No evidence of linkage between the transforming growth factor-alpha gene in families with apparently autosomal dominant inheritance of cleft lip and palate

Fine-Mapping of 18q21.1 Locus Identifies Single Nucleotide Polymorphisms Associated with Nonsyndromic Cleft Lip with or without Cleft Palate

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital birth defects. NSCL/P is a complex multifactorial disease caused by interactions between multiple environmental and genetic factors. However, the causal single nucleotide polymorphism (SNP) signature profile underlying the risk of familial NSCL/P still remains unknown. We previously reported a 5.7-Mb genomic region on chromosome 18q21.1 locus that potentially contributes to autosomal dominant, low-penetrance inheritance of NSCL/P. In the current study, we performed exome sequencing on 12 familial genomes (six affected individuals, two obligate carriers, and four seemingly unaffected individuals) of a six-generation family to identify candidate SNPs associated with NSCL/P risk. Subsequently, targeted bidirectional DNA re-sequencing of polymerase chain reaction (PCR)-amplified high-risk regions of MYO5B gene and sequenom iPLEX genotpying of 29 candidate SNPs were performed on a larger set of 33 members of this NSCL/P family (10 affected + 4 obligate carriers + 19 unaffected relatives) to find SNPs significantly associated with NSCL/P trait. SNP vs. NSCL/P association analysis showed the MYO5B SNP rs183559995 GA genotype had an odds ratio of 18.09 (95% Confidence Interval = 1.86–176.34; gender-adjusted P = 0.0019) compared to the reference GG genotype. Additionally, the following SNPs were also found significantly associated with NSCL/P risk: rs1450425 (LOXHD1), rs6507992 (SKA1), rs78950893 (SMAD7), rs8097060, rs17713847 (SCARNA17), rs6507872 (CTIF), rs8091995 (CTIF), and rs17715416 (MYO5B). We could thus identify mutations in several genes as key candidate SNPs associated with the risk of NSCL/P in this large multi-generation family.

Genetic Effect of Transforming Growth Factor Alpha Gene Variants on the Risk of Nonsyndromic Cleft Lip with or without Palate in Korean Populations

Objective

To identify the contribution of TGFA gene variants to the risk of nonsyndromic cleft lip with or without palate (NS-CL±P).

Design

The samples were from 142 Korean NS-CL±P families and 119 control parents having nonaffected children. Minor allele frequency, heterozygosity, and χ2 test for Hardy-Weinberg equilibrium were calculated for each of 10 selected single-nucleotide polymorphisms (SNPs). Ten SNPs were used to examine the association of case-parent trios with the transmission disequilibrium test (TDT) and conditional logistic regression models (CLRMs). Both allelic and genotypic TDTs for individual SNPs and sliding windows of haplotypes consisting of two to five SNPs were tested using family- and haplotype-based association test programs. Genotypic odd ratios (GORs) were obtained from CLRMs using STATA software. The parent-of-origin effect was evaluated for 10 SNPs, and a comparison between 218 case parents and 119 control parents was performed to investigate paternal and maternal ORs.

Results

Family-based TDT and haplotype analysis exhibited no statistical significance, but a relatively meaningful association was shown with rs3771497 (all P < .05; two SNPs, rs3771497 and rs3755377; five SNPs, rs3771497, rs3755377, rs3771485, rs11466212, and rs3771475). G/G homozygotes at rs3771497 have a significant decreased risk of NS-CL±P (GOR = 0.30, P < .01). No SNPs showed parent-of-origin effects. However, in the comparison between case parents and control parents, a single-marker analysis of maternal line showed a significant association with NS-CL±P in rs3771497 ( P < .001, recessive model).

Conclusion

The association of the TGFA gene with NS-CL±P in Korean populations was not clearly found. However, the etiologic effect of the TGFA gene on NS-CL±P patients should be investigated in terms of maternal genotype influence.

Transforming Growth Factor-α and Nonsyndromic Cleft Lip with or without Palate or Cleft Palate Only in Kelantan, Malaysia

Objective:

To determine the frequency of the transforming growth factor-alpha (TGFα) Taq1 polymorphism in nonsyndromic cleft lip with or without cleft palate (CL±P) and cleft palate only (CP) in Kelantan, Malaysia.

Setting:

The study was conducted at the Combined Cleft Clinic and at the Human Genome Centre in Hospital Universiti Sains Malaysia in Kelantan, Malaysia.

Design:

We examined the C2/Taq1 variant of the TGFα gene in 46 patients with nonsyndromic CL±P or CP only and in 33 controls. The TGFα genotype frequencies in patients were compared with those in controls using the chi-square or Fisher exact test. DNA samples were obtained from peripheral blood.

Results:

No association was found between TGFαTaq1 polymorphism and CL±P or CP in this case-control study. In addition, no homozygosity for the rare allele C2 was noted in CL±P, CP, or the controls.

Conclusion:

No evidence of TGFαTaq1 polymorphism was observed in association with CL±P and CP in this study.

TGF alpha has low protein expression in nonsyndromic clefts

Genetic studies have demonstrated that nonsyndromic cleft is composed of two separate entities: the cleft palate only and cleft of the lip, alveolus with or without cleft palate; both have a heterogeneous genetic background and environmental factors contribute to the onset of these malformations. The role of transforming growth factor alpha (TGF-A) was considered possible, but conflicting results have been reported. To detect if TGF-A is involved in the onset of cleft diseases, a series of patients with nonsyndromic clefts and control subjects were analyzed with regard to protein expression. Forty-three patients with nonsyndromic clefts and 21 unaffected subjects were enrolled in this study. Paraffin-embedded specimens were matched with TGF-A antibody and then scanned with a computerized image analyzer. TGF-A was scored as absent, moderately (from 10% to 30%), and highly expressed in epithelium, gland, and muscle. Data were statistically analyzed with a Kruskal-Wallis test. Comparison between control subjects and patients with clefts showed that only gland and epithelium reached a significant P value. A subsequent comparison between cleft of the lip, alveolus with or without cleft palate and cleft palate only groups demonstrated a statistically significant difference only for gland. TGF-A was decreasingly expressed in unaffected, cleft of the lip, alveolus with or without cleft palate, and patient with cleft palate only and thus further strength has been given to its role in the onset of the disease.

