Assessment of candidate genes and genetic heterogeneity in human non syndromic orofacial clefts specifically non syndromic cleft lip with or without palate

Association of selected gene variants with nonsyndromic orofacial clefts in Kuwait

INTRODUCTION AND OBJECTIVES

Non-syndromic orofacial clefts (NSOFCs) are complex congenital abnormalities involving both environmental and genetic factors involved in orofacial development. This study aimed to investigate the genetic association of specific genetic variants at different CYRIA gene loci with the development of NSOFCs in Kuwait.

METHODS

Four genetic variants (rs7552, rs3758249, rs3821949, and rs3917201) at four selected gene loci (CYRIA, FOXE1, MSX1, and TGFB3) were genotyped in a total of 240 DNA samples (patients (n = 114) and random controls (n = 126)) employing TaqMan® allele discrimination assay. For each variant and its genotype, the frequencies were determined and tested for Hardy-Weinberg Equilibrium. Genotype frequencies was compared between patients and controls using Pearson's test. Logistic regression analyses were employed to test for the associations of the four selected variants with the occurrence of NSOFCSs.

RESULTS

Significant differences in the distribution of genotypes between cases and controls, rs7552, rs3821949, and rs3917201 were found to have a positive association with NSOFCs. After adjusting for gender, the GG genotype of the rs7552 variant, the AG genotype of the rs3821949 variant, and the CC genotype of the rs3917201 variant showed nearly a two-fold increased risk of NSOFC (p < 0.05).

CONCLUSION

This study reports significant findings on the contribution and modest effect of CYRIA rs7552, MSX1 rs3821949, and TGFB3 rs3917201 in the development of NSOFCs. Our findings provide further evidence on the molecular mechanism and the role of the selected genes in NSOFCs.

Rethinking speech sound disorder (SSD) in non-syndromic cleft lip and palate: The importance of recognizing phonological and language difficulties

BACKGROUND

Children born with cleft palate ± lip (CP ± L) are at risk of speech sound disorder (SSD). Up to 40% continue to have SSD at age 5-6 years. These difficulties are typically described as articulatory in nature and often include cleft speech characteristics (CSC) hypothesized to result from structural differences. In non-CP ± L SSD comorbidity with language difficulties is often reported. There is growing evidence of concomitant language difficulties in children with CP ± L and of a higher prevalence of developmental speech errors in children compared with non-CP ± L peers. The impact of underlying phonological and language skills on speech production in children with CP ± L is poorly understood.

AIMS

To investigate language outcomes in children with CP ± L and the relationship to speech production, by answering the following research questions: (1) Does the profile of language skills in children with CP ± L differ from normative samples? (2) Do children with CP ± L and SSD have poorer language skills than those with typically developing speech? (3) Is there an association between language skills and speech profile in children with CP ± L at age 5-8 years?

METHODS & PROCEDURES

In this prospective cross-sectional, observational study, 95 participants were recruited from regional cleft lip and palate services in the UK. They were aged 5;0-7;11 with non-syndromic CP ± L. Those with a syndromic diagnosis, global learning disability, sensorineural hearing loss and first language other than English were excluded. Assessments of speech (Diagnostic Evaluation of Articulation and Phonology-DEAP) and language (Clinical Evaluation of Language Fundamentals-5th UK edition-CELF) were completed. Language outcomes were analysed and compared with normative samples and according to speech error analysis.

OUTCOMES & RESULTS

Average language scores were within the expected range. For those presenting with SSD, language scores were significantly lower than those with typically developing speech. Analysis of speech errors showed four distinct speech profiles: typical speech, CSC only, developmental speech characteristics (DSC), and combined CSC + DSC. Language scores were lower for participants with DSC (±CSC). A significant association was found between the presence of CSC + DSC and expressive language outcomes (odds ratio (OR) = 10.82; 95% confidence interval (CI) = 2.42, 48.32, p = 0.002).

CONCLUSIONS & IMPLICATIONS

An association between language skills and speech production was observed. The distribution of speech errors in children with CP ± L varied with a high level of DSC as well as CSC. Those with CSC + DSC had significantly lower language scores than those with typically developing speech or CSC only. Speech and language therapists working with this caseload should be alerted to potential ongoing phonological and language difficulties in children presenting with this profile.

WHAT THIS PAPER ADDS

What is already known on this subject Children born with CP ± L are known to be at risk of SSD. There is also evidence of language delay in the early years. Evidence for persistent language difficulties is equivocal but some studies have shown a higher than average prevalence of developmental phonological errors in addition to cleft articulation errors in speech production. What this paper adds to the existing knowledge This study investigates links between speech development and language skills in children aged 5-8 years with non-syndromic CP ± L. It adds to our understanding of the nature of SSD in children with CP ± L and in particular the relationship between language skills and speech production. It shows that children with CP ± L have varied speech profiles and that those presenting with delayed phonological processes are also at risk of language difficulties. What are the potential or actual clinical implications of this work? Speech and language therapists working with children with CP ± L should be aware of the varied nature of SSD in this population. They should be alert to the need for additional assessment of language for those presenting with delayed phonological processes and the implications this has for educational attainment.

Whole exome sequencing in 18 Brazilian families with vertical transmission of non-syndromic oral clefts

This study describes the results of whole exome sequencing in the etiological investigation and genetic counseling of families presenting with non-syndromic oral clefts with vertical transmission recorded in the Brazilian Database on Craniofacial Anomalies. Whole exome sequencing was performed in 18 families presenting with non-syndromic oral clefts with vertical transmission, and variant filtering was used to identify rare, and also possibly pathogenic variants in genes associated with oral clefts. Overall, our study identified seven families (38.88%) presented with segregating variants possibly related to oral clefts in our cohort: SETX, NOTCH1, FRAS1, ARHGAP29, KMT2D, ANKRD11, SIX1, BMP6, LRP2 and TFAP2A. In another family, all affected members (5.55%) presented a rare variant in FAM193A, which has no recognized function yet, but has prediction of deleterious effect. Our study highlights oral clefts clinical and etiological heterogeneity and shows the complexity of using whole exome sequencing for genetic counseling in non-syndromic oral clefts with vertical transmission.

The IRF6 rs2013162 and MTHFR A1298C rs1801131 Gene Polymorphisms Related to non-Syndromic Cleft lip and Palate among Deutero-Malay in Indonesia

OBJECTIVE

This study aimed to identify risk factors for NSCLP by analyzing polymorphisms in IRF6 rs2013162 and MTHFR A1298C rs1801131 in the Deutero Malay Population in Indonesia.

