Exploring parent-of-origin effects for non-syndromic cleft lip with or without cleft palate on PTCH1, PTCH2, SHH, SMO genes in Chinese case-parent trios / 北京大学学报(医学版)

OBJECTIVE@#Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect, affecting 1.4 per 1 000 live births, and multiple genetic and environmental risk factors influencing its risk. All the known genetic risk factors accounted for a small proportion of the heritability. Several authors have suggested parent-of-origin effects (PoO) may play an important role in the etiology of this complex and heterogeneous malformation. To clarify the genetic association between PTCH1, PTCH2, SHH and SMO in hedgehog (HH) pathway and NSCL/P, as well as testing for potential PoO effects in Chinese case-parent trios.@*METHODS@#We tested for transmission disequilibrium tests (TDT) and PoO effects using 83 common single nucleotide polymorphic (SNP) markers of HH pathway genes from 806 NSCL/P case-parent trios. These trios were drawn from an international consortium established for a genome-wide association studies (GWAS) of non-syndromic oral clefts of multiple ethnicities. DNA samples were collected from each trio. Single marker and haplotype based analysis were performed both in TDT tests and PoO effects. SNPs were excluded if they (ⅰ) had a call rate of < 95%, (ⅱ) had a minor allele frequency (MAF) of < 0.05, (ⅲ) had Mendelian errors over all trios of >5%, (ⅳ) had a genotype distribution in the parents that deviated from the Hardy-Weinberg equilibrium (HWE) (<i>P</i> < 0.000 1). The process was done using Plink (version 1.07, <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml</a>). TDT test was performed in Plink v1.07. A log-linear model was used to explore PoO effects using Haplin v6.2.1 as implemented in R package v3.4.2. Significance level was assessed using the Bonferroni correction.@*RESULTS@#A total of 18 SNPs were dropped due to low MAF, thus leaving 65 SNPs available for the analysis. Thus the Bonferroni threshold was 7.7×10-4 (0.05/65). Nominal significant association with NSCL/P was found at a SNP (rs4448343 in PTCH1, P=0.023) and six haplotypes (rs10512249-rs4448343, rs1461208-rs7786445, rs10512249-rs4448343, rs16909865-rs10512249-rs4448343, rs1461208-rs7786445-rs12698335, and rs288756-rs288758-rs1151790, P < 0.05). A total of six haplotypes (rs288765-rs1233563, rs12537550-rs11765352, rs872723-rs288765-rs1233563, rs288765-rs1233563-rs288756, rs6459952-rs12537550-rs11765352, and rs12537550-rs11765352-rs6971211) showed PoO effect (P < 0.05). None of the results remained significant after the Bonferroni correction (P>7.7×10-4).@*CONCLUSION@#Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.

Association of single nucleotide polymorphisms in AXIN2, BMP4, and IRF6 with Non-Syndromic Cleft Lip with or without Cleft Palate in a sample of the southeast Iranian population

Abstract Non-syndromic cleft lip with or without palate (NSCL/P) is a common congenital malformation worldwide, with complex etiology. It has been proposed that interaction of genes and environmental factors play a role in the predisposition to this disease. Objectives: The aim of this study was to examine the association between AXIN2 (axis inhibition protein 2) rs7224837, BMP4 (bone morphogenetic protein 4) rs17563, and IRF6 (interferon regulatory factor 6) rs861019 and 2235371 polymorphisms and NSCL/P in an Iranian population. Material and Methods: This case-control study was carried out on 132 unrelated NSCL/P patients and 156 healthy subjects. The variants were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results: The findings suggest that BMP4 rs17563 polymorphism significantly decreased the risk of NSCL/P in codominant (OR=0.36, 95%CI=0.17-0.79, p=0.012, CT vs CC and OR=0.11, 95%CI=0.01-0.88, p = 0.019, TT vs CC), dominant (OR=0.30, 95%CI=0.15-0.62, p = 0.0007, CT+TT vs CC), recessive (OR=0.12, 95%CI=0.02-0.99, p = 0.023, TT vs CC+CT), overdominant (OR=0.39, 95%CI = 0.18-0.84, p=0.021, CT vs CC+TT), and allele (OR=0.28, 95%CI=0.15-0.55, p<0.0001, T vs C) inheritance models. Our findings did not support an association between AXIN2 rs7224837 and IRF6 rs861019 polymorphism and risk/protection of NSCL/P. The IRF6 2235371 variant was not polymorphic in our population. Conclusion: The results indicate that the BMP4 rs17563 variant is likely to confer a protective effect against the occurrence of NSCL/P in a sample of the southeast Iranian population.

Association between non-syndromic cleft lip with or without cleft palate and environmental factors in Ningxia / 华西口腔医学杂志

<p><b>OBJECTIVE</b>To investigate the association between non-syndromic cleft lip with or without cleft palate (NSCL/P) and environmental factors in Ningxia population.</p><p><b>METHODS</b>This case-control study involved 453 NSCL/P patients and 452 normal newborns from Ningxia. A questionnaire focusing on various factors, including family history, pregnancy reaction, drug use during pregnancy, and infections, was used and responses were analyzed through Chi-square test and Logistic regression analysis with SPSS 16.0.</p><p><b>RESULTS</b>The constituent ratio of different types of NSCL/P was cleft lip∶cleft lip and palate∶cleft palate equal to 1︰2.02︰1.51. Logistic regression analysis revealed that abnormal pregnancy, infection, abortion, drugs, drinking, smoking, and living near factories likely increased the risk of NSCL/P (P<0.05). Single fetus, pregnancy-related nausea, vomiting, parents' moderate tastes, and eating soy foods and fruits decreased the risk of NSCL/P (P<0.05).</p><p><b>CONCLUSIONS</b>The incidence of NSCL/P should be reduced to enhance the conditions of women during pregnancy by maintaining a balanced diet and avoiding infections, abortion, drugs, and negative habits. 
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Research progress on susceptible gene loci of non-syndromic cleft lip with or without deft palate / 国际儿科学杂志

Non-syndromic cleft lip with or without cleft palate is a common birth defect with complex causes,now widely considered as the result of interactions between genetic and environmental factors.Susceptible genes of congenital cleft lip with or without cleft palate have become a focus since the whole genome sequencing was available.Numerous candidate genes which were screened out are being constantly validated by gene polymorphism detection,case-control study and meta analysis.But the results are inconsistent.In this article,we review the research progress on susceptible genes of non-syndromic cleft lip with or without cleft palate and the relationship between environmental factors and cleft lip with or without palate in recent years.

The association of MAFB gene polymorphism with nonsyndromic cleft lip with or without cleft palate in Ningxia Hui and Han population / 实用口腔医学杂志

Objective:To study the association between non-syndrome cleft lip and palate (NSCL/P)and MAFB (rs6072081, rs6065259,rs17820943,rs11696257)gene polymorphism in NingXia Hui and Han population.Methods:512 cases of NSCL/P,258 case of Hui nationality and 254 of Han,174 cases of complete 3 core family members(patients and their parents),142 cases of single parents families(patients and their single parents),were collected in patient group.505 cases of healthy newborns were collected in control group.The MAFB gene SNPs were determined with TaqMan SNPs genotyping methods and the data were analyzed by case-con-trol analysis,transmission disequilibrium test(TDT)and family based association test(FBAT).Results:Case-control analysis found that,there was a statistical significance of the genotypes and allele frequency between patients and the controls in MAFB of the 4 locus (P 0.05).Conclusion:The 4 locus single nucle-otide polymorphism was associated with NSCL/P in Ningxia population.