Human genetic factors in nonsyndromic cleft lip and palate: an update

Nonsyndromic cleft lip and/or palate (or orofacial cleft, OFC) is a malformation characterized by an incomplete separation between nasal and oral cavities without any associated anomalies. The last point defines the distinction between syndromic and nonsyndromic OFC. Nonsyndromic OFC is one of the most common malformations among live births and is composed of two separate entities: cleft lip with or without cleft palate (CL+/-P) and cleft palate isolated (CPI). Because of the complex etiology of nonsyndromic OFC, which is due to the differences between CL+/-P and CPI, and the heterogeneity of each group, caused by the number of genes involved, the type of inheritance, and the interaction with environmental factors, we reviewed those genes and available loci in the literature whose involvement in the onset of nonsyndromic OFC has more sound scientific evidence. Genetic studies on human populations have demonstrated that CL+/-P and CPI have distinct genetic backgrounds and, therefore, environmental factors probably disclose only these malformations. In CL+/-P several loci, OFC from 1 to 10 have been identified. The first locus, OFC1, has been mapped to chromosome 6p24. Other CL+/-P loci have been mapped to 2p13 (OFC2), 19q13.2 (OFC3) and 4q (OFC4). OFC5-8 are identified by mutations in the MSX1, IRF6, PVRL1, and TP73L gene, respectively. OFC9 maps to 13q33.1-q34, whereas OFC10 is associated with haploinsufficiency of the SUMO1 gene. In addition, MTHFR, TGF-beta3, and RARalpha play a role in cleft onset. In CPI one gene has been identified (TBX22) at present, but others are probably involved. Greater efforts are necessary in order to have a complete picture of the main factors involved in lip and palate formation. These elements will permit us to better understand and better treat patients affected by OFC.

Autosomal dominant nonsyndromic cleft lip and palate: significant evidence of linkage at 18q21.1

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital facial defects, with an incidence of 1 in 700-1,000 live births among individuals of European descent. Several linkage and association studies of NSCL/P have suggested numerous candidate genes and genomic regions. A genomewide linkage analysis of a large multigenerational family (UR410) with NSCL/P was performed using a single-nucleotide-polymorphism array. Nonparametric linkage (NPL) analysis provided significant evidence of linkage for marker rs728683 on chromosome 18q21.1 (NPL=43.33 and P=.000061; nonparametric LOD=3.97 and P=.00001). Parametric linkage analysis with a dominant mode of inheritance and reduced penetrance resulted in a maximum LOD score of 3.61 at position 47.4 Mb on chromosome 18q21.1. Haplotype analysis with informative crossovers defined a 5.7-Mb genomic region spanned by proximal marker rs1824683 (42,403,918 bp) and distal marker rs768206 (48,132,862 bp). Thus, a novel genomic region on 18q21.1 was identified that most likely harbors a high-risk variant for NSCL/P in this family; we propose to name this locus "OFC11" (orofacial cleft 11).

Association between the transforming growth factor alpha gene and nonsyndromic oral clefts: a HuGE review

Transforming growth factor alpha (TGFA) is a well-characterized mammalian growth factor. Since the first report of an association between DNA sequence variants at the TGFA genetic locus and nonsyndromic oral clefts, 47 studies have been carried out, producing conflicting results. In this review, the author synthesizes findings from published reports on the association between the TGFA gene and clefting in humans. Bias, lack of statistical power, and genuine population diversity can explain the diverse results. In the aggregate, TGFA is probably a genetic modifier of clefting in humans, which is consistent with the oligogenic model suggested for nonsyndromic oral clefts.

Linkage analysis between BCL3 and nearby genes on 19q13.2 and non-syndromic cleft lip with or without cleft palate in multigenerational Japanese families

OBJECTIVE

To investigate the linkage between candidate genes on chromosome 19 and cleft lip with or without cleft palate in Japanese using a parametric method.

MATERIALS AND METHODS

After informed consent was obtained, blood samples were drawn from 90 individuals in 14 families, 30 of whom were affected, and genomic DNAs were extracted. PCR-amplified products using four microsatellite markers, D19S178, BCL3, APOC2[007/008] and APOC2[AC1/AC2] located in 19q13.2, were separated by 8% polyacrylamide gel electrophoresis. Linkage analysis was carried out using the MLINK and LINKMAP programs, and logarithm of odds (LOD) scores were calculated for each family.

RESULTS

Before undertaking linkage analysis, we analyzed 74 healthy Japanese subjects and found racial differences in that the observed number of alleles and their heterozygosity were lower in Japanese than in Caucasians, and that both populations tended to show a different allele distribution. In 14 families, two-point maximum LOD score (Zmax) for BCL3 was 0.341 and multi-point Zmax was less than -2 excluding linkage. But in 9 families with left and bilateral CL/P, two-point Zmax for APOC2[AC1/AC2] was 1.701 and multi-point Zmax at APOC2 locus was 1.909.

CONCLUSION

The LOD score was relatively high but provided no evidence of linkage for CL/P to BCL3 and nearby genes in Japanese subjects.