SETTING

DNA isolation from venous blood samples was done followed by PCR and PCR-RFLPs method.

PATIENTS/PARTICIPANTS

115 NSCLP subjects and 120 healthy control subjects.

MAIN OUTCOME MEASURE(S)

The odds ratio (OR) determined to evaluate the risk factors is the main outcome measure.

MATERIAL AND METHODS

The study is a case-control design using samples from the venous blood of 115 NSCLP subjects and 120 healthy control subjects. After DNA was extracted, the PCR-RFLPs method was performed using the DdeI restriction enzyme on 100 blood samples of the IRF6 rs2013162 group and Mboll restriction enzyme on 135 blood samples of the MTHFR A1298C rs1801131 group. The Chi-Square test was used with the Exact Fisher alternatives, depending on the expected count value.

RESULTS

The results showed that the T mutant allele (OR = 4.125, P < .05) and GT genotype (OR = 21.00, P < .05) of IRF6 rs2013162 and the C mutant allele (OR = 3.781, P < .05), AC genotype (OR = 5, P < .05) and CC genotype (OR = 9,681, P < .05) of the MTHFR A1298C is associated to a greater risk of NSCLP.

CONCLUSIONS

IRF6 rs2013162 and MTHFR A1298C rs1801131 gene polymorphisms are strongly associated with NSCLP among the Deutero Malay population in the Indonesian population.

Epithelial-mesenchymal crosstalk: the scriptwriter of craniofacial morphogenesis

Epithelial-mesenchymal interactions (EMI) are fundamental mechanisms in regulating development and organogenesis. Here we summarized the signaling mechanisms involved in EMI in the major developmental events during craniofacial morphogenesis, including neural crest cell induction, facial primordial growth as well as fusion processes. Regional specificity/polarity are demonstrated in the expression of most signaling molecules that usually act in a mutually synergistic/antagonistic manner. The underlying mechanisms of pathogenesis due to disrupted EMI was also discussed in this review.

Cleft lip and palate and periconception COVID-19 infection in five arab countries

BACKGROUND

Little is known about factors associated with the severity of cleft lip with or without cleft palate (CL/P) especially during the COVID-19 pandemic with its dramatic changes.

OBJECTIVES

The aim of this multi-national study is to measure the association between CL/P severity, COVID-19 infection, and fear of COVID-19 in five Arab countries.

METHODS

This cross-sectional study took place in major governmental hospitals in five Arab countries from November 2020 to April 2023. Participants were infants born with CL/P and their mothers who were in their 1st trimester during the COVID-19 pandemic. Clinical examination was carried out, and CL/P cases were grouped according to phenotype: cleft lip and palate (CLP) versus cleft lip (CL), cleft extension (incomplete versus complete), and site (unilateral versus bilateral) to assess severity. Information on maternal COVID-19 infection and fear of COVID-19 were gathered.

RESULTS

The study recruited 273 CL/P infants. Maternal COVID-19 infection during one-month pre-gestation and 1st trimester was significantly associated with higher odds of CL/P severity (AOR = 2.707; P = 0.002) than mothers without the COVID-19 infection. Using supplements during pregnancy showed a protective effect (AOR = 0.573; P = 0.065).

CONCLUSION

Mothers infected with COVID-19 before and during pregnancy had more than twofold higher odds of having an infant with a more severe CL/P phenotype.

Molecular investigation in individuals with orofacial clefts and microphthalmia-anophthalmia-coloboma spectrum

This study describes genomic findings among individuals with both orofacial clefts (OC) and microphthalmia/anophthalmia/coloboma (MAC) recorded in the Brazilian Database on Craniofacial Anomalies (BDCA). Chromosomal microarray analysis (CMA) and Whole Exome Sequencing (WES) were performed in 17 individuals with OC-MAC. Clinical interpretation of molecular findings was based on data available at the BDCA and on re-examination. No copy number variants (CNVs) classified as likely pathogenic or pathogenic were detected by CMA. WES allowed a conclusive diagnosis in six individuals (35.29%), two of them with variants in the CHD7 gene, and the others with variants in the TFAP2A, POMT1, PTPN11, and TP63 genes with the following syndromes: CHARGE, CHD7-spectrum, Branchiooculofacial, POMT1-spectrum, LEOPARD, and ADULT. Variants of uncertain significance (VUS) possibly associated to the phenotypes were found in six other individuals. Among the individuals with VUSes, three individuals presented variants in genes associated to defects of cilia structure and/or function, including DYNC2H1, KIAA0586, WDR34, INTU, RPGRIP1L, KIF7, and LMNA. These results show that WES was the most effective molecular approach for OC-MAC in this cohort. This study also reinforces the genetic heterogeneity of OC-MAC, and the importance of genes related to ciliopathies in this phenotype.

A comprehensive consolidation of data on the relationship between IRF6 polymorphisms and non-syndromic cleft lip/palate susceptibility: From 79 case-control studies

BACKGROUND

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a prevalent craniofacial birth defect on a global scale. A number of candidate genes have been identified as having an impact on NSCL/P. However, the association between interferon regulatory factor 6 (IRF6) polymorphisms and NSCL/P has yielded inconsistent results, prompting the need for a meta-analysis to obtain more accurate estimates.

METHODS

We conducted a thorough screening of all relevant articles published up until November 15, 2023, in online bibliographic databases. The statistical analysis of the collected data was performed using the Comprehensive Meta-Analysis (Version 4.0) software.

RESULTS

A total of 79 case-control studies, comprising 14,003 cases and 19,905 controls, were included in our analysis. The combined data indicated that the IRF6 rs642961 and rs2235371 polymorphisms were associated with an increased risk of NSCL/P in the overall population. However, no significant association was found between the rs2013162 and rs2235375 polymorphisms and the risk of NSCL/P in the overall population. Furthermore, subgroup analyses revealed significant correlations between the IRF6 rs642961, rs2235371, and rs2235375 polymorphisms and the risk of NSCL/P based on ethnic background and country of origin. Nevertheless, the rs2013162 polymorphism plays a protective role in Caucasians and mixed populations.

CONCLUSIONS

Our collective data indicates a significant association between the rs642961 and rs2235371 polymorphisms and the risk of NSCL/P in the overall population. The rs2235375 polymorphism could influence the susceptibility to NSCL/P based on ethnic background. Meanwhile, the rs2013162 polymorphism provides protective effects in Caucasian, mixed populations, and the Brazilian population.

