Replication of two novel susceptibility loci for non-syndromic orofacial clefts in a Chinese population

Association Between Nonsyndromic Cleft Lip and Palate and 2 Polymorphic Loci: A Meta-Analysis

OBJECTIVES

The relationship between Noggin (NOG) and methylenetetrahydrofolate reductase and nonsyndromic cleft lip and palate (NSCLP) has been reported participate in craniofacial development but need further evidence. To indicate the susceptibility between the 2 genes and NSCLP, rs227731 and rs1801131 polymorphisms were included in the present research. This research may provide some genetic clues for disease detection and surveillance.

DESIGN

Seventeen studies including 4023 cases and 5691 controls were provided for meta-analysis, and odds ratio (OR) with 95% CI were obtained to estimate NSCLP risk.

RESULTS

Our analysis suggested potential association of rs227731C on increasing the risk of NSCLP in the Caucasian group and total group but not Asian group under all models: allele (OR = 1.45, 95% CI = 1.21-1.75, P < .0001), homozygote (OR = 2.03, 95% CI = 1.42-2.90, P < .0001), heterozygote (OR = 1.44, 95% CI = 1.19-1.73, P = .0001), dominant (OR = 1.61, 95% CI = 1.27-2.04, P < .0001), and recessive models (OR = 1.63, 95% CI = 1.25-2.12, P = .0003). Besides, increased risk is related to rs1801131 in Asian group under 3 models: allele (OR = 1.24, 95% CI = 1.06-1.44, P = .006), heterozygote (OR = 1.24, 95% CI = 1.02-1.52, P = .03), and dominant models (OR = 1.29, 95% CI = 1.06-1.56, P = .009).

CONCLUSIONS

Our analysis indicates polymorphisms rs227731 and rs1801131 are associated with NSCLP, with predominance of different ethnic group and deepen understanding of NSCLP.

Genetic variants of MGMT, RHPN2, and FAM49A contributed to susceptibility of nonsyndromic orofacial clefts in a Chinese population

BACKGROUND

The role of underlying genetic factors in the pathogenesis of nonsyndromic orofacial clefts (NSOC) remains poorly understood. Although genomewide association studies (GWASs) of NSOC have successfully identified a large number of novel genetic risk loci, association results of replication studies are inconsistent across different populations.

METHODS

Six single nucleotide polymorphisms (SNPs) (rs7922405 at 10q26.3, rs73039426 at 19q13.11, rs7552 at 2p24.2, rs1788160 at 8q22.2, rs9381107 at 6p24.3, and rs17095681 at 10q25.3) were analyzed for an association with NSOC in 1062 participants of Chinese descent (596 patients and 466 controls). We applied the multifactor dimensionality reduction (MDR) method to detect potential gene-gene (G × G) interactions in the six SNPs.

RESULTS

The genotype or allele frequencies of SNPs rs7922405, rs73039426, and rs7552 showed significant differences between the controls and patients with NSOC, whereas no association was shown between three SNPs (rs1788160, rs17095681, and rs9381107) and NSOC. MDR analysis did not reveal significant G × G interactions for susceptibility to NSOC.

CONCLUSION

We confirmed that three genes (rs7922405 of MGMT, rs73039426 of RHPN2, and rs7552 of FAM49A) may contribute to NSOC in Chinese populations. MGMT and RHPN2 are associated with NSOC, which is herein demonstrated for the first time.

Polymorphic variants in VAX1 and the risk of nonsyndromic cleft lip with or without cleft palate in a population from northern China

BACKGROUND

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common craniofacial birth defects, and the etiology of NSCL/P involves both genetic and environmental factors. Genome-wide association study (GWAS) identified a novel susceptibility locus of ventral anterior homeobox 1 (VAX1) in patients with NSCL/P. However, the association of single nucleotide polymorphisms (SNPs) of VAX1 with NSCL/P is inconclusive due to the differences in the racial and ethnic populations. The aim of this study was to replicate the association between VAX1 and NSCL/P in a northern Chinese Han population.

METHODS

Our study included 186 patients with NSCL/P and 223 healthy individuals from northern China. Five SNPs (rs4752028, rs10787760, rs7078160, rs6585429, and rs1871345) on VAX1 were genotyped using the SNaPshot method.