Transforming growth factor-alpha and nonsyndromic cleft lip with or without palate in Brazilian patients: results of a large case-control study

OBJECTIVE

Transforming growth factor-alpha (TGFA) was the first gene suggested to be associated with nonsyndromic cleft lip, cleft palate, or both (CL/ P). There are, however, still controversies of the effect of TGFA on the predisposition of this malformation. To contribute to a better understanding of the role of this gene in the occurrence of CL/P we undertook a case-control study including patients and controls ascertained in different regions of the country.

DESIGN

We examined the C2/TaqI variant of the TGFA gene in 536 patients with nonsyndromic CL/P and 412 controls. The TGFA genotype frequencies in patients were compared with controls using chi-square or Fisher exact test. DNA, obtained from peripheral blood or buccal swabs, was genotyped for the TaqI polymorphism of TGFA.

SETTING

The probands and corresponding controls were ascertained in different centers of Brazil, partly representing the ethnic admixture of our population.

RESULTS

The TGFA genotype distribution was very similar in patients with CL/P ascertained in the three different regions of Brazil. However, a discrete difference was observed between controls of Säo Paulo and Ceará (chi-square = 3.605; p = 0.058), with a lower value of the C2/Taq allele frequency in controls of CE (0.04). These data reinforce that this polymorphic system is heterogenous among different ethnic groups. In addition, no evidence was found for an association of TGFA with CL/P in this case-control study.

CONCLUSION

These data further suggest that TGFA is not a relevant modifier locus for the occurrence of CL/P.

Evidence for linkage of nonsyndromic cleft lip with or without cleft palate to a region on chromosome 2

Results from a genome-wide screen of 10 multiplex families ascertained through probands with nonsyndromic cleft lip with or without cleft palate (CL/P) in Mexico, Argentina, and the United States yielded suggestive evidence of linkage to chromosomes 2, 6, 17 and 18. Fine mapping excluded all regions except chromosome 2. Subsequent analysis was performed on the original 10 families plus an additional 16 families using 31 markers on chromosome 2. This analysis showed intriguing evidence of linkage to 2q (Zlr=2.26, empirical P-value=0.028 in a chromosome-wide analysis). Transmission disequilibrium tests also revealed evidence of linkage and disequilibrium for two markers in this region (D2S168 and D2S1400 with P-values=0.022 and 0.006, respectively). A subset of these 26 families provided additional evidence for a susceptibility gene for CL/P on 2q, suggesting that further studies of genes in this region are warranted.

Variants of developmental genes (TGFA, TGFB3, and MSX1) and their associations with orofacial clefts: a case-parent triad analysis

We selected 262 case-parent triads from a population-based study of orofacial clefts in Norway, and examined variants of developmental genes TGFA, TGFB3, and MSX1 in the etiology of orofacial clefts. One hundred seventy-four triads of cleft lip cases (CL+/-P) and 88 triads of cleft palate only cases (CPO) were analyzed. There was little evidence for an association of any of these genes with CL+/-P. The strongest association was a 1.7-fold risk with two copies of the TGFB3-CA variant (95% CI=0.9-3.0). Among CPO cases, there was a 3-fold risk with two copies of the TGFA TaqI A2 allele, and no increase with one copy. Assuming this to be a recessive effect, we estimated a 3.2-fold risk among babies homozygous for the variant (95% CI=1.1-9.2). Furthermore, there was strong evidence of gene-gene interaction. While there was only a weak association of the MSX1-CA variant with CPO, the risk was 9.7-fold (95% CI=2.9-32) among children homozygous for both the MSX1-CA A4 allele and the TGFA A2 allele. No association of CPO with the TGFA variant was seen among the other MSX1-CA genotypes. In conclusion, no strong associations were found between CL+/-P and variants at these three genes. There was a possible recessive effect of the TGFA TaqI variant on the risk of CPO, with a 3-fold risk among children homozygous for the variant. The effect of this TGFA genotype was even stronger among children homozygous for the MSX1-CA A4 allele, raising the possibility of interaction between these two genes.

Recent developments in orofacial cleft genetics

Nonsyndromic cleft of the lip and/or palate (CLP or orofacial cleft) derives from an embryopathy with consequent failure of the nasal process and/or palatal shelves fusion. This severe birth defect is one of the most common malformations among live births. Nonsyndromic CLP is composed of two separate entities: cleft lip and palate (CL+/-P) and cleft palate only (CPO). Both have a genetic background, and environmental factors probably disclose these malformations. In CL+/-P, several loci have been identified, and, in one case, a specific gene has also been found. In CPO, one gene has been identified, but many more are probably involved. Because of the complexity of the genetics of nonsyndromic CLP as a result of the difference between CL+/-P and CPO, heterogeneity of each group caused by the number of involved genes, type of inheritance, and interaction with environmental factors, we discuss the more sound results obtained with different approaches: epidemiological studies, animal models, human genetic studies, and in vitro studies.

Folate and the face: evaluating the evidence for the influence of folate genes on craniofacial development

OBJECTIVE

Genetics has been thought to play a crucial role in the etiology of non-syndromic cleft lip and palate (CL/P) for over 60 years, but we are still no closer to finding contributing genes. The main hindrance to the progress of CL/P genetic research is the complex multifactorial nature of the disorder with environmental factors playing a significant, if not equally important role. Thus, CL/P is the likely outcome of several developmental and biochemical events that may be different in different individuals or families.

