Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate

Genomic expression in non syndromic cleft lip and palate patients: A review

Cleft lip and palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications, affecting one in seven hundred live births. Genetic causes of non syndromic cleft lip and/or palate (NSCLP) include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. Development of the orofacial clefts in an individual will depend on the interaction of several moderately effecting genes with environmental factors. Several candidate genes have been genotyped in different population types, using case parent trio or case control design; also genes have been sequenced and SNPs have been reported. Quantitative and molecular analysis have shown linkage and association studies to be more relevant. Recent literature search shows genome wide association studies using microarray. The aim of this paper was to review the approaches to identify genes associated with NSCLP and to analyze their differential expressions. Although no major gene has been confirmed, a lot of research is ongoing to provide an understanding of the pathophysiology of the orofacial clefts.

DLX4 is associated with orofacial clefting and abnormal jaw development

Cleft lip and/or palate (CL/P) are common structural birth defects in humans. We used exome sequencing to study a patient with bilateral CL/P and identified a single nucleotide deletion in the patient and her similarly affected son—c.546_546delG, predicting p.Gln183Argfs*57 in the Distal-less 4 (DLX4) gene. The sequence variant was absent from databases, predicted to be deleterious and was verified by Sanger sequencing. In mammals, there are three Dlx homeobox clusters with closely located gene pairs (Dlx1/Dlx2, Dlx3/Dlx4, Dlx5/Dlx6). In situ hybridization showed that Dlx4 was expressed in the mesenchyme of the murine palatal shelves at E12.5, prior to palate closure. Wild-type human DLX4, but not mutant DLX4_c.546delG, could activate two murine Dlx conserved regulatory elements, implying that the mutation caused haploinsufficiency. We showed that reduced DLX4 expression after short interfering RNA treatment in a human cell line resulted in significant up-regulation of DLX3, DLX5 and DLX6, with reduced expression of DLX2 and significant up-regulation of BMP4, although the increased BMP4 expression was demonstrated only in HeLa cells. We used antisense morpholino oligonucleotides to target the orthologous Danio rerio gene, dlx4b, and found reduced cranial size and abnormal cartilaginous elements. We sequenced DLX4 in 155 patients with non-syndromic CL/P and CP, but observed no sequence variants. From the published literature, Dlx1/Dlx2 double homozygous null mice and Dlx5 homozygous null mice both have clefts of the secondary palate. This first finding of a DLX4 mutation in a family with CL/P establishes DLX4 as a potential cause of human clefts.

BMP7 Gene involved in nonsyndromic orofacial clefts in Western Han Chinese

Background

Nonsyndromic orofacial clefts (NSOCs) are the most common craniofacial birth defects with complex etiology in which multiple genes and environmental exposures are involved. Bone morphogenetic protein 7 (BMP7), as a member of the transforming growth factor-beta (TGF-beta) superfamily, has been shown to play crucial roles in palate and other orofacial ectodermal appendages development in animal models.

Material and Methods

This study was designed to investigate the possible associations between BMP7 gene and the NSOCs (221 case-parent trios) in Western Han Chinese. Five tagSNPs at BMP7, rs12438, rs6099486, rs6127973, rs230188 and rs6025469 were picked and tried to cover the entire gene. In order to identify the contribution of BMP7 gene to the etiology of NSOCs, we performed several statistical analysis from different aspects including transmission disequilibrium test (TDT), pairwise linkage disequilibrium (LD), parent-of-origin effect and Chi-squared/Fisher’s exact tests.

Results

Rs6127973 G allele and G/G homozygotes were over-transmitted for both NSOCs (P=0.005 and P=0.011, respectively) and NSCL/P (P=0.0061 and P=0.011, respectively), rs6127973 G allele was also paternally over-transmitted for both NSOCs (P=0.0061) and NSCL/P (P=0.011).

Conclusions

This study suggested that rs6127973 may be a risk factor of being NSOCs and confirmed the role of BMP7 gene in orofacial deformity from Western Han Chinese, which will also supply scientific evidence for future research and genetic counseling.

Key words: Single nucleotide polymorphisms, nonsyndromic orofacial clefts, BMP7.

IRF6 Is a Marker of Severity in Nonsyndromic Cleft Lip/Palate

Nonsyndromic cleft lip with or without palate (CL/P) is thought to be caused by the interplay of genetic and environmental factors, and this has thus hindered the process of identifying genetic causative factors. Numerous studies in the past decade have implicated IRF6 in CL/P, but this has not often been replicated in other populations. In specific, the only etiologic single-nucleotide polymorphism (SNP) identified in the IRF6 locus (rs642961) has recently been shown not to be associated with CL/P in diverse populations. We therefore used a genewide tagging SNP (tagSNP) haplotyping approach (including rs642961 as a tagSNP) to detect all potential risk-conferring haplotypes and combined this with detailed subphenotyping of CL/P cases ( N = 150) according to severity. We observed a significant overrepresentation of a tagSNP haplotype carrying the rs642961 risk allele in the most severe subphenotype of CL/P (complete bilateral CL/P; P = 0.008, odds ratio = 4.97, 95% confidence interval = 1.33 to 18.46). It was recently shown that >80% of IRF6 mutations in syndromic CL/P occur on the same haplotype background. We therefore suggest that IRF6 is a marker of CL/P severity.

IRF6 polymorphisms in Mexican patients with non-syndromic cleft lip

Cleft lip with or without cleft palate (CL/P) is one of the most common birth defects; it is a multifactorial disease affecting > 1/1,000 live births in Europe, and its etiology is largely unknown, although it is very likely genetic and environmental factors contribute to this malformation. Orofacial development is a complex process involving many genes and signaling pathways. Mutations in the gene for the interferon regulatory factor 6 (IRF6) cause a hereditary dominant malformation syndrome including CL/P, and polymorphisms are associated with non-syndromic CL/P (MIM 119530). Five SNPs at the locus with high heterozygosity in Caucasian populations were chosen for the present research due to their very strong association with CL/P. A case–parent trio study was performed using 292 samples from Mexico. Association with the rs1319435-C/C genotype (P = 0.02) was found in patients (73) as compared to pseudocontrols (219), while the genotype rs1319435-T/C was related with protection (P = 0.041) in the triad design. Significant over-transmission of the G allele for marker rs2235375 (P = 0.049) was found. Only the TACGT haplotype was diminished in the affected child, either in single (P = 0.0208) or double (P = 0.0208) dose. The pairwise analysis showed rs2235543 and rs2235371 were in strong linkage disequilibrium. These results point to a substantial contribution of IRF6 in the etiology of non-syndromic CL/P in a sample of the Mexican population.

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Cleft lip with or without cleft palate (CL/P) is one of the most common birth defects.

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Association with the rs1319435-C/C genotype was found in patients as compared to pseudocontrols.