Association of prenatal Cleft Lip and Palate ultrasound abnormalities with copy number variants at a single Chinese tertiary center

BACKGROUD

A systematic analysis was conducted to investigate the molecular etiology of fetal cleft lip and/or palate (CL/P) and the association between various types of CL/P and copy number variations (CNVs), as well as their impact on birth outcomes.

METHODS

In this retrospective study conducted between January 2016 and July 2022, a cohort of pregnancies diagnosed with fetal CL/P was enrolled and comprehensive clinical data for all cases were extracted from our medical record database, including demographic data about the pregnancies, ultrasound findings, results of Chromosomal microarray (CMA), as well as relevant pregnant and perinatal outcomes.

RESULTS

Among the 358 cases, 32 clinically significant variants in 29 (8.1%) fetuses with CL/P were detected by CMA. In 338 singleton pregnancies, the diagnostic yield of CMA in the context of CL/P fetuses was determined to be 7.7% (26/338). CP cases exhibited a relatively higher prevalence of pathogenic/likely pathogenic CNVs at a rate of 25% (3/12), followed by CLP cases at 8.0% (23/288). Notably, the CL group did not demonstrate any pathogenic/likely pathogenic CNV findings among the examined cases (0/38). The diagnostic rate of clinically significant variants was notably higher in the non-isolated CL/P group than in the isolated CL/P group (11/33, 33.3% vs. 15/305, 4.9%, p < 0.001). Within the remaining 20 twin pregnancies, three clinically significant variants (15%) were observed.

CONCLUSIONS

This study provides powerful evidence supporting the efficacy of CMA as a valuable tool for facilitating the prenatal genetic diagnosis of fetal CL/P. The presence of CP and CLP in fetal cases demonstrated a relatively higher incidence of pathogenic/likely pathogenic CNVs. Moreover, when these cases were accompanied by additional ultrasound abnormalities, the likelihood of identifying diagnostic CNVs significantly increased. Conversely, cases of CL alone might not be associated with positive CNVs. The present data may significantly enhance prenatal diagnosis accuracy and facilitate informed genetic counseling for cases of fetal CL/P.

Pattern of Cleft Lip and Palate Clefts at a Tertiary Care Hospital in Saudi Arabia

BACKGROUND

Clefts of the lip and palate (CL/P) and cleft palate (CP) are the most common craniofacial congenital anomalies. Clefts are classified as syndromic and nonsyndromic. Nonsyndromic clefts have no known genetic causes.

OBJECTIVES

This study combines prospective and retrospective studies to review the patterns of CL/P and CP and associated syndromes and conditions in patients registered for CL/P surgery at a tertiary care pediatric center in our tertiary care hospital in Saudi Arabia.

METHODS

It included patient data from May 2015 through April 2023. Patient record forms and SPSS (IBM version 20.0) were used to collect and analyze data. A significance level of 5% was used, with p ≤ 0.05 considered statistically significant.

RESULTS

Of the 319 patients who met our inclusion criteria, 175 were male. Of the total, 99 had a left unilateral isolated cleft lip, 61 had a right unilateral isolated cleft lip, 69 had a bilateral cleft lip, and 90 had an isolated CP. Of the total, 140 had CL/P. Around 242 were nonsyndromic. The Chi-square test revealed a significant association between the prevalence of isolated CP and CLP and gender. The prevalence of left unilateral isolated cleft lip and bilateral and isolated CP was significantly associated with syndromic and nonsyndromic cases.

CONCLUSION

Males are more likely to be affected by orofacial clefts, which is consistent with the global trend. Isolated CP was the most common orofacial cleft. Within the sample, syndromes' association with orofacial clefts was significantly weaker than that of isolated and bilateral clefts.

Testing Reported Associations of Gene Variants with Non-Syndromic Orofacial Clefts in the Polish Population

Orofacial clefts (OFCs) are the second most common birth defect worldwide. The etiology of OFCs involves complex interactions between genetics and environment. Advances in genomic technologies have identified gene variants associated with OFCs. This study aimed to investigate whether selected SNPs in the MYH9, MTHFR, MAFB, and SUMO1 genes influence the occurrence of non-syndromic OFCs in the Polish population. The study included 209 individuals with non-syndromic OFCs and 418 healthy controls. Saliva and umbilical cord blood samples were collected for DNA extraction. Four SNPs in the MYH9, MTHFR, MAFB, and SUMO1 genes were genotyped using real-time PCR-based TaqMan assays. Statistical analysis was performed using logistic regression to assess the association between SNPs and OFCs. A significant association was found between the rs7078 CC polymorphism and OFCs (OR = 3.22, CI 1.68-6.17, p < 0.001). No significant associations were identified for the rs1081131, rs13041247, and rs3769817 polymorphisms. The research indicates that the rs7078 polymorphism significantly influences the occurrence of orofacial cleft palate in the Polish population, whereas the rs3769817, rs1801131, and rs13041247 SNPs do not show such a correlation.

Stem Cell-Based Regenerative Approaches for the Treatment of Cleft Lip and Palate: A Comprehensive Review

Cleft lip and/or palate (CLP) is a prevalent congenital craniofacial abnormality that can lead to difficulties in eating, speaking, hearing, and psychological distress. The traditional approach for treating CLP involves bone graft surgery, which has limitations, post-surgical complications, and donor site morbidity. However, regenerative medicine has emerged as a promising alternative, employing a combination of stem cells, growth factors, and scaffolds to promote tissue regeneration. This review aims to provide a comprehensive overview of stem cell-based regenerative approaches in the management of CLP. A thorough search was conducted in the Medline/PubMed and Scopus databases, including cohort studies, randomized controlled trials, case series, case controls, case reports, and animal studies. The identified studies were categorized into two main groups: clinical studies involving human subjects and in vivo studies using animal models. While there are only a limited number of studies investigating the combined use of stem cells and scaffolds for CLP treatment, they have shown promising results. Various types of stem cells have been utilized in conjunction with scaffolds. Importantly, regenerative methods have been successfully applied to patients across a broad range of age groups. The collective findings derived from the reviewed studies consistently support the notion that regenerative medicine holds potential advantages over conventional bone grafting and represents a promising therapeutic option for CLP. However, future well-designed clinical trials, encompassing diverse combinations of stem cells and scaffolds, are warranted to establish the clinical efficacy of these interventions with a larger number of patients.