CONCLUSIONS

Because of the known advantages of folate therapy during pregnancy and the developmental problems that may occur when diets are folate deficient, recent research has looked toward a possible genetic explanation for susceptibility to low folate status. Several gene variants have been identified which, when combined with an inadequate diet, may impede human development, but it still remains to be seen whether these are a major contributor to CL/P. Here we review some of the current viewpoints and the possible impact of folic acid supplementation on clefting incidence.

Gene/environment causes of cleft lip and/or palate

Craniofacial anomalies, and in particular cleft lip and palate, are major human birth defects with a worldwide frequency of 1 in 700 and substantial clinical impact. A wide range of studies in developmental biology has contributed to a better knowledge of how both genes and environmental exposures impact head organogenesis. Specific causes have now been identified for some forms of cleft lip and palate, and we are at the beginning of a time in which the common nonsyndromic forms may also have specific etiologies identified. Mouse models have an especially important role in disclosing cleft etiologies and providing models for environmental cotriggers or interventions. An overview of the gene-environment contributions to nonsyndromic forms of clefting and their implications for developmental biology and clinical counseling is presented.

Genetic and teratogenic approaches to craniofacial development

Craniofacial malformations are the most common birth defects that occur in humans, with facial clefting representing the majority of these defects. Facial clefts can arise at any stage of development due to perturbations that alter the extracellular matrix as well as affect the patterning, migration, proliferation, and differentiation of cells. In this review, we focus on recent advances in the understanding of the developmental basis for facial clefting through the analysis of the effects of gene disruption experiments and treatments with teratogens in both chickens and mice. Specifically, we analyze the results of disruptions to genes such as Sonic hedgehog (Shh), epidermal growth factor receptor (EGFR), Distal-less (Dlx), and transforming growth factor beta 3 (TGFbeta3). We also describe the effects that teratogens such as retinoic acid, jervine, and cyclopamine have on facial clefting and discuss mechanisms for their action. In addition to providing insight into the bases for abnormal craniofacial growth, genetic and teratogenic techniques are powerful tools for understanding the normal developmental processes that generate and pattern the face.

Linkage analysis of candidate regions in Swedish nonsyndromic cleft lip with or without cleft palate families

OBJECTIVE

To analyze linkage of five candidate regions for nonsyndromic cleft lip with or without palate (CLP) on chromosome 2p13, 4q, 6p23, and 19q13; in addition chromosome 1q32, the locus for van der Woude syndrome, on Swedish CLP families.

DESIGN

Three to five linked microsatellite markers were selected from each candidate region. Polymerase chain reaction (PCR) with fluorescent-labeled microsatellite markers was performed on DNA samples from the participating families. Electrophoresis of the PCR products was performed on a laser-fluorescent DNA sequencer. The genotype data were analyzed with multipoint linkage analysis. Modes of inheritance tested included two autosomal dominant, an autosomal recessive, and a nonparametric model. Multipoint logarithm of odds (LOD) scores were also calculated by assuming genetic heterogeneity.

PARTICIPANTS

Nineteen Swedish multigenerational families with at least two first-degree relatives affected with CLP. Greater than 50% of the families studied show vertical transmission of the clefting phenotype and both inter- and intrafamilial variability were noted.

RESULTS

Cumulative multipoint LOD scores for the whole group of families calculated under autosomal dominant modes of inheritance were negative in all regions and less than -2 except chromosome 6p23. LOD scores calculated under recessive inheritance and the nonparametric model were inconclusive. There was no significant evidence of genetic heterogeneity among the sample group.

CONCLUSIONS

The group of Swedish CLP families did not demonstrate significant linkage to any of the five candidate regions examined. This might suggest a new but yet unknown CLP locus or loci in this family group. However, because linkage could not be excluded in some individual families, they should still be tested with candidate genes from these regions.

Transforming growth factor alpha locus and nonsyndromic cleft lip with or without cleft palate: a reappraisal

An association between nonsyndromic cleft lip with or without cleft palate (CL +/- P) and genetic variation at the transforming growth factor alpha (TGFA) locus was originally reported in 1989. Subsequent population-based studies of this association have provided conflicting results. The present analyses were undertaken to determine if the cumulative weight of the available data convincingly supports or refutes this association. The published data were analyzed for differences in allele frequencies between Caucasian CL +/- P patients (i.e., cases) and controls, and for heterogeneity between Caucasian samples. When all data except the original report were considered, there was a statistically significant association between TGFA and CL +/- P (M.H.O.R. = 1.43; 95% C.I. 1.12-1.80). However, there was evidence of significant heterogeneity in the TGFA allele frequencies between cases, but not controls, from different studies. The data suggest that the observed heterogeneity is unlikely to be attributable to differences in the ethnic composition of the cases among the various studies but may reflect differences in the proportion of cases with bilateral lip defects and/or with positive family histories of CL +/- P. Definitive conclusions regarding the source(s) of the observed heterogeneity could not, however, be drawn on the basis of the available data. Hence, at present, the evidence regarding an association between genetic variation at the TGFA locus and CL +/- P remains inconclusive.

