nerve palsies and chest abnormalities. We analyzed 7 personal and 62 previously reported cases and found: 1. that the severity in the upper limbs and, particularly, malformations of the feet, but not the presence or absence of cranial nerve palsies, is a significant feature in the differentiation of cases, and 2. that the group of patients with cranial nerve palsies includes some with limb defects similar to those in the Hanhart syndrome and others with features which overlap the manifestations of the Poland syndrome. Still other cases had cranial nerve palsy as an isolated trait or as a component manifestation of several different syndromes. These findings permit re-definition and nosologic delimitation of the various syndromes as follows: 1. The Hanhart-syndrome: usually severe limb defect of at least one hand or foot, frequently associated with severe oral abnormalities and sometimes also with cranial nerve palsy. Most cases reported as aglossia-adactylia syndrome, aglossia-hypomelia syndrome, and some cases reported as glossopalatine ankylosis, ankyloglossia superior and Mobius syndrome describe instances of the Hanhart syndrome. 2. The Poland-Mobius syndrome: we suggest this term to refer to those cases of "Mobius syndrome" which have a chest defect and/or symbrachydactyly of the type seen in the Poland syndrome. We suspect that these cases of the "Mobius syndrome," and most of the cases which are usually diagnosed as Poland syndrome represent a different spectrum of the same condition, hence the term Poland-Mobius syndrome. 3. The autosomal dominant cleft palate/lateral synechiae syndrome delineated by Fuhrmann et al. and other apparently less frequent conditions are mentioned in the discussion. Cranial nerve palsy obviously occurs in several etiologically distinct conditions. An analogous situation is present, although less obvious, in the Hanhart and the Poland-Mobius syndrome. Both of these conditions are formal genesis malformation syndromes which implies that they are etiologically non-specific developmental field complexes. In the Hanhart syndrome Bersu et al. postulate a common pathogenetic disturbance for oral and limb defects, thus suggesting that the manifestations represent a single anomaly rather than a "syndrome." This anomaly, for which we suggest the term Kettner anomaly, may occur not only in the Hanhart syndrome but also in other conditions. Similarly, the Poland anomaly, i.e...

Abducens Nerve↗
PubMed1979

Multiple-abutment fixed partial dentures in maxillofacial prosthetics.

Ten patients were presented to illustrate multiple-abutment fixed partial dentures used in combination with auxiliary prosthetic attachments of a fixed or removable design to solve diverse problems encountered in the rehabilitation of congenital and acquired orofacial defects. While such fixed prostheses have high initial costs, their effectiveness and long-term cost-benefits suggest that, where appropriate, they represent optimum therapy that will prove most economical over the long term.

Adolescent↗