Rare loss-of-function variants in FLNB cause non-syndromic orofacial clefts

Orofacial clefts (OFCs) are the most common congenital craniofacial disorders, of which the etiology is closely related to rare coding variants. Filamin B (FLNB) is an actin-binding protein implicated in bone formation. FLNB mutations have been identified in several types of syndromic OFCs and previous studies suggest a role of FLNB in the onset of non-syndromic OFCs (NSOFCs). Here, we report two rare heterozygous variants (p.P441T and p.G565R) in FLNB in two unrelated hereditary families with NSOFCs. Bioinformatics analysis suggests that both variants may disrupt the function of FLNB. In mammalian cells, p.P441T and p.G565R variants are less potent to induce cell stretches than wild type FLNB, suggesting that they are loss-of-function mutations. Immunohistochemistry analysis demonstrates that FLNB is abundantly expressed during palatal development. Importantly, Flnb-/- embryos display cleft palates and previously defined skeletal defects. Taken together, our findings reveal that FLNB is required for development of palates in mice and FLNB is a bona fide causal gene for NSOFCs in humans.

Incidence of non-syndromic orofacial cleft during the COVID-19 pandemic in Saudi Arabia

OBJECTIVES

This is the first national study to investigate the incidence of non-syndromic oro-facial clefts (NSOFC) and Pierre-Robin-Sequence in Saudi Arabia over the Covid-19 pandemic period.

METHODS

All maternity hospitals (30-hospitals) in the major regions and cities of Saudi from November 2020-to-2021 were included in the study. Patients were evaluated for cleft phenotype using the LASHAL-classification system. The incidence of NSOFC in Saudi Arabia was calculated by comparing the number of NSOFCs cases born out of all live births during the study period at the included hospitals. Clinical examination was performed and information was gathered using a validated data collection form.

RESULTS

In one year, 140,380 live-infants were born at the selected hospitals. Of these, 177 were diagnosed with NSOFC giving an incidence of 1.26/1,000 live-births in Saudi Arabia and the highest incidence in Medina city (2.46/1000 live-births). The incidence of cleft lip-and-palate (0.67/1000 live-births) was higher than that of cleft-palate (0.37/1000 live-births) and cleft-lip (0.22/1000 live-births). Pierre-Robin Sequence incidence was (0.04/1000 live-births). There were 21(12.1) or 23(13.2%) of NSOFC's mothers exposed or vaccinated with Covid-19, respectively.

CONCLUSION

The national incidence of NSOFC in Saudi Arabia was 1.26/1000 live births with variation between phenotypes and regions in the country. In addition, to reporting Covid-19 infection prevalence and vaccine exposure among NSOFC's mothers, this study represents the first of its type to evaluate NSOFC prevalence in Saudi Arabia on a national level.

Exome sequencing improves genetic diagnosis of congenital orofacial clefts

Objective: This retrospective study aims to evaluate the utility of exome sequencing (ES) in identifying genetic causes of congenital orofacial clefts (OFCs) in fetuses with or without other structural abnormalities, and to further explore congenital OFCs genetic causes. Methods: The study enrolled 107 singleton pregnancies diagnosed with fetal OFCs between January 2016 and May 2022, and categorized them into two groups: isolated cleft lip and/or palate (CL/CP) and syndromic CL/CP. Cases with positive karyotyping and chromosomal microarray analysis results were excluded. Whole-exome sequencing was performed on eligible fetuses and their parents. Monogenic variants identified by ES and perinatal outcomes were recorded and evaluated during postnatal follow-up. Results: Clinically significant variants were identified in 11.2% (12/107) of fetuses, with no significant difference in detection rate between the isolated CL/CP group and the syndromic CL/CP group (8/83, 9.6% vs. 4/24, 16.7%, p = 0.553). Additionally, sixteen (16/107, 15.0%) fetuses had variants of uncertain significance. We identified 12 clinically significant variations that correlated with clinical phenotypes in 11 genes from 12 fetuses, with CHD7 being the most frequently implicated gene (n = 2). Furthermore, we observed a significant difference in termination rates and survival rates between the isolated CL/CP and syndromic CL/CP groups (41.0% vs. 70.8% and 56.6% vs. 20.8%, p < 0.05 for both). Conclusion: Based on our findings, it is clear that ES provides a significant increase in diagnostic yield for the molecular diagnosis of congenital OFCs, thereby substantially improving the existing prenatal diagnostic capabilities. This study also sheds light on seven novel pathogenic variants, broadening our understanding of the genetic underpinnings of OFCs and expanding the disease spectrums of relevant genes.

Orofacial Clefts: Genetics of Cleft Lip and Palate

Orofacial clefting is considered one of the commonest birth defects worldwide. It presents as cleft lip only, isolated cleft palate or cleft lip and palate. The condition has a diverse genetic background influenced by gene-gene and gene-environment interaction, resulting in two main types, syndromic and nonsyndromic orofacial clefts. Orofacial clefts lead to significant physiological difficulties that affect feeding, speech and language development and other developmental aspects, which results in an increased social and financial burden on the affected individuals and their families. The management of cleft lip and palate is solely based on following a multidisciplinary team approach. In this narrative review article, we briefly summarize the different genetic causes of orofacial clefts and discuss some of the common syndromes and the approach to the management of orofacial clefts.

Simultaneous Occurrence of Hypospadias and Bilateral Cleft Lip and Jaw in a Crossbred Calf: Clinical, Computer Tomographic, and Genomic Characterization

Congenital abnormalities in animals, including abnormalities of the cleft lip and jaw and hypospadias have been reported in all domesticated species. They are a major concern for breeders due to the increased economic loss they entail. In this article, we described a congenital bilateral cheilognathoschisis (cleft lip and jaw) with campylognathia in association with penile hypospadias and preputial hypoplasia with failure of preputial fusion in a Bos taurus crossbred Piedmontese × Wagyu calf. Clinical examination, computed tomography, and whole genome sequencing were performed to describe and identify a possible cause of the abnormalities. Clinical examination revealed a bilateral cheilognathoschisis of approximately 4 cm in length and 3 cm in width in the widest part, with computer tomography analyses confirming the bilateral absence of the processus nasalis of the incisive bone and the lateral deviation of the processus palatinus towards the left side. Genomic data analyses identified 13 mutations with a high impact on the products of the following overlapped genes: ACVR1, ADGRA2, BHMT2, BMPR1B, CCDC8, CDH1, EGF, F13A1, GSTP1, IRF6, MMP14, MYBPHL, and PHC2 with ADGRA2, EGF, F13A1, GSTP1, and IRF6 having mutations in a homozygous state. The whole genome investigation indicates the involvement of multiple genes in the birth defects observed in this case.

