A polymorphic marker associated with non-syndromic cleft lip with or without cleft palate in a population in Heilongjiang Province, northern China

Polymorphisms of ATP-Binding Cassette, Sub-Family A, Member 4 (rs560426 and rs481931) and Non-Syndromic Cleft Lip/Palate: A Meta-Analysis

Background: A number of genes are associated with the incidence of non-syndromic cleft lip/palate (NSCL/P). Studies have shown a significant association between polymorphisms of ATP-binding cassette, sub-family A, member 4 (ABCA4) with the risk of NSCL/P. The present meta-analysis assessed the association between ABCA4 polymorphisms (rs560426 and rs481931) and the NSCL/P risk by reviewing case-control studies. Methods: Four databases (Scopus; Cochrane Library; Web of Science; and PubMed) were searched for articles published up to June 2020. The Review Manager 5.3 software was used to calculate the crude odds ratio (OR) and 95% confidence interval (CI). Both subgroup analyses for ethnicity and source of controls and a meta-regression related to publication year were conducted. Results: Of 94 retrieved studies, 12 were analyzed in this meta-analysis (2859 NSCL/P patients and 3792 controls for ABCA4 rs560426 polymorphism and 1333 NSCL/P patients and 1884 controls for ABCA4 rs481931 polymorphism). Overall, there was no significant association between both polymorphisms and the risk of NSCL/P. However, subgroup analysis demonstrated that there was a higher risk of NSCL/P for specific models: the allelic model (OR = 1.13; p = 0.03), the homozygote model (OR = 1.53; p = 0.04), and the recessive model (OR = 1.30; p = 0.03) in the Asian ethnicity for the rs560426 polymorphism. Conclusion: The findings confirmed that the NSCL/P risk was significantly associated with the G allele and GG genotype of rs560426 polymorphism but not for rs481931 polymorphism. There were no associations between both polymorphisms (rs560426 and rs481931) and the NSCL/P risk in those of European descent and the mixed ethnicities.

Genetic Factors in Nonsyndromic Orofacial Clefts

Orofacial clefts (OFCs) are the most common congenital birth defects in humans and immediately recognized at birth. The etiology remains complex and poorly understood and seems to result from multiple genetic and environmental factors along with gene-environment interactions. It can be classified into syndromic (30%) and nonsyndromic (70%) clefts. Nonsyndromic OFCs include clefts without any additional physical or cognitive deficits. Recently, various genetic approaches, such as genome-wide association studies (GWAS), candidate gene association studies, and linkage analysis, have identified multiple genes involved in the etiology of OFCs. This article provides an insight into the multiple genes involved in the etiology of OFCs. Identification of specific genetic causes of clefts helps in a better understanding of the molecular pathogenesis of OFC. In the near future, it helps to provide a more accurate diagnosis, genetic counseling, personalized medicine for better clinical care, and prevention of OFCs.

Environmental mechanisms of orofacial clefts

Orofacial clefts (OFCs) are among the most common birth defects and impart a significant burden on afflicted individuals and their families. It is increasingly understood that many nonsyndromic OFCs are a consequence of extrinsic factors, genetic susceptibilities, and interactions of the two. Therefore, understanding the environmental mechanisms of OFCs is important in the prevention of future cases. This review examines the molecular mechanisms associated with environmental factors that either protect against or increase the risk of OFCs. We focus on essential metabolic pathways, environmental signaling mechanisms, detoxification pathways, behavioral risk factors, and biological hazards that may disrupt orofacial development.

The SNP rs560426 Within ABCA4-ARHGAP29 Locus and the Risk of Nonsyndromic Oral Clefts

OBJECTIVE

Nonsyndromic oral clefts are common birth defect with complex etiology. In the present study, we attempt to further validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts.

DESIGN

We performed allelic transmission disequilibrium test analysis, on 10 eligible single nucleotide polymorphisms (SNPs) and SNP haplotypes using the Family-Based Association Test.

PARTICIPANTS

The study sample consisted of 334 case-parent trios of nonsyndromic oral clefts from Taiwanese population, separated into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO) groups.

RESULTS

We found only the SNP rs560426 within the ABCA4 gene showed strong association with NSCPO (P = .03498; Permuted P = .05382). No association between other 9 selected SNPs in ABCA4-ARHGAP29 region and the risk of nonsyndromic oral clefts was found. For the haplotype analyses, we found only haplotype T-C (rs570926 and rs3789431) in ABCA4 block 2 showed significant association with nonsyndromic NSCL/P in these Taiwanese trios.

CONCLUSIONS

We used a family-based analysis in 334 Taiwanese case-parent trios to validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. This study provides a new evidence for an association between the intron variant rs560426 within ABCA4 and nonsyndromic cleft palate which may contribute their regulatory role in craniofacial development.

Investigation of candidate genes of non-syndromic cleft lip with or without cleft palate, using both case-control and family-based association studies

OBJECTIVE

Non-syndromic cleft of the lip and/or palate (NSCL/P) is one of the most common polygenic diseases. In this study, both case-control and family-based association study were used to confirm whether the Single Nucleotide Polymorphisms (SNPs) were associated with NSCL/P.

METHODS

A total of 37 nuclear families and 189 controls were recruited, whose blood DNA was extracted and subjected to genotyping of SNPs of 27 candidate genes by polymerase chain reaction-improved multiple ligase detection reaction technology (PCR-iMLDR). Case-control statistical analysis was performed using the SPSS 19.0. Haplotype Relative Risk (HRR), transmission disequilibrium test (TDT), and Family-Based Association Test (FBAT) were used to test for over-transmission of the target alleles in case-parent trios. The gene-gene interactions on NSCL/P were analyzed by Unphased-3.1.4.

RESULTS

In case-control statistical analysis, only C14orf49 chr14_95932477 had statistically significant on genotype model (P = .03) and allele model (P = .03). Seven SNPs had statistically significant on TDT. None of 26 alleles has association with NSCL/P on FBAT. Some SNPs had haplotype-haplotype interactions and genotype-genotype interactions.

CONCLUSION

C14orf49 chr14_95932477 was significantly different between cases and controls on genotype model and allele model by case-control design. Seven SNPs were significantly different on HRR. Four SNPs were significantly different on TDT.