The impact of molecular genetics on oral health paradigms

As a result of our increased understanding of the human genome, and the functional interrelationships of gene products with each other and with the environment, it is becoming increasingly evident that many human diseases are influenced by heritable alterations in the structure or function of genes. Significant advances in research methods and newly emerging partnerships between private and public sector interests are creating new possibilities for utilization of genetic information for the diagnosis and treatment of human diseases. The availability and application of genetic information to the understanding of normal and abnormal human growth and development are fundamentally changing the way we approach the study of human diseases. As a result, the issues and principles of medical genetics are coming to bear across all disciplines of health care. In this review, we discuss some of the potential applications of human molecular genetics for the diagnosis and treatment of oral diseases. This discussion is presented in the context of the ongoing technological advances and conceptual changes that are occurring in the field of medical genetics. To realize the promise of this new molecular genetics, we must be prepared to foresee the possibilities and to incorporate these newly emergent technologies into the evolving discipline of dentistry. By using examples of human conditions, we illustrate the broad application of this emerging technology to the study of simple as well as complex genetic diseases. Throughout this paper, we will use the following terminology: Penetrance--In a population, defined as the proportion of individuals possessing a disease-causing genotype who express the disease phenotype. When this proportion is less than 100%, the disease is said to have reduced or incomplete penetrance. Polymerase chain reaction (PCR)--A technique for amplifying a large number of copies of a specific DNA sequence flanked by two oligonucleotide primers. The DNA is alternately heated and cooled in the presence of DNA polymerase and free nucleotides, so that the specified DNA segment is denatured, hybridized with primers, and extended by DNA polymerase. MIM--Mendelian Inheritance in Man catalogue number from V. McKusick's Mendelian Inheritance in man (OMIM, 1998).

Genetics of nonsyndromic cleft lip and palate: a review of international studies and data regarding the Italian population

The aims of this review are (1) to illustrate current knowledge of the mode of inheritance and the loci involved in the cleft lip and palate and (2) to summarize the results of our investigations, which were carried out in Italy. It is well established that nonsyndromic cleft of the lip with or without the palate (CL+/-P) and cleft palate only (CPO) are separate entities. Genetic heterogeneity has been observed in CL+/-P, which involves different chromosome regions, mainly 6p23 (OFC1), 2q13 (OFC2), and 19q13.2 (OFC3), as well as other loci, such as 4q25-4q31.3 and 17q21. Furthermore, an interaction between different genes has been suggested in the oligogenic model. In one case at least, an OFC1 and OFC2 interaction has been demonstrated. The mode of inheritance of CPO is compatible with a recessive single major gene model, while an association with a candidate gene, mapping on the chromosome region 2q13/TGFalpha, remains to be confirmed.

Transforming growth factor-alpha (TGFA): genomic structure, boundary sequences, and mutation analysis in nonsyndromic cleft lip/palate and cleft palate only

Transforming growth factor-alpha (TGFA) has been proposed as a candidate gene in the etiology of nonsyndromic cleft lip with or without cleft palate (NS-CL/P) and of nonsyndromic cleft palate only (NS-CPO). Biologic support for a role of TGFA arises from its presence at high levels in the epithelial tissue of the medial edge of the palatal shelves at the time of shelf fusion in mice. Genetic support for the role of TGFA in clefting comes from the reported association of TGFA alleles with human NS-CPO and NS-CL/P. In this study we report the sequence and structure of human genomic TGFA and the search for causal TGFA mutations in 250 individuals with NS-CL/P or NS-CPO by conformational analysis of the coding sequence, splice junctions, and a portion of the 3' untranslated region strongly homologous between human and mouse. We confirm that human TGFA is composed of six exons and here report several new sequence substitutions and their frequencies. Five variants in conserved segments may represent rare causes for clefting in humans and provide support for the role of TGFA in facial morphogenesis.

Candidate genes for nonsyndromic cleft lip and palate and maternal cigarette smoking and alcohol consumption: evaluation of genotype-environment interactions from a population-based case-control study of orofacial clefts

Previous studies suggest that the relationship between genes and nonsyndromic cleft lip +/- cleft palate (CLP) or cleft palate only (CP) may be modified by the environment. Using data from a population-based case-control study, we examined allelic variants for three genes, i.e., transforming growth factor alpha (TGFA), transforming growth factor beta 3 (TGFB3), and Msh (Drosophila) homeobox homolog 1 (MSX1), and their interactions with two exposures during pregnancy (maternal cigarette smoking and alcohol consumption) as risk factors for CLP and CP. For each cleft phenotype, risk estimates associated with most allelic variants tended to be near unity. Risk estimates for maternal smoking (> or = 10 cigarettes/day) were significantly elevated for CP and were most elevated among infants with allelic variants at the TGFB3 or MSX1 sites. By comparison, risk estimates for maternal alcohol consumption (> or = 4 drinks/month) were significantly elevated for CLP and were most elevated among infants with allelic variants at the MSX1 site. Our results suggest that development of CLP and CP may be influenced independently by maternal exposures but more significantly by interaction of such exposures and specific allelic variants.

Association of MSX1 and TGFB3 with nonsyndromic clefting in humans

Nonsyndromic cleft lip with or without cleft palate (CL/P) and nonsyndromic cleft palate only (CPO) are common congenital anomalies with significant medical, psychological, social, and economic ramifications. Both CL/P and CPO are examples of complex genetic traits. There exists sufficient evidence to hypothesize that disease loci for CL/P and CPO can be identified by a candidate-gene linkage-disequilibrium (LD) strategy. Candidate genes for clefting, including TGFA, BCL3, DLX2, MSX1, and TGFB3, were screened for LD with either CL/P or CPO in a predominantly Caucasian population, with both case-control- and nuclear-family-based approaches. Previously reported LD for TGFA with both CL/P and CPO could not be confirmed, except in CL/P patients with a positive family history. Also, in contrast to previous studies, no LD was found between BCL3 and either CL/P or CPO. Significant LD was found between CL/P and both MSX1 and TGFB3 and between CPO and MSX1, suggesting that these genes are involved in the pathogenesis of clefting. In addition, a mutation search in the genes DLX2, MSX1, and TGFB3 was performed in 69 CPO patients and in a subset of the CL/P patients. No common mutations were found in the coding regions of these genes; however, several rare variants of MSX1 and TGFB3 were found that may alter the latters' normal function. These results form the basis for future research, including (a) mutation searches in the MSX1 and TGFB3 genes in Caucasian CL/P patients and (b) extension of the search for MSX1 mutations in CPO patients to the noncoding regions.

