Association between the JAG2 gene polymorphism and the occurrence of nonsyndromic cleft lip with or without cleft palate in northwest Chinese population / 中华医学遗传学杂志

Objective@#To assess the association of JAG2 gene single nucleotide polymorphisms with the occurrence of nonsyndromic cleft lip with or without cleft palate (NSCLP) among northwest Chinese population.@*Methods@#A case-control study was carried out on 301 NSCLP patients and 304 healthy controls. An iMLDR™ genotyping technique was used to detect three single nucleotide polymorphisms (SNPs) [rs741859 (T/C), rs11621316 (A/G) and rs1057744(C/T)] of the JAG2 gene. Allelic and genotypic frequencies and haplotypic distribution among the two groups were compared.@*Results@#A significant difference was found in the frequency of C and T alleles for rs741859 between the two groups. The CT genotype of rs741859 could significantly reduce the risk for NSCLP to 65% (P < 0.05) and the risk for cleft lip with or without cleft palate (CL/P) to 62% (P < 0.05). rs11621316 and rs1057744 are in the same linkage disequilibrium (LD) region with a high degree of linkage (r2 > 0.8), whose distribution difference between the two groups was not statistically significant (P > 0.05).@*Conclusion@#The CT genotype of the JAG2 gene rs741859 may confer a protective effect for NSCLP among northwest Chinese population.

Association between platelet-derived growth factor-C single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate in Western Chinese population / 华西口腔医学杂志

OBJECTIVE@#To explore the association between two single nucleotide polymorphisms (SNPs), namely, rs4691383 and rs7667857, in the platelet-derived growth factor-C (PDGF-C) gene, the genotypes, environmental exposure factors, and nonsyndromic cleft lip with or without cleft palate (NSCL/P) in Western Chinese population.@*METHODS@#A total of 268 case-parent trios were selected, and two SNPs (rs4691383 andrs7667857) were genotyped by using polymerase chain reaction and restriction enzyme fragment length polymorphic method and direct sequencing method. Hardy-Weinberg equilibrium, linkage disequilibrium test, transmission disequilibrium test, and haplotype analysis were conducted to analyze the data. Meanwhile, the questionnaires on the epidemiology of cleft lip and palate filled by the included samples were collected, and the interaction between the genotypes of the two SNPs and environmental exposure factors was assessed by conditional logistic regression.@*RESULTS@#The A allele at rs4691383 and the G allele at rs7667857 of PDGF-C gene were over-transmitted for NSCL/P (P0.05).@*CONCLUSIONS@#The rs4691383 and rs7667857 at PDGF-C gene are closely related to the occurrence of NSCL/P in Western Chinese population. However, the interaction between environmental exposure factors and PDGF-C genotypes is not obvious in the occurrence of NSCL/P.

Associations among PRDM16 polymorphisms, environmental exposure factors during mother's pregnancy, and nonsyndromic cleft lip with or without cleft palate / 华西口腔医学杂志

OBJECTIVE@#We aimed to study the association between rs7525173, rs2236518, rs2493264 single nucleotide polymorphism (SNP) in the PRDM16 gene, smoking, alcohol exposures, and nonsyndromic cleft lip with or without cleft palate (NSCL/P).@*METHODS@#A total of 157 case-parent trios were selected, and SNPs were genotyped by using ligase detection reaction (LDR) and direct sequencing methods. Transmission disequilibrium test (TDT) and linkage disequilibrium (LD) tests were con-ducted to analyze the data. A total of 1 710 patients with orofacial clefts and 956 healthy newborns were enrolled in the epidemiological survey. The smoking and drinking exposures of parents during early pregnancy were analyzed.@*RESULTS@#The C allele at rs2236518 was over-transmitted for NSCPO (P<0.05). Statistical differences were observed among three factors, namely, maternal smoking, maternal passive smoking, and maternal drinking (P<0.05).@*CONCLUSIONS@#The rs2236518 at PRDM16 gene, maternal smoking, maternal passive smoking, and maternal drinking were closely related to the occurrence of NSCL/P.