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In the triad design, the genotype rs1319435-T/C was related with protection.

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The IRF6 contributes to the etiology of non-syndromic CL/P in a sample of the Mexican population.

Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci

Although genome-wide association studies (GWASs) for nonsyndromic orofacial clefts have identified multiple strongly associated regions, the causal variants are unknown. To address this, we selected 13 regions from GWASs and other studies, performed targeted sequencing in 1,409 Asian and European trios, and carried out a series of statistical and functional analyses. Within a cluster of strongly associated common variants near NOG, we found that one, rs227727, disrupts enhancer activity. We furthermore identified significant clusters of non-coding rare variants near NTN1 and NOG and found several rare coding variants likely to affect protein function, including four nonsense variants in ARHGAP29. We confirmed 48 de novo mutations and, based on best biological evidence available, chose two of these for functional assays. One mutation in PAX7 disrupted the DNA binding of the encoded transcription factor in an in vitro assay. The second, a non-coding mutation, disrupted the activity of a neural crest enhancer downstream of FGFR2 both in vitro and in vivo. This targeted sequencing study provides strong functional evidence implicating several specific variants as primary contributory risk alleles for nonsyndromic clefting in humans.

Ten-year experience of more than 35,000 orofacial clefts in Africa

BACKGROUND

Surgical correction of orofacial clefts greatly mitigates negative outcomes. However, access to reconstructive surgery is limited in developing countries. The present study reviews epidemiological data from a single charitable organization, Smile Train, with a database of surgical cases from 33 African countries from 2001-2011.

METHODS

Demographic and clinical patient data were collected from questionnaires completed by the participating surgeons. These data were recorded in Excel, analyzed using SPSS and compared with previously reported data.

RESULTS

Questionnaires were completed for 36,384 patients by 389 African surgeons. The distribution of clefts was: 34.44% clefts of the lip (CL), 58.87% clefts of the lip and palate (CLP), and 6.69% clefts of the palate only (CP). The male to female ratio was 1.46:1, and the unilateral: bilateral ratio 2.93:1, with left-sided predominance 1.69:1. Associated anomalies were found in 4.18% of patients. The most frequent surgeries included primary lip/nose repairs, unilateral (68.36%) and bilateral (11.84%). There was seasonal variation in the frequency of oral cleft births with the highest in January and lowest by December. The average age at surgery was 9.34 years and increased in countries with lower gross domestic products. The average hospital stay was 4.5 days. The reported complication rate was 1.92%.

CONCLUSIONS

With the exception of cleft palates, results follow trends of worldwide epidemiologic reports of 25% CL, 50% CLP, and 25% CP, 2:1 unilateral:bilateral and left:right ratios, and male predominance. Fewer than expected patients, especially females, presented with isolated cleft palates, suggesting that limitations in economic resources and cultural aesthetics of the obvious lip deformity may outweigh functional concerns and access to treatment for females. A fewer than expected associated anomalies suggests either true ethnic variation, or that more severely-affected patients are not presenting for treatment. The epidemiology of orofacial clefting in Africa has been difficult to assess due to the diversity of the continent and the considerable variation among study designs. The large sample size of the data collected provides a basis for further study of the epidemiology of orofacial clefting in Africa.

Association of single-nucleotide polymorphisms in the IRF6 gene with non-syndromic cleft lip with or without cleft palate in the Xinjiang Uyghur population

Our main aim was to investigate the association between the interferon regulatory factor (IRF6) gene and non-syndromic cleft lip and palate (nsCLP) in the Xinjiang Uyghur population. Twelve single nucleotide polymorphisms (SNP) were screened in a group of 100 patients with nsCLP and in a control group of 60 unaffected subjects by next generation sequencing using a MiSeq Benchtop Sequencer (Illumina). Our case-control association analysis showed that the SNP marker rs7545538 differed significantly in genotype (codominant model; CC compared with CG compared with GG; p=0.038) and allele frequencies (odds ratio (OR)=1.89, 95% CI 1.18-3.03, p=0.007) between patients with nsCLP and controls. Analysis of the recessive model of inheritance showed that distribution of the recessive model of rs7545538 (GG compared with CC+GC) was significantly higher in patients with nsCLP than in controls (OR=2.5, 95% CI 1.13-5.37, p=0.021) and had a borderline association with an increased risk of nsCLP (OR=2.5, 95% CI 1.13-5.37, p=0.021). Markers rs2235377 and rs2235371 also differed significantly in dominant and over-dominant models of inheritance (p=0.037) while increased G allele frequency was seen in SNP rs2235373 (p=0.03). A haplotype analysis showed four common haplotypes in Block 1: CCGGT>CCGAT>CACAT>TAGAC (in frequency). The 5-marker combination haplotype CCGAT was significantly more common in patients with nsCLP than in controls (p=0.032). In Block 2, the overall distribution of the haplotypes TAC and TAG predicted by the three SNP differed significantly between the patients with nsCLP and control subjects (p=0.009 and 0.003, respectively). Our results showed that genetic polymorphism of the IRF6 gene is associated with increased risk of nsCLP in a Xinjiang Uyghur population.

Functional analysis of SPECC1L in craniofacial development and oblique facial cleft pathogenesis

BACKGROUND

Oblique facial clefts, also known as Tessier clefts, are severe orofacial clefts, the genetic basis of which is poorly understood. Human genetics studies revealed that disruption in SPECC1L resulted in oblique facial clefts, demonstrating that oblique facial cleft malformation has a genetic basis. An important step toward innovation in treatment of oblique facial clefts would be improved understanding of its genetic pathogenesis. The authors exploit the zebrafish model to elucidate the function of SPECC1L by studying its homolog, specc1lb.

METHODS

Gene and protein expression analysis was carried out by reverse-transcriptase polymerase chain reaction and immunohistochemistry staining. Morpholino knockdown, mRNA rescue, lineage tracing and terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling assays were performed for functional analysis.

RESULTS

Expression of specc1lb was detected in epithelia juxtaposed to chondrocytes. Knockdown of specc1lb resulted in bilateral clefts between median and lateral elements of the ethmoid plate, structures analogous to the frontonasal process and the paired maxillary processes. Lineage tracing analysis revealed that cranial neural crest cells contributing to the frontonasal prominence failed to integrate with the maxillary prominence populations. Cells contributing to lower jaw structures were able to migrate to their destined pharyngeal segment but failed to converge to form mandibular elements.

CONCLUSIONS

These results demonstrate that specc1lb is required for integration of frontonasal and maxillary elements and convergence of mandibular prominences. The authors confirm the role of SPECC1L in orofacial cleft pathogenesis in the first animal model of Tessier cleft, providing morphogenetic insight into the mechanisms of normal craniofacial development and oblique facial cleft pathogenesis.