A locus in 2p13-p14 (OFC2), in addition to that mapped in 6p23, is involved in nonsyndromic familial orofacial cleft malformation

An allelic association between the transforming growth factor alpha gene (TGFA) situated in the chromosome 2p13 region and nonsyndromic cleft lip with or without cleft palate, also named orofacial cleft (OFC), was found in several population studies. However, no linkage between gene and malformation has shown up until now, probably due to the presence of genetic heterogeneity and the small sample size analyzed. Previously, we employed a collection of 38 OFC families to demonstrate linkage to the 6p23 chromosome region with the presence of genetic heterogeneity. In the present study we tested whether, in the same sample, linkage between OFC and markers on 2p13 could be determined. Evidence for genetic heterogeneity in our family set was apparent, by both pairwise and multipoint linkage analyses. Moreover, lod scores > 3 were found for marker D2S378 when families linked to the 6p23 markers were analyzed. Taken together these results indicate a role for the TGFA, or for another gene physically close to it, and suggest an interaction between two different genes, OFC1 and OFC2, mapped in 6p23 and 2p13, respectively, in the development of the cleft.

Application of transmission disequilibrium tests to nonsyndromic oral clefts: including candidate genes and environmental exposures in the models

Extensive epidemiological and genetic studies of the cause of oral clefts have demonstrated strong familial aggregation but have failed to yield definitive evidence of any single genetic mechanism. We used the transmission/disequilibrium test (TDT) to investigate the relationship between oral clefts and markers associated with five candidate genes by utilizing 160 parent-offspring trios. Conditional logistic regression models extended the TDT to include covariates as effect modifiers, thus permitting tests for gene-environment interactions. For four of these candidates [transforming growth factor alpha (TGFA), transforming growth factor beta 3 (TGFB3), retinoic acid receptor (RARA), and the proto-oncogene BCL3], we detected modestly elevated odds ratios for the transmission of one marker allele to cleft probands when all the trios were analyzed together. These odds ratios increased when information on type of cleft, race, family history, or maternal smoking were incorporated as effect modifiers. We detected significant interaction between maternal smoking and the transmission of alleles for markers near TGFA and TGFB3; excess transmission of allele 3 at BCL3 was most significant among cleft lip probands; and the odds ratios for transmission of alleles at D19S178 and THRA1 were significant when ethnic group was included in the model. We suggest that utilizing an analytical strategy that allows for stratification of data and incorporating environmental effects into a single analysis may be more effective for detecting genes of small effect.

Genetics of nonsyndromic oral clefts revisited

Nonsyndromic oral clefts are among the most common birth defects, affecting approximately 1 in 1000 Caucasian newborns. In recent decades, many investigators have used genetic and epidemiologic methods to identify etiologic factors, but results have often been inconclusive or contradictory. Etiologic heterogeneity is undoubtedly a major component in these birth defects, and there may not be a single answer to this problem. Here, we describe the main features of published studies pointing out their strengths and limitations. Additionally, we give insight into current methods for detecting the presence of interaction between genetic markers and environmental exposures in the etiology of oral clefts.

Molecular basis of familial cleft lip and palate

Cleft lip and palate (CLP) is one of the commonest congenital malformations and although the aetiology is still very unclear, a familial genetic component is considered to be an important factor in certain individuals. Molecular biology techniques are being used to identify the genes involved and this paper reviews current knowledge and the advances that have already been made. Recent evidence suggests a potential major gene on 6p, and a modifying role for transforming growth factor alpha (TGFA). Moreover retinoic acid receptor alpha (RARA) (17q), MSXI (4p), 4q and BCL3 (19q) could all be implicated in certain CLP families. In addition, the potential modifying role of various genes with the environment are considered to be important areas of research in the future. The identification of a genetic locus associated with this disease would be an important advance in CLP genetic counselling and lead to a better understanding of the genetic basis of CLP.

Evidence for an association between nonsyndromic cleft lip with or without cleft palate and a gene located on the long arm of chromosome 4

Recent studies suggest that the familial aggregation of nonsyndromic cleft lip with or without cleft palate (CL +/- P) is likely to be attributable to the effects of several susceptibility loci, acting in a multiplicative fashion. Two potential CL +/- P susceptibility loci (CSL), transforming growth factor alpha (TGFA) and retinoic acid receptor (RARA), have been identified through association studies. In addition, recent evidence of linkage between CL +/- P and two markers (D4S175 and D4S192) in the region 4q25-4q31.3 raised the possibility that a CSL, with a larger effect than either TGFA or RARA, may reside within this region of the human genome. The present analyses were undertaken to determine whether D4S175 or D4S192 is significantly associated with CL +/- P in a sample of unrelated patients that have previously provided evidence of associations between CL +/- P and both TGFA and RARA. The results of these analyses provide further, tentative, evidence for the presence of a CSL locus on the long arm of chromosome 4 and help to refine the location of this locus in the region of D4S175 and D4S192.