Rs28446116 in PTCH1 is associated with non-syndromic cleft lip with or without palate in the Ningxia population, China

OBJECTIVES

To investigate the association between PTCH1 single nucleotide polymorphism(SNP) and non-syndromic cleft lip with or without palate (NSCL/P) in the Ningxia Hui Autonomous region and predict the function of single nucleotide polymorphism through bioinformatics analysis.

DESIGN

A case-control analysis of 31 single nucleotide polymorphism locus alleles on PTCH1 gene (504 cases and 455 controls) was performed to explore the association between PTCH1 gene polymorphisms and non-syndromic cleft lip with or without palate in Ningxia region. Transcription factors, 3D single nucleotide polymorphism and other related information of single nucleotide polymorphism loci with statistical significance were screened by the case-control experiments, and then analyzed the corresponding transcription factors through the NCBI database.

RESULTS

The case-control study showed that 5 of the 31 single nucleotide polymorphism loci rs357564 (P = 0.0233), rs1805155 (P = 0.0371), rs28446116 (P = 0.0408), rs2282041 (P = 0.0439), rs56119276 (P = 0.0256) had statistically significant differences in allele frequencies between the case and control groups. Bioinformatics analysis revealed that EP300 and RUNX3, among the transcription factors associated with rs28446116, may be associated with the development of non-syndromic cleft lip with or without palate.

CONCLUSION

PTCH1 gene may be associated with the occurrence of non-syndromic cleft lip with or without palate in the Ningxia region, which may be related to the role of EP300 and RUNX3 in the development of cleft lip and palate.

Morphometric analysis of the size-adjusted linear dimensions of the skull landmarks revealed craniofacial dysmorphology in Mid1-cKO mice

BACKGROUND

The early craniofacial development is a highly coordinated process involving neural crest cell migration, proliferation, epithelial apoptosis, and epithelial-mesenchymal transition (EMT). Both genetic defects and environmental factors can affect these processes and result in orofacial clefts. Mutations in MID1 gene cause X-linked Opitz Syndrome (OS), which is a congenital malformation characterized by craniofacial defects including cleft lip/palate (CLP). Previous studies demonstrated impaired neurological structure and function in Mid1 knockout mice, while no CLP was observed. However, given the highly variable severities of the facial manifestations observed in OS patients within the same family carrying identical genetic defects, subtle craniofacial malformations in Mid1 knockout mice could be overlooked in these studies. Therefore, we propose that a detailed morphometric analysis should be necessary to reveal mild craniofacial dysmorphologies that reflect the similar developmental defects seen in OS patients.

RESULTS

In this research, morphometric study of the P0 male Mid1-cKO mice were performed using Procrustes superimposition as well as EMDA analysis of the size-adjusted three-dimensional coordinates of 105 skull landmarks, which were collected on the bone surface reconstructed using microcomputed tomographic images. Our results revealed the craniofacial deformation such as the increased dimension of the frontal and nasal bone in Mid1-cKO mice, in line with the most prominent facial features such as hypertelorism, prominent forehead, broad and/or high nasal bridge seen in OS patients.

CONCLUSION

 While been extensively used in evolutionary biology and anthropology in the last decades, geometric morphometric analysis was much less used in developmental biology. Given the high interspecies variances in facial anatomy, the work presented in this research suggested the advantages of morphometric analysis in characterizing animal models of craniofacial developmental defects to reveal phenotypic variations and the underlining pathogenesis.

Cognitive functioning and clinical characteristics of children with non-syndromic orofacial clefts: A case-control study

Introduction

The higher rate of neuropsychiatric disorders in individuals with non-syndromic orofacial clefts has been well documented by previous studies. Our goal was to identify children with non-syndromic orofacial clefts that are at risk for abnormal neurodevelopment by assessing their developmental history and present cognitive functioning.

Materials and methods

A single-center, case-controlled study was carried out at the Department of Pediatrics of the University of Pécs in Hungary. The study consisted of three phases including questionnaires to collect retrospective clinical data and psychometric tools to assess IQ and executive functioning.

Results

Forty children with non-syndromic oral clefts and 44 age-matched controls participated in the study. Apgar score at 5 min was lower for the cleft group, in addition to delays observed for potty-training and speech development. Psychiatric disorders were more common in the cleft group (15%) than in controls (4.5%), although not statistically significant with small effect size. The cleft group scored lower on the Continuous Performance Test. Subgroup analysis revealed significant associations between higher parental socio-economic status, academic, and cognitive performance in children with non-syndromic orofacial clefts. Analyzes additionally revealed significant associations between early speech and language interventions and higher scores on the Verbal Comprehension Index of the WISC-IV in these children.

Discussion

Children with non-syndromic orofacial clefts seem to be at risk for deficits involving the attention domain of the executive system. These children additionally present with difficulties that affect cognitive and speech development. Children with non-syndromic orofacial clefts show significant skill development and present with similar cognitive strengths as their peers. Longitudinal studies with larger sample sizes are needed to provide more conclusive evidence on cognitive deficits in children with non-syndromic orofacial clefts at risk for neurodevelopmental difficulties.

Gene×environment associations in orofacial clefting

This chapter reviews the evidence of gene×environment interactions (G×E) in the etiology of orofacial cleft birth defects (OFCs), specifically cleft lip (CL), cleft palate (CP), and cleft lip with or without cleft palate (CL/P). We summarize the current state of our understanding of the genetic architecture of nonsyndromic OFCs and the evidence that maternal exposures during pregnancy influence risk of OFCs. Further, we present possible candidate gene pathways for these exposures including metabolism of folates, metabolism of retinoids, retinoic acid receptor signaling, aryl hydrocarbon receptor signaling, glucocorticoid receptor signaling, and biotransformation and transport. We review genes in these pathways with prior evidence of association with OFCs, genes with evidence from prior candidate gene G×E studies, and genes identified from genome-wide searches specifically for identifying G×E. Finally, we suggest future directions for G×E research in OFCs.

Bilateral Cleft Lip Repair: Lessons from History

LEARNING OBJECTIVES

After studying this article, the participant should be able to: 1. Describe the bilateral cleft lip and nasal deformity and associated anatomical variations. 2. Understand the history and evolution of the bilateral cleft lip repair. 3. Understand the key principles of the surgical repair.