Palatogenesis and cutaneous repair: A two-headed coin

BACKGROUND

The reparative mechanism that operates following post-natal cutaneous injury is a fundamental survival function that requires a well-orchestrated series of molecular and cellular events. At the end, the body will have closed the hole using processes like cellular proliferation, migration, differentiation and fusion.

RESULTS

These processes are similar to those occurring during embryogenesis and tissue morphogenesis. Palatogenesis, the formation of the palate from two independent palatal shelves growing towards each other and fusing, intuitively, shares many similarities with the closure of a cutaneous wound from the two migrating epithelial fronts.

CONCLUSIONS

In this review, we summarize the current information on cutaneous development, wound healing, palatogenesis and orofacial clefting and propose that orofacial clefting and wound healing are conserved processes that share common pathways and gene regulatory networks.

Investigation of genetic factors underlying typical orofacial clefts: mutational screening and copy number variation

Typical orofacial clefts (OFCs) comprise cleft lip, cleft palate and cleft lip and palate. The complex etiology has been postulated to involve chromosome rearrangements, gene mutations and environmental factors. A group of genes including IRF6, FOXE1, GLI2, MSX2, SKI, SATB2, MSX1 and FGF has been implicated in the etiology of OFCs. Recently, the role of the copy number variations (CNVs) has been studied in genetic defects and diseases. CNVs act by modifying gene expression, disrupting gene sequence or altering gene dosage. The aims of this study were to screen the above-mentioned genes and to investigate CNVs in patients with OFCs. The sample was composed of 23 unrelated individuals who were grouped according to phenotype (associated with other anomalies or isolated) and familial recurrence. New sequence variants in GLI2, MSX1 and FGF8 were detected in patients, but not in their parents, as well as in 200 control chromosomes, indicating that these were rare variants. CNV screening identified new genes that can influence OFC pathogenesis, particularly highlighting TCEB3 and KIF7, that could be further analyzed. The findings of the present study suggest that the mechanism underlying CNV associated with sequence variants may play a role in the etiology of OFC.

Classification, epidemiology, and genetics of orofacial clefts

Orofacial clefts (OFCs) include a broad range of facial conditions that differ in cause and disease burden. In the published literature, there is substantial ambiguity in both terminology and classification of OFCs. This article discusses the terminology and classification of OFCs and the epidemiology of OFCs. Demographic, environmental, and genetic risk factors for OFCs are described, including suggestions for family counseling. This article enables clinicians to counsel families regarding the occurrence and recurrence of OFCs. Although much of the information is detailed, it is intended to be accessible to all health professionals for use in their clinical practices.

ACTN3 R577X genotypes associate with Class II and deepbite malocclusions

INTRODUCTION

α-Actinins are myofibril anchor proteins that influence the contractile properties of skeletal muscles. ACTN2 is expressed in slow type I and fast type II fibers, whereas ACTN3 is expressed only in fast fibers. ACTN3 homozygosity for the 577X stop codon (ie, changing 577RR to 577XX, the R577X polymorphism) results in the absence of α-actinin-3 in about 18% of Europeans, diminishes fast contractile ability, enhances endurance performance, and reduces bone mass or bone mineral density. We have examined ACTN3 expression and genetic variation in the masseter muscle of orthognathic surgery patients to determine the genotype associations with malocclusion.

METHODS

Clinical information, masseter muscle biopsies, and saliva samples were obtained from 60 subjects. Genotyping for ACTN3 single nucleotide polymorphisms, real-time polymerase chain reaction quantitation of muscle gene message, and muscle morphometric fiber type properties were compared to determine statistical differences between genotype and phenotype.

RESULTS

Muscle mRNA expression level was significantly different for ACTN3 single nucleotide polymorphism genotypes (P <0.01). The frequency of ACTN3 genotypes was significantly different for the sagittal and vertical classifications of malocclusion, with the clearest association being elevated 577XX genotype in skeletal Class II malocclusion (P = 0.003). This genotype also resulted in significantly smaller diameters of fast type II fibers in masseter muscles (P = 0.002).

CONCLUSION

ACTN3 577XX is overrepresented in subjects with skeletal Class II malocclusion, suggesting a biologic influence during bone growth. ACTN3 577XX is underrepresented in subjects with deepbite malocclusion, suggesting that muscle differences contribute to variations in vertical facial dimensions.

Association between NOGGIN and SPRY2 polymorphisms and nonsyndromic cleft lip with or without cleft palate

Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common congenital malformation with a worldwide prevalence rate of 0.4-2.0% among live births, depending on race and ethnic background. Single-nucleotide polymorphisms (SNPs) of genes may contribute to NSCLP risk, although the risk factors and pathogenesis of NSCLP remain unknown. The objective of this study was to investigate association of SNPs of noggin (NOG) and sprouty homolog 2 (SPRY2) with NSCLP risk. A total of 188 NSCLP patients and 228 healthy controls from northern China were recruited for genotyping of these SNPs using the SNaP shot method. The frequency of the NOG rs227731 genotype was significantly lower among NSCLP cases than among controls. Logistic regression analysis showed rs227731 CC genotype was associated with decreased NSCLP susceptibility (OR = 0.31, 95% CI = 0.12-0.80) compared to the AA homozygote. However, no association between SPRY2, SNPs, and NSCLP risk were observed in this cohort of patients. In conclusion, NOG rs227731 genotype was associated with decreased NSCLP risk in a Northern Chinese population.

Anatomic Severity, Midfacial Growth, and Speech Outcomes in Van der Woude/Popliteal Pterygium Syndromes Compared to Nonsyndromic Cleft Lip/Palate

OBJECTIVE

To summarize the clinical characteristics and surgical and speech outcomes for patients with Van der Woude/popliteal pterygium syndromes (VWS/PPS) and to compare them with a historic cohort of patients with nonsyndromic cleft lip/cleft palate (CL/P).

DESIGN

Retrospective chart review.

SETTING

Tertiary care center.

PATIENTS

All patients with VWS/PPS seen at Boston Children's Hospital from 1979 to 2012: 28 patients with VWS (n = 21)/PPS (n = 7) whose mean age was 17.3 ± 10.4 years, including 18 females (64%) and 10 males (36%); 18 patients (64%) had a family history of VWS/PPS.

MAIN OUTCOME MEASURES

Cleft type, operative procedures, speech, and midfacial growth. Data were compared with historic cohorts of patients with nonsyndromic CL/P treated at one tertiary care center.

RESULTS

There were 24 patients (86%) with CP±L, Veau types I (n = 4, 17%), II (n = 4, 17%), III (n = 5, 21%), and IV (n = 11, 46%). Nine patients (38%) had palatal fistula after palatoplasty. Fourteen of 23 (61%) patients with CL/P age 5 years or older had midfacial retrusion, and 10 (43%) required a pharyngeal flap for velopharyngeal insufficiency. Fisher's exact test demonstrated higher frequencies of Veau type IV CP±L (P = .0016), bilateral CL±P (P = .0001), and complete CL±P (P < .0001) in VWS/PPS compared with nonsyndromic patients. Incidences of midfacial retrusion (P = .0001), palatal fistula (P < .0001), and need for pharyngeal flap (P = .0014) were significantly greater in patients with VWS/PPS.