RESULTS

Recessive genetic model analysis revealed that homozygous genotype CC of VAX1 rs4752028 was associated with an increased risk of NSCL/P (odds ratio = 1.89, 95% confidence interval = 1.12-3.19, P = 0.017), but the results were not significant after the Bonferroni correction for multiple comparisons. The allele and genotype frequencies of rs10787760, rs7078160, rs6585429, and rs1871345 and the allele frequencies of rs4752028 showed no significant differences between cases and controls. Haplotype and SNP-SNP interaction analyses did not detect any significant association of VAX1 with the occurrence of NSCL/P.

CONCLUSION

VAX1 rs4752028 was weakly associated with NSCL/P development in the studied northern Chinese Han population.

Associations between the NOGGIN rs227731 polymorphism and NSCL/P risk may be associated with ethnicities: A meta-analysis

BACKGROUND

The aim of this study was to evaluate the association between the noggin rs227731 polymorphism on chromosome 17q22 and risk of nonsyndromic cleft lip with or without palate (NSCL/P).

METHODS

Three online databases were searched, including Embase, PubMed, and Chinese National Knowledge Infrastructure. The strength of the associations was evaluated by odds ratios (ORs) and 95% confidence intervals (CIs). We also made a subgroup analysis to explore sources of heterogeneity.

RESULTS

Nine comparisons from seven studies were included in this meta-analysis. We used five genetic models and found that the noggin rs227731 polymorphism may increase NSCL/P risk in Caucasians: C versus A: OR = 1.43, 95% CI, 1.30-1.58; CC versus AA: OR = 2.00, 95% CI, 1.59-2.52; CA versus AA: OR = 1.50, 95% CI, 1.27-1.77; CC+CA versus AA: OR = 1.64, 95% CI, 1.40-1.92; CC versus CA+AA: OR = 1.56, 95% CI, 1.30-1.87. However, for the Chinese population, no significant association between the rs227731 polymorphism and NSCL/P risk was found: C vs. A: OR = 1.04, 95% CI, 0.81-1.33; CC vs. AA: OR = 1.01, 95% CI, 0.52-1.95; CA vs. AA: OR = 1.03, 95% CI, 0.75-1.40; CC+CA vs. AA: OR = 1.04, 95% CI, 0.76-1.43; CC vs. CA+AA: OR = 1.01, 95% CI, 0.56-1.81.

CONCLUSION

Our meta-analysis suggested that the rs227731 polymorphism may increase NSCL/P risk in Caucasians and may have no significant association in the Chinese population. Effects of individual and environmental risk factors and of gene-environment interactions may play a different role in Caucasians than in the Chinese population. More relevant case-control studies are required to obtain more precise results. Birth Defects Research 109:445-451, 2017. © 2017 Wiley Periodicals, Inc.

Is Chromosome 15q13.3 Duplication Involving CHRNA7 Associated With Oral Clefts?

Copy number variants have been associated with intellectual disability, multiple congenital anomalies and craniofacial disorders. It has been reported that microduplication of 15q13.3 is associated with autism, cognitive impairment, seizures, and attention-deficit hyperactivity disorder. Here, the author identified microduplications in the 15q13.3 region in 4 cases from 3 Chinese families using chromosomal microarray analysis-single nucleotide polymorphism array (CMA-SNP). These 4 cases include 2 fetuses from 2 unrelated families and a father and a daughter from a third family. The identified microduplications of 15q13.3 are approximately 400 kb in size, encompassing just 1 gene, cholinergic receptor, neuronal nicotinic, alpha polypeptide 7 (CHRNA7). Three-fourths of the probands exhibit oral clefts, which has not been previously reported in cases with this duplication genotype. Therefore, in this study, the author describes for the first time the common feature of oral clefts in patients carrying a microduplication of 15q13.3 encompassing the CHRNA7 gene, which sheds light on the correlation between CHRNA7 and cleft palate.

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.

Analysis of susceptibility polymorphisms for nonsyndromic cleft lip with or without cleft palate in the Brazilian population

BACKGROUND

Although genome-wide association studies have identified several susceptibility loci for nonsyndromic cleft lip with or without cleft palate (NSCL/P) in populations around the world, the role of most loci is unknown in the highly heterogeneous Brazilian population.