SUMMARY

This article describes characteristics of the bilateral cleft lip and nasal deformity and its management, including presurgical orthopedics, operative techniques, and postsurgical care.

[Exploring the association between de novo mutations and non-syndromic cleft lip with or without palate based on whole exome sequencing of case-parent trios]

OBJECTIVE

To explore the association between de novo mutations (DNM) and non-syndromic cleft lip with or without palate (NSCL/P) using case-parent trio design.

METHODS

Whole-exome sequencing was conducted for twenty-two NSCL/P trios and Genome Analysis ToolKit (GATK) was used to identify DNM by comparing the alleles of the cases and their parents. Information of predictable functions was annotated to the locus with SnpEff. Enrichment analysis for DNM was conducted to test the difference between the actual number and the expected number of DNM, and to explore whether there were genes with more DNM than expected. NSCL/P-related genes indicated by previous studies with solid evidence were selected by literature reviewing. Protein-protein interactions analysis was conducted among the genes with protein-altering DNM and NSCL/P-related genes. R package "denovolyzeR" was used for the enrichment analysis (Bonferroni correction: P=0.05/n, n is the number of genes in the whole genome range). Protein-protein interactions among genes with DNM and genes with solid evidence on the risk factors of NSCL/P were predicted depending on the information provided by STRING database.

RESULTS

A total of 339 908 SNPs were qualified for the subsequent analysis after quality control. The number of high confident DNM identified by GATK was 345. Among those DNM, forty-four DNM were missense mutations, one DNM was nonsense mutation, two DNM were splicing site mutations, twenty DNM were synonymous mutations and others were located in intron or intergenic regions. The results of enrichment analysis showed that the number of protein-altering DNM on the exome regions was larger than expected (P < 0.05), and five genes (KRTCAP2, HMCN2, ANKRD36C, ADGRL2 and DIPK2A) had more DNM than expected (P < 0.05/(2×19 618)). Protein-protein interaction analysis was conducted among forty-six genes with protein-altering DNM and thirteen genes associated with NSCL/P selected by literature reviewing. Six pairs of interactions occurred between the genes with DNM and known NSCL/P-related genes. The score measuring the confidence level of the predicted interaction between RGPD4 and SUMO1 was 0.868, which was higher than the scores for other pairs of genes.

CONCLUSION

Our study provided novel insights into the development of NSCL/P and demonstrated that functional analyses of genes carrying DNM were warranted to understand the genetic architecture of complex diseases.

Association of soluble epoxide hydrolase 2 gene with the risk of non-syndromic cleft lip with or without cleft palate in western Han Chinese population

OBJECTIVES

This study aimed to explore the associations between soluble epoxide hydrolase 2 gene (EPHX2) variants and non-syndromic cleft lip with or without cleft palate (NSCL/P) in Chinese Han population.

METHODS

We recruited 159 NSCL/P cases from Chinese Han population and carried out targeted resequencing using the whole genome sequencing data of 542 healthy Chinese individuals from Novegene internal database as controls. We classified EPHX2 variants as common or rare according to their minor allele frequency and performed an association analysis for common variations and a burden analysis for rare variations.

RESULTS

The lowest P-value in NSCL/P was observed at rs57699806 (P=0.000 13, OR=2.849 and 95% CI: 1.691-4.800), followed by rs4732723 (P=0.006 50, OR=0.662 and 95%CI: 0.491-0.892), rs7829267 (P=0.009 20, OR=1.496 and 95%CI: 1.117-2.005), rs721619 (P=0.011 00, OR=1.474 and 95%CI: 1.098-1.980), and rs7816586 (P=0.040 00, OR=1.310 and 95%CI: 1.015-1.691). The odds ratios suggested the C allele at rs4732723 as a protective factor for NSCL/P and the reference alleles at other single nucleotide polymorphisms (SNPs) as the risk factors for NSCL/P. Burden analysis showed no statistical significance (P>0.05).

CONCLUSIONS

Through targeted resequencing, this study identified five SNPs named rs57699806, rs4732723, rs7829267, rs721619, and rs7816586 around the region of EPHX2 gene associated with NSCL/P in Chinese Han population. Four SNPs of rs57699806, rs4732723, rs7829267, and rs7816586 were first identified.

Association of genetic polymorphisms of VAX1, MAFB, and NTN1 with nonsyndromic cleft lip with or without cleft palate in Chinese population

Nonsyndromic cleft lip with or without palate (NSCL/P) is a common birth defect involving genetic factors. We conducted this case-control study to verify the association of ten single-nucleotide polymorphisms (SNPs) of six genes (VAX1, MAFB, PAX7, ABCA4, NTN1, and NOG) with NSCL/P in the Chinese population. The study included 249 NSCL/P patients, 62 nonsyndromic cleft palate only (NSCPO) patients and 480 controls. Three loci, namely, VAX1 rs7078160, MAFB rs11696257, and NTN1 rs4791774, were associated with NSCL/P (Bonferroni method adjusted p values were 0.020, 0.00031, and 0.030, respectively). We also found that the disease risk of individuals carrying both VAX1 rs7078160 and NTN1 rs4791774 was higher than those carrying only one of them (p = 4.50 × 10^-4 and 6.03 × 10^-3, respectively). SNPs of genes VAX1 rs7078160, MAFB rs11696257, and NTN1 rs4791774 increased NSCL/P risk in the Chinese population.

An overview of the trajectory of Brazilian individuals with 22q11.2 deletion syndrome until diagnosis

Background

22q11.2 deletion syndrome (22q11.2DS) is a rare disease with an important characteristic—clinical heterogeneity. The diversity of organs, regions, and systems of the body that can be affected requires periodic updating of health professionals so that they can recognize these clinical signs as belonging to 22q11.2DS. Updated professionals are equally important for the appropriate and timely clinical management of individuals with a positive diagnosis. In this context, this article aimed to map and analyze the access to healthcare for individuals with 22q11.2DS until the moment of diagnosis.