CONCLUSIONS

Patients with VWS/PPS have more severe forms of labiopalatal clefting and higher incidences of midfacial retrusion, palatal fistula, and velopharyngeal insufficiency following primary repair as compared with nonsyndromic CL/P.

First-trimester nonsystemic corticosteroid use and the risk of oral clefts in Norway

PURPOSE

Exposure of pregnant mice to corticosteroids can produce oral clefts in offspring. Although data in humans are more mixed, recent reports have suggested that dermatologic steroids are associated with oral clefts.

METHODS

We investigated maternal first-trimester exposure to corticosteroids (focusing on dermatologic uses) and oral clefts in offspring using two population-based studies. The Norway Cleft Study (1996-2001) is a national case-control study including 377 infants with cleft lip ± palate (CLP), 196 infants with cleft palate only (CPO), and 763 controls. The Norwegian Mother and Child Cohort Study (MoBa, 1998-2008) is a national birth cohort including 123 infants with CLP, 61 infants with CPO, and 551 controls.

RESULTS

In the case-control study, there was the suggestion of an association of dermatologic corticosteroids with both CLP (adjusted OR [aOR], 2.3; 95% confidence interval [CI], 0.71-7.7) and CPO (aOR, 3.4; CI, 0.87-13). There was no evidence of this association in the cohort data (odds ratio for CLP, 1.2; CI, 0.50-2.8 and odds ratio for CPO, 1.0; CI, 0.30-3.4), although exposure to dermatologic steroids was less specifically ascertained. There were no associations with other types of corticosteroids.

CONCLUSIONS

Our data add to the suggestive but inconsistent findings for this association.

Further evidence suggesting a role for variation in ARHGAP29 variants in nonsyndromic cleft lip/palate

BACKGROUND

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect of complex etiology. Several genes have been implicated in the etiology of NSCL/P, although only a few have been replicated across datasets.

METHODS

ARHGAP29 was suggested as a candidate gene for NSCL/P as it is located in close proximity to ABCA4 (1p22), a gene previously identified in a genome-wide association study of NSCL/P.

RESULTS

Rare, potentially damaging, coding variants in ARHGAP29 were found in NSCL/P cases, and its expression was detected during murine craniofacial development. In this study, we investigated whether variations in ARHGAP29 were associated with NSCL/P in our family based dataset. Five single-nucleotide polymorphisms (SNPs) flanking and within ARHGAP29 were genotyped in our NSCL/P datasets consisting of simplex and multiplex families of non-Hispanic white (NHW, primarily European) and Hispanic ethnicities. Results showed strong association of three ARHGAP29 SNPs with NSCL/P in the NHW families. Two intronic SNPs (rs1541098 and rs3789688) showed strong association with NSCL/P in all NHW families (p = 0.0005 and p = 0.0002, respectively), and simplex NHW families (p = 0.003 for both SNPs). A SNP in the 3' untranslated region (rs1576593) also showed strong association with NSCL/P in all NHW families (p = 0.002), and the multiplex subset (p = 0.002). ARHGAP29 SNP haplotypes were also associated with NSCL/P. Evidence of gene-gene interaction was found between ARHGAP29 and additional cleft susceptibility genes.

CONCLUSION

This study further supports ARHGAP29 as a candidate gene for human NSCL/P in families of Caucasian descent.

Association of JARID2 polymorphisms with non-syndromic orofacial clefts in northern Chinese Han population

OBJECTIVES

Non-syndromic orofacial clefts (NSOC) are the most common human craniofacial malformation in all worldwide populations. Recently, the jumoji AT-rich interaction domain 2 (JARID2) had been reported to be a novel candidate gene for non-syndromic cleft lip with or without cleft palate (CL/P). The SNPs rs2076056, rs2237138 and rs2299043 in JARID2 were highly significant in Italian families.

MATERIAL AND METHODS

In the current research, a case-control study was conducted to examine the association between these three SNPs and NSOC in a northern Chinese Han population. Genotyping of the three SNPs were performed using SNaPshot minisequencing technique.

RESULTS

Distribution of rs2237138 genotypes in CL/P group was different from those in the control group (P = 0.04), but significant results did not persist after Benjamini and Hochberg false discovery rate (FDR) correction for multiple tests. Further logistic regression analysis showed that rs2237138 GG genotypes were associated with decreased CL/P susceptibility (OR = 0.34, 95% CI = 0.13-0.84), compared with the AA wild-type homozygote. For the haplotype CGT, a statistically difference was identified between the CL/P group and controls (P = 0.04). And carriers of GAT haplotype were considered to be less frequent among cleft palate only group as compared to controls (P = 0.02). However, both of the haplotypes association did not remain statistically significant after Benjamini and Hochberg FDR correction.

CONCLUSION

We got a weak association between these polymorphisms and NSOC in both single-marker and haplotype analyses. Our data further strengthen the conclusion that JARID2 polymorphisms are associated with NSOC susceptibility.

Association between TGFB3 and nonsyndromic cleft lip with or without cleft palate in a Chilean population

OBJECTIVE

To assess the possible association between TGFB3 allele variants and nonsyndromic cleft lip with or without cleft palate in a Chilean population.

DESIGN

In our study we used a case-parents trios design. The sample consisted of 150 unrelated trios ascertained through probands affected with nonsyndromic cleft lip with or without cleft palate. Three TGFB3 polymorphisms were analyzed (rs2268626, rs2268625, and rs3917201). An allele/haplotype transmission disequilibrium test was used to evaluate the possible genotype-phenotype association.

RESULTS

An overtransmission from parents to affected progeny was observed for the A allele of rs3917201 (p = .03) and for the rs2268625-rs3917201 A-A haplotype (p = .022). A defect of transmission of rs2268625-rs3917201 G-G haplotype (p = .022) was observed also.

CONCLUSIONS

Allelic and haplotypic associations implicate a possible role of TGFB3 in nonsyndromic cleft lip with or without cleft palate in the Chilean population. Additional studies are needed in order to elucidate the possible mechanisms that can explain the role of TGFB3 genetic variants in the condition.