METHODS

To determine the association of 7 markers that showed genome-wide significant association in Brazilians with NSCL/P, we conducted a structured association study conditioned upon the individual ancestry proportions to evaluate markers at 1p36 (rs742071), 2p21 (rs7590268), 3p11.1 (rs7632427), 8q21.3 (rs12543318), 13q31.1 (rs8001641), 15q22.2 (rs1873147), and 17q22 (rs227731) in 505 patients with NSCL/P and 594 healthy controls recruited from 2 different geographical regions of Brazil. The polymorphisms were genotyped by TaqMan 5'-exonuclease allelic discrimination assay, and each sample was independently typed for 40 biallelic short insertion/deletion markers to characterize the genomic ancestry.

RESULTS

After Bonferroni correction for multiple tests, significant associations with NSCL/P were observed for rs742071, rs1873147, and rs227731. However, the frequency of the risk alleles varied between the geographical regions, according to the proportions of European and African genomic ancestry. The group enriched by European ancestry showed significant association with rs227731 (p = 0.001), whereas the group with high African ancestry was significantly associated with rs1873147 polymorphism (p = 0.005). The significant association with rs742071 was only detected in the combined sample (p = 0.005).

CONCLUSION

The findings of the present study revealed the associations of 1p36 (rs742071), 15q22 (rs1873147), and 17p22 (rs227731) with NSCL/P in the Brazilian population, and further confirmed that the genetic heterogeneity of NSCL/P may be related to the different ethnic background of the affected individuals.

Polymorphisms in FGF12, VCL, CX43 and VAX1 in Brazilian patients with nonsyndromic cleft lip with or without cleft palate

BACKGROUND

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common orofacial birth defect with a wide range prevalence among different populations. Previous association studies with populations from Europe and Asia have identified putative susceptibility markers for NSCL/P in fibroblast growth factor 12 (FGF12), vinculin (VCL), connexin 43 (CX43) and in a region close to the ventral anterior homeobox 1 (VAX1) gene. However, there have thus far been no studies of these markers in NSCL/P Brazilian patients, and as the genetic ancestry of the Brazilian population is highly varied, the predisposition to those disease markers can be different.

METHODS

Herein we conducted a structured association study conditioned on the individual ancestry proportions to determine the role of 16 polymorphic markers within those genes in 300 patients with NSCL/P and 385 unaffected controls.

RESULTS

None of the alleles and genotypes showed association with NSCL/P, though there was a significant association of the haplotype formed by VAX1 rs10787760, rs6585429 and rs1871345 polymorphisms with NSCL/P that did not persist Bonferroni correction for multiple tests.

CONCLUSIONS

Our results are consistent with a lack of involvement of FGF12, VCL and CX43 variants with NSCL/P pathogenesis in Brazilian patients. Furthermore, the higher frequency of a haplotype of VAX1 with NSCL/P patients suggests a low penetrant gene for oral cleft, and warrants further studies.

Resequencing of VAX1 in patients with nonsyndromic cleft lip with or without cleft palate

BACKGROUND

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common of all congenital anomalies, and has a multifactorial etiology involving both environmental and genetic factors. Recent genome-wide association studies (GWAS) identified strong association between a locus on chromosome 10q25.3 and NSCL/P in European samples. One gene at 10q25.3, the ventral anterior homeobox 1 (VAX1) gene, is considered a strong candidate gene for craniofacial malformations. The purpose of the present study was to provide further evidence that VAX1 is the causal gene at the 10q25.3 locus through identification of an excess of rare mutations in patients with NSCL/P.

METHODS

The 5'UTR, complete coding regions, and adjacent splice sites of the two known VAX1 isoforms were sequenced in 384 patients with NSCL/P and 384 controls of Central European descent. Observed variants were investigated with respect to familial cosegregation or de novo occurrence, and in silico analyses were performed to identify putative effects on the transcript or protein level.

RESULTS

Eighteen single-base variants were found, 15 of them rare and previously unreported. In the long VAX1 isoform, predicted functionally relevant variants were observed more often in NSCL/P cases, although this difference was not significant (p = 0.17). Analysis of family members demonstrated incomplete cosegregation in most pedigrees.

CONCLUSION

Our data do not support the hypothesis that highly penetrant rare variants in VAX1 are a cause of NSCL/P. To determine whether VAX1 is the causative gene at 10q25.3 further research, in particular into the biologic function of its long isoform, is warranted. Birth Defects Research (Part A), 2012.