Results

We analyzed the clinical data of 111 individuals with 22q11.2DS registered in the Brazilian Database on Craniofacial Anomalies (BDCA) from 2008 to 2020. In this study, individuals were diagnosed at a median age of 9 years (mean = 9.7 years). Before the genetic investigation, they accessed 68.75% of the internationally recommended evaluations available at BDCA. Recurrent 22q11.2DS clinical manifestations such as delayed neuropsychomotor development, lip and/or palate defects, cardiac malformation and/or hematological/immunological alteration co-occurred in at least 72.06% of individuals. Cardiac malformation was the only clinical alteration that lowered the median diagnostic age, corresponding to 6.5 years of age with a cardiac malformation versus 11 years of age without one (p = 0.0006).

Conclusions

In Brazil, 22q11.2 DS is under-recognized, and early diagnosis and management of affected individuals are still a distant reality. In this sense, 22q11.2 DS suspicion followed by the elimination of obstacles for its diagnosis confirmation is essential to increase life expectancy and improve the quality of life of these individuals in Brazil.

Orofacial Cleft and Mandibular Prognathism-Human Genetics and Animal Models

Many complex molecular interactions are involved in the process of craniofacial development. Consequently, the network is sensitive to genetic mutations that may result in congenital malformations of varying severity. The most common birth anomalies within the head and neck are orofacial clefts (OFCs) and prognathism. Orofacial clefts are disorders with a range of phenotypes such as the cleft of the lip with or without cleft palate and isolated form of cleft palate with unilateral and bilateral variations. They may occur as an isolated abnormality (nonsyndromic-NSCLP) or coexist with syndromic disorders. Another cause of malformations, prognathism or skeletal class III malocclusion, is characterized by the disproportionate overgrowth of the mandible with or without the hypoplasia of maxilla. Both syndromes may be caused by the presence of environmental factors, but the majority of them are hereditary. Several mutations are linked to those phenotypes. In this review, we summarize the current knowledge regarding the genetics of those phenotypes and describe genotype-phenotype correlations. We then present the animal models used to study these defects.

Environmental factors in non-syndromic orofacial clefts: A review based on meta-analyses results

Non-syndromic orofacial clefts (NSOFCs) are prevalent birth defects with a complex etiology where several interacting genetic and environmental factors have been observed. This narrative review describes maternal exposures that have been significantly associated with protective effects or risk factors. The statistically significant information reported here was found in meta-analysis studies, taking advantage of their precision in defining intervention effects and their management of heterogeneity between studies. In addition, I propose a hypothesis explaining the biological basis for the results of the meta-analyses. This review aims to improve the evidence available in parent counseling, to prevent the occurrence of orofacial clefts by suggesting lifestyle changes.

The Role of the Pediatric Dentist in the Multidisciplinary Management of the Cleft Lip Palate Patient

The focus of this paper is the pediatric dental care of Cleft Lip and Palate (CLP) children and the role of the pediatric dentist in the CLP team. The management of children with cleft lip and palate presents many challenges and a multidisciplinary and prepared team is always required. Affected individuals present a multiplicity of problems: effective management involves a wide range of specialities. The value of a multidisciplinary team is widely known and mentioned in the literature, but very few papers focus on the role and the importance of the pediatric dentist. Therefore, the purpose of this article is to underline the role of the pediatric dentist as a member of the cleft lip and palate team which ranges from prenatal counseling, presurgical prevention and orthopedics, to post-treatment rehabilitation and restoration.

Update in Unilateral Cleft Lip Surgery

LEARNING OBJECTIVES

After studying this article, the participant should be able to: 1. Describe the unilateral cleft lip and nasal deformity and associated anatomical variations. 2. Understand the history and evolution of the unilateral cleft lip repair. 3. List different presurgical treatment options. 4. Differentiate between surgical techniques.

SUMMARY

This article describes characteristics of the unilateral cleft lip and nasal deformity and its management, including presurgical orthopedics, operative techniques, and postsurgical care. The rotation-advancement and straight-line repairs are discussed in detail, as are the current concepts in primary cleft nose repair.

Cleft Candidate Genes and Their Products in Human Unilateral Cleft Lip Tissue

Cleft lip and palate are common congenital pathologies that affect the human population worldwide. The formation of cleft lip is associated with multiple genes and their coded proteins, which regulate the development of craniofacial region, but the exact role of these factors is not always clear. The use of morphological studies for evaluation of human cleft-affected tissue has been limited because of insufficiency of available pathological material. The aim of this study was to detect and compare the immunohistochemical expression of cleft candidate gene coded proteins (DLX4, MSX2, HOXB3, SHH, PAX7, SOX3, WNT3A, and FOXE1) in the non-syndromic unilateral cleft lip patient tissue and control group tissue. A semiquantitative counting method was used to evaluate the tissue in biotin-streptavidin-stained slides. Statistically significant differences between the patient and control groups were found for the number of immunoreactive structures for SHH (p = 0.019) and FOXE1 (p = 0.011) in the connective tissue and SOX3 (p = 0.012) in the epithelium. Multiple statistically significant very strong and strong correlations were found between the immunoreactives in cleft-affected tissue. These significant differences and various correlations indicate that multiple morphopathogenetic pathways are possibly involved in unilateral cleft lip pathogenesis. Therefore, we further discuss these possible interactions.

Altered regulation of cell migration in IRF6-mutated orofacial cleft patients-derived primary cells reveals a novel role of Rho GTPases in cleft/lip palate development

Orofacial clefts are the most common congenital craniofacial birth defects. They occur from a failure in cell proliferation and fusion of neural crest cells of the lip buds and/or palatal shelves. In this study, we investigate the genetic basis and molecular mechanisms in primary cells derived from a cleft and lip palate patient presenting van der Woude syndrome (VWS). Since mutations in the integrin genes are widely correlated with VWS, Interferon Regulatory Factor 6 (IRF6) screening was conducted in a cohort of 200 participants presenting with orofacial anomalies. Primary fibroblastic cells derived from the upper right gingiva and palatal regions were isolated and two cellular populations from two participants were obtained: a control with no cleft phenotype and a patient with a cleft phenotype typical of van der Woude syndrome (VWS). IRF6 targeted sequencing revealed mutations in two distinct families. Our results showed no alteration in the viability of the CLP/VWS patient cells, suggesting the phenotype associate with the disease is not secondary to a defect in cell proliferation. We did however detect a significant decrease in the migratory ability of the CLP with Van der Woude syndrome (CLP/VWS) patient cells, which could account for the phenotype. When compared to normal cells, patient cells showed a lack of polarization, which would account for their lack of mobility. Patient cells showed protrusions all around the cells and a lack of defined leading edge. This was reflected with actin staining, WAVE2 and Arp2 around the cell, and correlated with an increase in Rac1 activation. Consistently with the increase in Rac1 activation, patient cells showed a loss in the maturation of focal adhesions needed for contractility, which also accounts for the lack in cell migration. Our findings give increased understanding of the molecular mechanisms of VWS and expands the knowledge of van der Woude syndrome (VWS) occurrence by providing a strong molecular evidence that CLP with Van der Woude syndrome (CLP/VWS) phenotype is caused by a defect in normal physiological processes of cells.