Exploratory genotype-phenotype correlations of facial form and asymmetry in unaffected relatives of children with non-syndromic cleft lip and/or palate

Family relatives of children with nonsyndromic cleft lip with or without cleft palate (NSCL/P) who presumably carry a genetic risk yet do not manifest overt oral clefts, often present with distinct facial morphology of unknown genetic etiology. This study investigates distinct facial morphology among unaffected relatives and examines whether candidate genes previously associated with overt NSCL/P and left-right body patterning are correlated with such facial morphology. Cases were unaffected relatives of individuals with NSCL/P (n = 188) and controls (n = 194) were individuals without family history of NSCL/P. Cases and controls were genotyped for 20 SNPs across 13 candidate genes for NSCL/P (PAX7, ABCA4-ARHGAP29, IRF6, MSX1, PITX2, 8q24, FOXE1, TGFB3 and MAFB) and left-right body patterning (LEFTY1, LEFTY2, ISL1 and SNAI1). Facial shape and asymmetry phenotypes were obtained via principal component analyses and Procrustes analysis of variance from 32 coordinate landmarks, digitized on 3D facial images. Case-control comparisons of phenotypes obtained were performed via multivariate regression adjusting for age and gender. Phenotypes that differed significantly (P < 0.05) between cases and controls were regressed on the SNPs one at a time. Cases had significantly (P < 0.05) more profile concavity with upper face retrusion, upturned noses with obtuse nasolabial angles, more protrusive chins, increased lower facial heights, thinner and more retrusive lips and more protrusive foreheads. Furthermore, cases showed significantly more directional asymmetry compared to controls. Several of these phenotypes were significantly associated with genetic variants (P < 0.05). Facial height and width were associated with SNAI1. Midface antero-posterior (AP) projection was associated with LEFTY1. The AP position of the chin was related to SNAI1, IRF6, MSX1 and MAFB. The AP position of the forehead and the width of the mouth were associated with ABCA4-ARHGAP29 and MAFB. Lastly, facial asymmetry was related to LEFTY1, LEFTY2 and SNAI1. This study demonstrates that, genes underlying lip and palate formation and left-right patterning also contribute to facial features characteristic of the NSCL/P spectrum.

Nonsyndromic cleft lip with or without cleft palate: Increased burden of rare variants within Gremlin-1, a component of the bone morphogenetic protein 4 pathway

BACKGROUND

The genes Gremlin-1 (GREM1) and Noggin (NOG) are components of the bone morphogenetic protein 4 pathway, which has been implicated in craniofacial development. Both genes map to recently identified susceptibility loci (chromosomal region 15q13, 17q22) for nonsyndromic cleft lip with or without cleft palate (nsCL/P). The aim of the present study was to determine whether rare variants in either gene are implicated in nsCL/P etiology.

METHODS

The complete coding regions, untranslated regions, and splice sites of GREM1 and NOG were sequenced in 96 nsCL/P patients and 96 controls of Central European ethnicity. Three burden and four nonburden tests were performed. Statistically significant results were followed up in a second case-control sample (n = 96, respectively). For rare variants observed in cases, segregation analyses were performed.

RESULTS

In NOG, four rare sequence variants (minor allele frequency < 1%) were identified. Here, burden and nonburden analyses generated nonsignificant results. In GREM1, 33 variants were identified, 15 of which were rare. Of these, five were novel. Significant p-values were generated in three nonburden analyses. Segregation analyses revealed incomplete penetrance for all variants investigated.

CONCLUSION

Our study did not provide support for NOG being the causal gene at 17q22. However, the observation of a significant excess of rare variants in GREM1 supports the hypothesis that this is the causal gene at chr. 15q13. Because no single causal variant was identified, future sequencing analyses of GREM1 should involve larger samples and the investigation of regulatory elements.

Ethnic heterogeneity of IRF6 AP-2a binding site promoter SNP association with nonsyndromic cleft lip and palate

OBJECTIVE

The goal of this study was to confirm the reported association between a noncoding SNP (rs642961) in IRF6 and nonsyndromic cleft lip and palate.

DESIGN, SETTING, AND PARTICIPANTS

Two SNPs in IRF6 (rs2235371 and rs64296) were genotyped in Hispanic and non-Hispanic white multiplex (122) and simplex (308) nonsyndromic cleft lip and palate families. Linkage and family-based association analyses were performed on the individual SNPs as well as the 2-SNP haplotype.

RESULTS

Only modest evidence was found for an association with rs642961 and the 2-SNP haplotype. In contrast, strong evidence was found for the association with rs2235371; this was most evident in the non-Hispanic white simplex families.

CONCLUSIONS

Although it is confirmed that variation in IRF6 is associated with nonsyndromic cleft lip and palate, the results do not support the reported association with SNP rs64296. Importantly, the association varies between ethnic groups. This finding underscores the need for evaluating additional variations in IRF6 across multiple populations to better determine its role in nonsyndromic cleft lip and palate.

Disrupting hedgehog and WNT signaling interactions promotes cleft lip pathogenesis

Cleft lip, which results from impaired facial process growth and fusion, is one of the most common craniofacial birth defects. Many genes are known to be involved in the etiology of this disorder; however, our understanding of cleft lip pathogenesis remains incomplete. In the present study, we uncovered a role for sonic hedgehog (SHH) signaling during lip fusion. Mice carrying compound mutations in hedgehog acyltransferase (Hhat) and patched1 (Ptch1) exhibited perturbations in the SHH gradient during frontonasal development, which led to hypoplastic nasal process outgrowth, epithelial seam persistence, and cleft lip. Further investigation revealed that enhanced SHH signaling restricts canonical WNT signaling in the lambdoidal region by promoting expression of genes encoding WNT inhibitors. Moreover, reduction of canonical WNT signaling perturbed p63/interferon regulatory factor 6 (p63/IRF6) signaling, resulting in increased proliferation and decreased cell death, which was followed by persistence of the epithelial seam and cleft lip. Consistent with our results, mutations in genes that disrupt SHH and WNT signaling have been identified in both mice and humans with cleft lip. Collectively, our data illustrate that altered SHH signaling contributes to the etiology and pathogenesis of cleft lip through antagonistic interactions with other gene regulatory networks, including the canonical WNT and p63/IRF6 signaling pathways.

Digital imaging analysis to assess scar phenotype

In order to understand the link between the genetic background of patients and wound clinical outcomes, it is critical to have a reliable method to assess the phenotypic characteristics of healed wounds. In this study, we present a novel imaging method that provides reproducible, sensitive, and unbiased assessments of postsurgical scarring. We used this approach to investigate the possibility that genetic variants in orofacial clefting genes are associated with suboptimal healing. Red-green-blue digital images of postsurgical scars of 68 patients, following unilateral cleft lip repair, were captured using the 3dMD imaging system. Morphometric and colorimetric data of repaired regions of the philtrum and upper lip were acquired using ImageJ software, and the unaffected contralateral regions were used as patient-specific controls. Repeatability of the method was high with intraclass correlation coefficient score > 0.8. This method detected a very significant difference in all three colors, and for all patients, between the scarred and the contralateral unaffected philtrum (p ranging from 1.20(-05) to 1.95(-14) ). Physicians' clinical outcome ratings from the same images showed high interobserver variability (overall Pearson coefficient = 0.49) as well as low correlation with digital image analysis results. Finally, we identified genetic variants in TGFB3 and ARHGAP29 associated with suboptimal healing outcome.