Prenatal craniofacial development: new insights on normal and abnormal mechanisms

Technical advances are radically altering our concepts of normal prenatal craniofacial development. These include concepts of germ layer formation, the establishment of the initial head plan in the neural plate, and the manner in which head segmentation is controlled by regulatory (homeobox) gene activity in neuromeres and their derived neural crest cells. There is also a much better appreciation of ways in which new cell associations are established. For example, the associations are achieved by neural crest cells primarily through cell migration and subsequent cell interactions that regulate induction, growth, programmed cell death, etc. These interactions are mediated primarily by two groups of regulatory molecules: "growth factors" (e.g., FGF and TGF alpha) and the so-called steroid/thyroid/retinoic acid superfamily. Considerable advances have been made with respect to our understanding of the mechanisms involved in primary and secondary palate formation, such as growth, morphogenetic movements, and the fusion/merging phenomenon. Much progress has been made on the mechanisms involved in the final differentiation of skeletal tissues. Molecular genetics and animal models for human malformations are providing many insights into abnormal development. A mouse model for the fetal alcohol syndrome (FAS), a mild form of holoprosencephaly, demonstrates a mid-line anterior neural plate deficiency which leads to olfactory placodes being positioned too close to the mid-line, and other secondary changes. Work on animal models for the retinoic acid syndrome (RAS) shows that there is major involvement of neural crest cells. There is also major crest cell involvement in similar syndromes, apparently including hemifacial microsomia. Later administration of retinoic acid prematurely and excessively kills ganglionic placodal cells and leads to a malformation complex virtually identical to the Treacher Collins syndrome. Most clefts of the lip and/or palate appear to have a multifactorial etiology. Genetic variations in TGF alpha s, RAR alpha s, NADH dehydrogenase, an enzyme involved in oxidative metabolism, and cytochrome P-450, a detoxifying enzyme, have been implicated as contributing genetic factors. Cigarette smoking, with the attendant hypoxia, is a probable contributing environmental factor. It seems likely that few clefts involve single major genes. In most cases, the pathogenesis appears to involve inadequate contact and/or fusion of the facial prominences or palatal shelves. Specific mutations in genes for different FGF receptor molecules have been identified for achondroplasia and Crouzon's syndrome, and in a regulatory gene (Msx2) for one type of craniosynostosis. Poorly co-ordinated control of form and size of structures, or groups of structures (e.g., teeth and jaws), by regulatory genes should do much to explain the very frequent "mismatches" found in malocclusions and other dentofacial "deformities". Future directions for research, including possibilities for prevention, are discussed.

Association between alleles of the transforming growth factor alpha locus and cleft lip and palate in the Chilean population

Two RFLPs at the TGFA locus were studied in 39 unrelated Chilean (Caucasoid-Mongoloid) patients with non-syndromic cleft lip/palate [CL(P)] and 51 control individuals. A highly significant association between BamHI A2 allele and CL(P) was detected (chi 2 = 6.00; P = 0.014), while no association was found between TaqI RFLPs and clefting. No significant differences were found when comparing genotypes by type of cleft and a positive or negative family history of clefting. Our results seem to support rather definitively the association between TGFA and clefting but do not support the hypothesis that TGFA is a major causal gene of CL(P).

The major locus for multifactorial nonsyndromic cleft lip maps to mouse chromosome 11

Cleft lip with or without cleft palate, CL(P), a common human birth defect, has a genetically complex etiology. An animal model with a similarly complex genetic basis is established in the A/WySn mouse strain, in which 20% of newborns have CL(P). Using a newly created congenic strain, AEJ.A, and SSLP markers, we have mapped a major CL(P)-causing gene derived from the A/WySn strain. This locus, here named clf1 (cleft lip) maps to Chromosome (Chr) 11 to a region having linkage homology with human 17q21-24, supporting reports of association of human CL(P) with the retinoic acid receptor alpha (RARA) locus.

Prenatal craniofacial development: new insights on normal and abnormal mechanisms

Technical advances are radically altering our concepts of normal prenatal craniofacial development. These include concepts of germ layer formation, the establishment of the initial head plan in the neural plate, and the manner in which head segmentation is controlled by regulatory (homeobox) gene activity in neuromeres and their derived neural crest cells. There is also a much better appreciation of ways in which new cell associations are established. For example, the associations are achieved by neural crest cells primarily through cell migration and subsequent cell interactions that regulate induction, growth, programmed cell death, etc. These interactions are mediated primarily by two groups of regulatory molecules: "growth factors" (e.g., FGF and TGFalpha) and the so-called steroid/thyroid/retinoic acid superfamily. Considerable advances have been made with respect to our understanding of mechanisms involved in primary and secondary palate formation, such as growth, morphogenetic movements, and the fusion/merging phenomenon. Much progress has been made on the mechanisms involved in the final differentiation of skeletal tissues. Molecular genetics and animal models for human malformations are providing many insights into abnormal development. A mouse model for the fetal alcohol syndrome(FAS), a mild form of holoprosencephaly, demonstrates a mid-line anterior neural plate deficiency which leads to olfactory placodes being positioned too close to the mid-line, and other secondary changes. Work on animal models for the retinoic acid syndrome (RAS) shows that there is major involvement of neural crest cells. There is also major crest cell involvement in similar syndromes, apparently including hemifacial microsomia. Later administration of retinoic acid prematurely and excessively kills ganglionic placodal cells and leads to a malformation complex virtually identical to the Treacher Collins syndrome. Most clefts of the lip and/or palate appear to have a multifactorial etiology. Genetic variations in TGF alpha s, RAR alpha s, NADH dehydrogenase, an enzyme involved in oxidative metabolism, and cytochrome P-450, a detoxifying enzyme, have been implicated as contributing genetic factors. Cigarette smoking, with the attendant hypoxia, is a probable contributing environmental factor. It seems likely that few clefts involve single major genes. In most cases, the pathogenesis appears to involve inadequate contact and/or fusion of the facial prominences or palatal shelves. Specific mutations in genes for different FGF receptor molecules have been identified for achondroplasia and Crouzon's syndrome, and in a regulatory gene (Msx2) for one type of craniosynostosis.(ABSTRACT TRUNCATED AT 400 WORDS)

Evidence, from family studies, for linkage disequilibrium between TGFA and a gene for nonsyndromic cleft lip with or without cleft palate

The inheritance of alleles of the transforming growth factor alpha (TGFA) locus has been studied in families affected with cleft lip with or without cleft palate (CL/P), by using the transmission/disequilibrium test described by Spielman and colleagues. Only heterozygous parents with an affected child can be included in this test, but within such families a significantly greater frequency of C2 alleles were transmitted to affected children than would be expected by chance. There was no evidence that the total number of C2 alleles transmitted to affected and unaffected children differed significantly from random segregation. These data provide evidence from within families that a gene for susceptibility to CL/P is in significant linkage disequilibrium with the C2 allele of the TGFA locus.