"Unexpected event": Having an infants with cleft lip and/or palate

This study aimed to determine the difficulties that the mothers of infants with a cleft lip and/or palate (CL/P) go through, the problems they encounter in this process, and how they perceive the support of healthcare professionals, families, and friends. The study used a phenomenological approach from qualitative research methods. The study sample included 18 mothers of 0 to 3-month-old infants with CL/P. The data were collected using socio-demographic information form and semi-structured interview form. The data obtained from the interviews were evaluated using content and thematic analysis approaches. On the basis of the interviews conducted with mothers of infants with CL/P, the following themes emerged: (a) "unexpected event: having an infant with CL/P," (b) "using social media," (c) "stigma," and (d) "uncertainty of long-term treatment." In this study, it was determined that mothers experienced shock, confusion, sadness, and disappointment in this process; therefore, they used social media to seek support from the families as well as conducted research on the disease that involved a lot of uncertainty due to long-term treatments. The present study can help healthcare professionals, who play a role in the care and treatment of infants with CL/P, to understand and know what mothers need in the preoperative period.

Genetic variants in S-adenosyl-methionine synthesis pathway and nonsyndromic cleft lip with or without cleft palate in Chile

BACKGROUND

The S-adenosyl-methionine (SAM) availability is crucial for DNA methylation, an epigenetic mechanism involved in nonsyndromic cleft lip with or without cleft palate (NSCL/P) expression. The aim of this study was to assess the association between single-nucleotide polymorphisms (SNPs) of genes involved in SAM synthesis and NSCL/P in a Chilean population.

METHODS

In 234 cases and 309 controls, 18 SNPs in AHCY, MTR, MTRR, and MAT2A were genotyped, and the association between them and the phenotype was evaluated based on additive (allele), dominant, recessive and haplotype models, by odds ratio (OR) computing.

RESULTS

Three deep intronic SNPs of MTR showed a protective effect on NSCL/P expression: rs10925239 (OR 0.68; p = 0.0032; q = 0.0192), rs10925254 (OR 0.66; p = 0.0018; q = 0.0162), and rs3768142 (OR 0.66; p = 0.0015; q = 0.0162). Annotations in expression database demonstrate that the protective allele of the three SNPs is associated with a reduction of MTR expression summed to the prediction by bioinformatic tools of its potentiality to modify splicing sites.

CONCLUSIONS

The protective effect against NSCL/P of these intronic MTR SNPs seems to be related to a decrease in MTR enzyme expression, modulating the SAM availability for proper substrate methylation. However, functional analyses are necessary to confirm our findings.

IMPACT

SAM synthesis pathway genetic variants are factors associated to NSCL/P. This article adds new evidence for folate related genes in NSCL/P in Chile. Its impact is to contribute with potential new markers for genetic counseling.

Orofacial clefts embryology, classification, epidemiology, and genetics

Orofacial clefts (OFCs) rank as the second most common congenital birth defect in the United States after Down syndrome and are the most common head and neck congenital malformations. They are classified as cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO). OFCs have significant psychological and socio-economic impact on patients and their families and require a multidisciplinary approach for management and counseling. A complex interaction between genetic and environmental factors contributes to the incidence and clinical presentation of OFCs. In this comprehensive review, the embryology, classification, epidemiology and etiology of clefts are thoroughly discussed and a "state-of-the-art" snapshot of the recent advances in the genetics of OFCs is presented.

The influence of genetic syndromes on the algorithm of cleft lip and palate repair – A retrospective study

Introduction:

This study aimed to determine if the treatment algorithm used for nonsyndromic cleft patients required alteration to manage syndromic cleft lip and/or palate patients.

Methods:

The records of patients managed by the Pécs Cleft Team between January 1999 and December 2015 were analyzed retrospectively. The sources of the data included clinical and genetic records.

Results:

A total of 607 patients were managed by the cleft team during the study. Sixteen patients (2.6%) were noted to be afflicted with a particular identifiable syndrome. Seven different genetic syndromes and one sequence were present in the study. The Pierre Robin sequence occurred most often, comprising 50% of the cohort. The treatment algorithm used in managing nonsyndromic clefts required modification in 13 of the 16 syndromic patients.

Discussion:

The presence of a genetic syndrome may notably affect the treatment algorithm in children born with cleft lip and/or palate. The surgical treatment of certain associated anomalies has by necessity, priority over the timing of the reconstruction of the cleft lip and/or cleft palate in syndromic patients.

Assessment of the correlation between various risk factors and orofacial cleft disorder spectrum: a retrospective case-control study

Background

Orofacial clefts (OFCs) comprise a wide range of malformations, including cleft lip, cleft palate, and cleft lip with cleft palate, which can vary in terms of etiology, severity, and disease burden.

Objective(s)

This study aimed to evaluate the correlation between various risk factors and orofacial cleft disorder spectrum in newborns.

Study design

A total of 323 cases and 400 controls were enrolled in this study and evaluated in terms of the maternal history of abortion or miscarriage, child’s sex, maternal and paternal age, maternal history of systemic disease, history of medication therapy during pregnancy, birth order, consanguineous marriage, and complications during pregnancy.

Results

Analysis of the results suggested that consanguineous marriage, a maternal history of abortion/miscarriage, and complications during pregnancy could potentially increase the risk of OFCs in children (P < 0.05). However, the analyses revealed that the other variables could not potentially increase the risk of OFCs (P > 0.05).

Conclusion(s)

Multiple cofactors may simultaneously contribute to the formation of such abnormalities; therefore, a comprehensive, multidisciplinary care program is necessary to ensure a successful pregnancy period and the birth of a healthy newborn.

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18

Genome-wide association studies for non-syndromic orofacial clefting (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effects of 14 OFC-associated SNPs at 12q13 near KRT18. All the classifiers picked the same SNP as having the strongest effect, but the significance was highest with the classifier trained on zebrafish periderm. Reporter and deletion analyses support this SNP as lying within a periderm enhancer regulating KRT18/KRT8 expression.