Investigation of Parental Transmission of RUNX2 Single Nucleotide Polymorphism and Its Association with Nonsyndromic Cleft Lip with or Without Palate

Objective

To investigate the association and parental transmission of RUNX2 single nucleotide polymorphisms (SNPs) with risk of nonsyndromic cleft lip with or without cleft palate (NS-CL±P).

Design

Four RUNX2 SNPs in 142 Korean NS-CL±P families (nine cleft lip, 26 cleft lip and alveolus, and 107 cleft lip and palate; 76 trios and 66 dyads) were genotyped. The minor allele frequency, heterozygosity, and chi-square test for Hardy-Weinberg equilibrium at each SNP were computed between parents. Pairwise linkage disequilibrium was computed as D′ and r2 for all SNPs. Both allelic and genotypic transmission disequilibrium tests (TDTs) were performed for individual SNPs using a family-based association test program. Sliding windows of haplotypes consisting of two to four SNPs were tested using a haplotype-based association test program. Genotypic odds ratios (GORs) were calculated from conditional logistic regression models. Parent-of-origin effects were assessed using transmission asymmetry test and parent-of-origin likelihood ratio test.

Results

The family-based TDT showed significant evidence of linkage and association at rs1934328 ( P = .001). In the haplotype analysis, two, three, and four haplotypes containing rs1934328 revealed significant associations ( P = .0017, P = .0022, and P = .0020, respectively). The genotypes A/T and T/T at rs1934328 were significantly associated with NS-CL±P compared with the genotype A/A (GOR = 2.75, 95% confidence interval [CI] = 1.39–5.45, P =0.0019 in the dominant model; GOR = 5.38, 95% CI = 1.34–21.68, P = .0046 in the additive model). However, no parent-of origin effect was observed.

Conclusion

These findings suggest possible involvement of RUNX2-rs 194328 in the etiology of NS-CL±P in Korean cleft-parent trios without excess parental transmission.

An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects

DNA variation in Interferon Regulatory Factor 6 (IRF6) causes Van der Woude syndrome (VWS), the most common syndromic form of cleft lip and palate (CLP). However, an etiologic variant in IRF6 has been found in only 70% of VWS families. To test whether DNA variants in regulatory elements cause VWS, we sequenced three conserved elements near IRF6 in 70 VWS families that lack an etiologic mutation within IRF6 exons. A rare mutation (350dupA) was found in a conserved IRF6 enhancer element (MCS9.7) in a Brazilian family. The 350dupA mutation abrogated the binding of p63 and E47 transcription factors to cis-overlapping motifs, and significantly disrupted enhancer activity in human cell cultures. Moreover, using a transgenic assay in mice, the 350dupA mutation disrupted the activation of MCS9.7 enhancer element and led to failure of lacZ expression in all head and neck pharyngeal arches. Interestingly, disruption of the p63 Motif1 and/or E47 binding sites by nucleotide substitution did not fully recapitulate the effect of the 350dupA mutation. Rather, we recognized that the 350dupA created a CAAAGT motif, a binding site for Lef1 protein. We showed that Lef1 binds to the mutated site and that overexpression of Lef1/β-Catenin chimeric protein repressed MCS9.7-350dupA enhancer activity. In conclusion, our data strongly suggest that 350dupA variant is an etiologic mutation in VWS patients and disrupts enhancer activity by a loss- and gain-of-function mechanism, and thus support the rationale for additional screening for regulatory mutations in patients with CLP.

Dominant mutations in GRHL3 cause Van der Woude Syndrome and disrupt oral periderm development

Mutations in interferon regulatory factor 6 (IRF6) account for ∼70% of cases of Van der Woude syndrome (VWS), the most common syndromic form of cleft lip and palate. In 8 of 45 VWS-affected families lacking a mutation in IRF6, we found coding mutations in grainyhead-like 3 (GRHL3). According to a zebrafish-based assay, the disease-associated GRHL3 mutations abrogated periderm development and were consistent with a dominant-negative effect, in contrast to haploinsufficiency seen in most VWS cases caused by IRF6 mutations. In mouse, all embryos lacking Grhl3 exhibited abnormal oral periderm and 17% developed a cleft palate. Analysis of the oral phenotype of double heterozygote (Irf6(+/-);Grhl3(+/-)) murine embryos failed to detect epistasis between the two genes, suggesting that they function in separate but convergent pathways during palatogenesis. Taken together, our data demonstrated that mutations in two genes, IRF6 and GRHL3, can lead to nearly identical phenotypes of orofacial cleft. They supported the hypotheses that both genes are essential for the presence of a functional oral periderm and that failure of this process contributes to VWS.

Association and Mutation Analyses of the IRF6 Gene in Families with Nonsyndromic and Syndromic Cleft Lip and/or Cleft Palate

Objectives

(1) To detect interferon regulatory factor 6 gene ( IRF6) mutations in newly recruited Van der Woude syndrome (VWS) and popliteal pterygium syndrome (PPS) families. (2) To test for association, in nonsyndromic cleft lip and/or cleft palate (NSCL/P) and in VWS/PPS families, the single nucleotide polymorphism (SNP) rs642961, from the IRF6 enhancer AP-2α region, alone or as haplotype with rs2235371, a coding SNP (Val274Ile).

Design

IRF6 mutation screening was performed by direct sequencing and genotyping of rs642961 and rs2235371 by TaqMan technology.

Patients

Seventy-one Swedish NSCL/P families, 24 Finnish cleft palate (CP) families, and 24 VWS/PPS families (seven newly recruited) were studied.

Results

Allelic and genotypic frequencies in each phenotype were compared to those of the controls, and no significant difference could be observed. IRF6 gene mutation was detected in six of the seven new VWS/PPS families. Association analysis of the entire VWS/PPS sample set revealed the A allele from rs642961 to be a risk allele. Significant association was detected in the Swedish CP subset of our NSCL/P collection where the G-C haplotype for rs642961-rs2235371 were at risk ( P= .013).

Conclusions

Our results do not support the previously reported association between the A allele of rs642961 and the NSCL phenotype. However, in the VWS/PPS families, the A allele was a risk allele and was, in a large majority (>80%), transmitted on the same chromosome as the IRF6 mutation.

Cleft lip - a comprehensive review

Orofacial clefts comprise a range of congenital deformities and are the most common head and neck congenital malformation. Clefting has significant psychological and socio- economic effects on patient quality of life and require a multidisciplinary team approach for management. The complex interplay between genetic and environmental factors play a significant role in the incidence and cause of clefting. In this review, the embryology, classification, epidemiology, and etiology of cleft lip are discussed. The primary goals of surgical repair are to restore normal function, speech development, and facial esthetics. Different techniques are employed based on surgeon expertise and the unique patient presentations. Pre-surgical orthopedics are frequently employed prior to definitive repair to improve outcomes. Long term follow up and quality of life studies are discussed.