Association of transforming growth-factor alpha gene polymorphisms with nonsyndromic cleft palate only (CPO)

Genetic analysis and tissue-specific expression studies support a role for transforming growth-factor alpha (TGFA) in craniofacial development. Previous studies have confirmed an association of alleles for TGFA with nonsyndromic cleft lip with or without cleft palate (CL/P) in humans. We carried out a retrospective association study to determine whether specific allelic variants of the TGFA gene are also associated with cleft palate only (CPO). The PCR products from 12 overlapping sets of primers to the TGFA cDNA were examined by using single-strand conformational polymorphism analysis. Four DNA polymorphic sites for TGFA were identified in the 3' untranslated region of the TGFA gene. These variants, as well as previously identified RFLPs for TGFA, were characterized in case and control populations for CPO by using chi 2 analysis. A significant association between alleles of TGFA and CPO was identified which further supports a role for this gene as one of the genetic determinants of craniofacial development. Sequence analysis of the variants disclosed a cluster of three variable sites within 30 bp of each other in the 3' untranslated region previously associated with an antisense transcript. These studies extend the role for TGFA in craniofacial morphogenesis and support an interrelated mechanism underlying nonsyndromic forms of CL/P.

Exclusion of candidate genes from a role in cleft lip with or without cleft palate: linkage and association studies

Candidate genes and marker loci for cleft lip/palate (CL/P) were tested using linkage analyses and association studies. Eight British families with apparent autosomal dominant inheritance of non-syndromic CL/P participated in the linkage analyses while the association analyses involved 61 unrelated British white people with CL/P and 60 controls. The report of an association between RARA (17q21) and unrelated Australian persons with CL/P (p = 0.016) was not confirmed in British CL/P persons (chi 2 = 0.954, p > 0.1). There was also no evidence of linkage between RARA and the eight CL/P families (Z = -3.211, theta = 0.001). Linkage was excluded between familial CL/P and F13A1 (map position 6p24-25) with an observed maximum lod score of Z = -2.052 at theta = 0.05. No association was found between alleles at VIM (10p13) and the British CL/P subjects (chi 2 = 0.110, p > 0.5). Multipoint analysis excluded linkage between familial CL/P and the markers D1S65 and D1S58 which flank the Van der Woude syndrome locus with a maximum lod score of Z = -4.0. This suggests that the genetic defect underlying VWS is not the same as in non-syndromic CL/P. There was no evidence of linkage between CRTL1 (5q15) and the eight CL/P families (Z = -3.466, theta = 0.05).

Genetic variation in transforming growth factor alpha: possible association of BamHI polymorphism with bilateral sporadic cleft lip and palate

Non-syndromic cleft lip with or without cleft palate (CL/P) is one of the most common birth defects affecting 1/1000 Caucasians. Genetic factors are thought to contribute to the development of this disorder. A significant association between two restriction fragment length polymorphisms, the TGF alpha TaqI 2.7-kb allele and the TGF alpha BamHI 40-kb allele, at the transforming growth factor alpha (TGF alpha) locus and the occurrence of clefting has previously been reported. A total of 98 Caucasian patients of Alsacian ancestry was recruited from our registry of congenital malformations. These patients had isolated CL/P but no other anomalies. In addition 57 patients with cleft palate, but without cleft lip, were studied. A control group comprised 99 unrelated healthy Caucasians of the same Alsacian ancestry. TaqI and BamHI identify two-allele polymorphisms. The TGFA Taq and BamHI alleles showed no significant association with the presence of clefting, the only exception being that the BamHI 10.0-kb allele was significantly more frequent in patients with bilateral CL/P.

Cleft lip with or without cleft palate: associations with transforming growth factor alpha and retinoic acid receptor loci

The first association study of cleft lip with or without cleft palate (CL/P), with candidate genes, found an association with the transforming growth-factor alpha (TGFA) locus. This finding has since been replicated, in whole or in part, in three independent studies. Here we extend our original analysis of the TGFA TaqI RFLP to two other TGFA RFLPs and seven other RFLPs at five candidate genes in 117 nonsyndromic cases of CL/P and 113 controls. The other candidate genes were the retinoic acid receptor (RARA), the bcl-2 oncogene, and the homeobox genes 2F, 2G, and EN2. Significant associations with the TGFA TaqI and BamHI RFLPs were confirmed, although associations of clefting with previously reported haplotypes did not reach significance. Of particular interest, in view of the known teratogenic role of retinoic acid, was a significant association with the RARA PstI RFLP (P = .016; not corrected for multiple testing). The effect on risk of the A2 allele appears to be additive, and although the A2A2 homozygote only has an odds ratio of about 2 and recurrence risk to first-degree relatives (lambda 1) of 1.06, because it is so common it may account for as much as a third of the attributable risk of clefting. There is no evidence of interaction between the TGFA and RARA polymorphisms on risk, and jointly they appear to account for almost half the attributable risk of clefting.

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

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