Haploinsufficiency of interferon regulatory factor 6 alters brain morphology in the mouse

Orofacial clefts are among the commonest birth defects. Among many genetic contributors to orofacial clefting, Interferon Regulatory Factor 6 (IRF6) is unique since mutations in this gene cause Van der Woude (VWS), the most common clefting syndrome. Furthermore, variants in IRF6 contribute to increased risk for non-syndromic cleft lip and/or palate (NSCL/P). Our previous work shows that individuals with either VWS or NSCL/P may have cerebral anomalies (larger anterior, smaller posterior regions), and a smaller cerebellum. The objective of this study was to test the hypothesis that disrupting Irf6 in the mouse will result in quantitative brain changes similar to those reported for humans with VWS and NSCL/P. Male mice heterozygous for Irf6 (Irf6(gt1/+); n = 9) and wild-type (Irf6(+/+) ; n = 6) mice at comparable age underwent a 4.7-T MRI scan to obtain quantitative measures of cortical and subcortical brain structures. There was no difference in total brain volume between groups. However, the frontal cortex was enlarged in the Irf6(gt1/+) mice compared to that of wild types (P = 0.028) while the posterior cortex did not differ. In addition, the volume of the cerebellum of Irf6(gt1/+) mice was decreased (P = 0.004). Mice that were heterozygous for Irf6 showed a similar pattern of brain anomalies previously reported in humans with VWS and NSCL/P. These structural differences were present in the absence of overt oral clefts. These results support a role for IRF6 in brain morphometry and provide evidence for a potential genetic link to abnormal brain development in orofacial clefting.

Detecting genetic association of common human facial morphological variation using high density 3D image registration

Human facial morphology is a combination of many complex traits. Little is known about the genetic basis of common facial morphological variation. Existing association studies have largely used simple landmark-distances as surrogates for the complex morphological phenotypes of the face. However, this can result in decreased statistical power and unclear inference of shape changes. In this study, we applied a new image registration approach that automatically identified the salient landmarks and aligned the sample faces using high density pixel points. Based on this high density registration, three different phenotype data schemes were used to test the association between the common facial morphological variation and 10 candidate SNPs, and their performances were compared. The first scheme used traditional landmark-distances; the second relied on the geometric analysis of 15 landmarks and the third used geometric analysis of a dense registration of ∼30,000 3D points. We found that the two geometric approaches were highly consistent in their detection of morphological changes. The geometric method using dense registration further demonstrated superiority in the fine inference of shape changes and 3D face modeling. Several candidate SNPs showed potential associations with different facial features. In particular, one SNP, a known risk factor of non-syndromic cleft lips/palates, rs642961 in the IRF6 gene, was validated to strongly predict normal lip shape variation in female Han Chinese. This study further demonstrated that dense face registration may substantially improve the detection and characterization of genetic association in common facial variation.

Heritability of human facial appearance is an intriguing question to the general public and researchers. Although it is known that some facial features are highly heritable, the exact genetic basis is unknown. Previous studies used simple linear measurements such as landmark distances, to evaluate the facial shape variation. Such approaches, although easy to carry out, may lack statistical power and miss complex morphological changes. In this study, we utilized a new 3D face registration method that enables subtle differences to be detected at high resolution 3D images. Based on this, we tried to test and characterize the associations of 10 candidate genetic variants to common facial morphological variations. Different types of phenotype data were extracted and compared in the association tests. Our results show that geometry based data performed better than simple distance based data. Furthermore, high density geometric data outstood the others in capturing small shape changes and modeling the 3D face visualization. Interestingly, a genetic variant from IRF6 gene, which is also a well-known risk factor of non-syndrome cleft lip, was found to strongly predispose the mouth shape in Han Chinese females.

Interferon-regulatory factors determine macrophage phenotype polarization

The mononuclear phagocyte system regulates tissue homeostasis as well as all phases of tissue injury and repair. To do so changing tissue environments alter the phenotype of tissue macrophages to assure their support for sustaining and amplifying their respective surrounding environment. Interferon-regulatory factors are intracellular signaling elements that determine the maturation and gene transcription of leukocytes. Here we discuss how several among the 9 interferon-regulatory factors contribute to macrophage polarization.

Germline mutation in the RAD51B gene confers predisposition to breast cancer

BACKGROUND

Most currently known breast cancer predisposition genes play a role in DNA repair by homologous recombination. Recent studies conducted on RAD51 paralogs, involved in the same DNA repair pathway, have identified rare germline mutations conferring breast and/or ovarian cancer predisposition in the RAD51C, RAD51D and XRCC2 genes. The present study analysed the five RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3) to estimate their contribution to breast and ovarian cancer predisposition.

METHODS

The study was conducted on 142 unrelated patients with breast and/or ovarian cancer either with early onset or with a breast/ovarian cancer family history. Patients were referred to a French family cancer clinic and had been previously tested negative for a BRCA1/2 mutation. Coding sequences of the five genes were analysed by EMMA (Enhanced Mismatch Mutation Analysis). Detected variants were characterized by Sanger sequencing analysis.

RESULTS

Three splicing mutations and two likely deleterious missense variants were identified: RAD51B c.452 + 3A > G, RAD51C c.706-2A > G, RAD51C c.1026 + 5_1026 + 7del, RAD51B c.475C > T/p.Arg159Cys and XRCC3 c.448C > T/p.Arg150Cys. No RAD51D and XRCC2 gene mutations were detected. These mutations and variants were detected in families with both breast and ovarian cancers, except for the RAD51B c.475C > T/p.Arg159Cys variant that occurred in a family with 3 breast cancer cases.

CONCLUSIONS

This study identified the first RAD51B mutation in a breast and ovarian cancer family and is the first report of XRCC3 mutation analysis in breast and ovarian cancer. It confirms that RAD51 paralog mutations confer breast and ovarian cancer predisposition and are rare events. In view of the low frequency of RAD51 paralog mutations, international collaboration of family cancer clinics will be required to more accurately estimate their penetrance and establish clinical guidelines in carrier individuals.

Genetics of cleft lip and cleft palate

Orofacial clefts are common birth defects and can occur as isolated, nonsyndromic events or as part of Mendelian syndromes. There is substantial phenotypic diversity in individuals with these birth defects and their family members: from subclinical phenotypes to associated syndromic features that is mirrored by the many genes that contribute to the etiology of these disorders. Identification of these genes and loci has been the result of decades of research using multiple genetic approaches. Significant progress has been made recently due to advances in sequencing and genotyping technologies, primarily through the use of whole exome sequencing and genome-wide association studies. Future progress will hinge on identifying functional variants, investigation of pathway and other interactions, and inclusion of phenotypic and ethnic diversity in studies.

Translational Genetics

Scientific opportunities have never been better than today! The completion of the Human Genome project has sparked hope and optimism that cures for debilitating conditions can be achieved and tailored to individuals and communities. The availability of reference genome sequences and genetic variations as well as more precise correlations between genotype and phenotype have facilitated the progress made in finding solutions to clinical problems. While certain craniofacial and oral diseases previously deemed too difficult to tackle have benefited from basic science and technological advances over the past decade, there remains a critical need to translate the fruits of several decades’ worth of basic and clinical research into tangible therapies that can benefit patients. The fifth Annual Fall Focused Symposium, “Translational Genetics – Advancing Fronts for Craniofacial Health”, was created by the American Association for Dental Research (AADR) to foster its mission to advance interdisciplinary research that is directed toward improving oral health. The symposium showcased progress made in identifying molecular targets that are potential therapeutics for common and rare dental diseases and craniofacial disorders. Speakers focused on translational and clinical applications of their research and, where applicable, on strategies for new technologies and therapeutics. The critical needs to transfer new knowledge to the classroom and for further investment in the field were also emphasized. The symposium underscored the importance of basic research, chairside clinical observations, and population-based studies in driving the new translational connections needed for the development of cures for the most common and devastating diseases involving the craniofacial complex.

Association between Interferon Regulatory Factor 6 Gene Polymorphisms and Nonsyndromic Cleft Lip with or without Cleft Palate in a Chinese Population

Objective

To further confirm the association between two IRF6 single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate in a Chinese population.

Participants

A total of 106 nonsyndromic cleft lip with or without cleft palate case trios and 129 control trios.

Intervention

Two IRF6 single nucleotide polymorphisms, rs2235371 and rs642961, were genotyped for all case and control families. Case-control analysis and family-based linkage analysis were both performed for the two single nucleotide polymorphisms.

Results

The genotype and allele frequencies of rs2235371 (odds ratioAG+AA vs. GG, 0.581; 95% confidence interval, 0.345 to 0.976; P = .039) and rs642961 (odds ratioAG+AA vs. GG, 5.389; 95% confidence interval, 2.936 to 9.893; P = 5e-08) were significantly higher in nonsyndromic cleft lip with or without cleft palate patients compared with controls. There was an obvious dosage effect of allele A at rs642961. The transmission of a major allele (G) of rs2235371 and a minor allele (A) of rs642961 was in disequilibrium ( P < .05) in complete case-parent trios. The association between the two single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate was confirmed by the Family-Based Association Test for rs642961 ( P = .008), but there was no significance for rs2235371 ( P = 0.057). Haplotype analysis found that rs2235371 G/rs642961 A haplotype increased the risk of nonsyndromic cleft lip with or without cleft palate ( P = 2.42e-07); whereas, rs2235371 A/rs642961 G haplotype reduced the risk of nonsyndromic cleft lip with or without cleft palate ( P = 4.37e-05). No evidence of linkage disequilibrium was found between the two single nucleotide polymorphisms (D′ = 0.303, r2 = 0.017).

Conclusion

Our results confirmed the involvement of the IRF6 variants rs642961 and rs2235371 in the etiology of nonsyndromic cleft lip with or without cleft palate in a Chinese population.

Search for genetic modifiers of IRF6 and genotype-phenotype correlations in Van der Woude and popliteal pterygium syndromes

Van der Woude syndrome is the most common form of syndromic orofacial clefting, accounting for 1-2% of all patients with cleft lip and/or cleft palate. Van der Woude and popliteal pterygium syndromes are caused by mutations in IRF6, but phenotypic variability within and among families with either syndrome suggests that other genetic factors contribute to the phenotypes. The aim of this study was to identify common variants acting as genetic modifiers of IRF6 as well as genotype-phenotype correlations based on mutation type and location. We identified an association between mutations in the DNA-binding domain of IRF6 and limb defects (including pterygia). Although we did not detect formally significant associations with the genes tested, borderline associations suggest several genes that could modify the VWS phenotype, including FOXE1, TGFB3, and TFAP2A. Some of these genes are hypothesized to be part of the IRF6 gene regulatory network and may suggest additional genes for future study when larger sample sizes are also available. We also show that families with the Van de Woude phenotype but in whom no mutations have been identified have a lower frequency of cleft lip, suggesting there may be locus and/or mutation class differences in Van de Woude syndrome.

SNPs and interaction analyses of IRF6, MSX1 and PAX9 genes in patients with non‑syndromic cleft lip with or without palate

Non‑syndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital deformity, often associated with missing or deformed teeth. The genes interferon regulatory factor 6 (IRF6), muscle segment homeobox 1 (MSX1) and paired box gene 9 (PAX9) are important for the development of the maxillofacial region and dentition. The aim of this study was to explore how genetic variations in IRF6, MSX1 and PAX9, as well as gene‑gene interactions, are associated with NSCL/P. We investigated 9 IRF6 tag single nucleotide polymorphisms (SNPs), 2 MSX1 tag SNPs and 8 PAX9 tag SNPs selected from HapMap data from the Chinese population. The SNPs were examined for associations with NSCL/P in 204 patients and 226 controls. The results demonstrated a significant association between NSCL/P and rs2073485, rs2235371, rs2236909 and rs861020 in the IRF6 gene, and haplotype analysis supported these findings. A marginally significant difference was observed in the NSCL/P group for rs17176643 in the PAX9 gene compared to the control group. The results of gene‑gene interaction analyses also indicated that the combination of rs2073485, rs2235371 or rs2236909 in IRF6 and rs17176643 in PAX9, increased the risk of NSCL/P. Thus, our study provided additional understanding of IRF6 variations in patients with NSCL/P and suggested that interactions between the IRF6 and PAX9 genes are potentially important for susceptibility to NSCL/P.

De novo 2.3 Mb microdeletion of 1q32.2 involving the Van der Woude Syndrome locus

Background

Van der Woude syndrome is the most common among syndromes which include cleft lip and/or cleft palate as one of the presentations. It is usually caused by mutations in the interferon regulatory factor 6 (IRF6) gene.

Case presentation

We previously reported on a patient with suspected deletion of the IRF6 gene. Using the Affymetrix Human SNP 6.0 Array, the interstitial deletion has been confirmed and found to be approximately 2.327–2.334 Mb within the 1q32.2 region. Although several known genes were deleted, the patient has no other phenotype apart from the orofacial presentations typical of VWS. The same deletion was not present in either parent and his two siblings were also phenotypically normal.

Conclusions

Other than IRF6, the genes which are deleted in this patient appear to be insensitive to copy number and haploinsufficiency. We compared the deletion in this patient with another case which was also mapped by high resolution array but had additional phenotypic features.