Genome-Wide Screening of Aberrant Methylation Loci for Nonsyndromic Cleft Lip / 中华医学杂志(英文版)

Background@#The pathogenicity of cleft lip (CL) is pretty complicated since it is influenced by the interaction of environment and genetic factors. The purpose of this study was to conduct a genome-wide screening of aberrant methylation loci in partial lesion tissues of patients with nonsyndromic CL (NSCL) and preliminarily validate candidate dysmethylated genes associated with NSCL.@*Methods@#Fifteen healthy and sixteen NSCL fetal lip tissue samples were collected. The Infinium HumanMethylation450 BeadChip was used to screen aberrant methylation loci in three NSCL and three healthy lip tissues. The differential methylation sites and functions of the annotated genes between NSCL and healthy lip tissues were analyzed using minfi package of R software, cluster analysis, Gene Ontology (GO) annotation, and metabolic pathway annotation. Gene expression was assessed in nine differentially methylated genes by real-time polymerase chain reaction (PCR). The transcriptions mRNA levels of three out of nine candidate genes were downregulated remarkably in NSCL lip tissues, and these three genes' abnormal methylation loci were validated by pyrosequencing in 16 NSCL cases and 15 healthy cases.@*Results@#In total, 4879 sites in the genes of NSCL odinopoeia fetuses showed aberrant methylation when compared with normal lip tissue genome. Among these, 3661 sites were hypermethylated and 1218 sites were hypomethylated as compared to methylation levels in healthy specimens. These aberrant methylation sites involved 2849 genes and were widely distributed among the chromosomes. Most differentially methylated sites were located in cytosine-phosphoric acid-guanine islands. Based on GO analysis, aberrantly methylated genes were involved in 11 cellular components, 13 molecular functions, and a variety of biological processes. Notably, the transcription of DAB1, REELIN, and FYN was significantly downregulated in lesion tissues of NSCL fetus (P < 0.05). Pyrosequencing results validated that there were two loci in DAB1 with high methylation status in patient tissues (P < 0.05).@*Conclusions@#We detected numerous aberrantly methylated loci in lesion tissues of NSCL fetus. Aberrant gene expression in the REELIN signaling pathway might be related with NSCL. Decreased transcription of DAB1, a member of REELIN signal pathway, resulted from its abnormal high methylation, which might be one of the factors underlying the occurrence of NSCL.

The 19-bp deletion polymorphism of dihydrofolate reductase (DHFR) and nonsyndromic cleft lip with or without cleft palate: evidence for a protective role

Objective Nonsyndromic cleft lip with or without cleft palate (NS-CL/P) are among the most common congenital birth defects worldwide. Several lines of evidence point to the involvement of folate, as well as folate metabolizing enzymes in risk reduction of orofacial clefts. Dihydrofolate reductase (DHFR) enzyme participates in the metabolic cycle of folate and has a crucial role in DNA synthesis, a fundamental feature of gestation and development. A functional polymorphic 19-bp deletion within intron-1 of DHFR has been associated with the risk of common congenital malformations. The present study aimed to evaluate the possible association between DHFR 19-bp deletion polymorphism and susceptibility to NS-CL/P in an Iranian population. Material and Methods The current study recruited 100 NS-CL/P patients and 100 healthy controls. DHFR 19-bp deletion was determined using an allele specific-PCR method. Results We observed the DHFR 19-bp homozygous deletion genotype (D/D) vs. homozygous wild genotype (WW) was more frequent in controls than in NS-CL/P patients (25% vs. 13%), being associated with a reduced risk of NS-CL/P in both codominant (OR=0.33, P=0.027) and recessive (OR=0.45, P=0.046) tested inheritance models. We also stratified the cleft patients and reanalyzed the data. The association trend for CL+CL/P group compared to the controls revealed that the DD genotype in both codominant (OR=0.30, P=0.032) and recessive models (OR=0.35, P=0.031) was associated with a reduced risk of CL+CL/P. Conclusions Our results for the first time suggested the DHFR 19-bp D/D genotype may confer a reduced risk of NS-CL/P and might act as a protective factor against NS-CL/P in the Iranian subjects. .

Association between MSX1 SNPs and Nonsyndromic Cleft Lip with or without Cleft Palate in the Korean Population

The purpose of this study was to investigate the contribution of MSX1 gene to the risk of nonsyndromic cleft lip with or without cleft palate (NS-CL +/- P) in the Korean population. The samples consisted of 142 NS-CL +/- P families (9 with cleft lip, 26 with cleft lip and alveolus, and 107 with cleft lip and palate; 76 trios and 66 dyads). Three single nucleotide polymorphisms (SNPs: rs3821949, rs12532, and rs4464513) were tested for association with NS-CL +/- P case-parent trios using transmission disequilibrium test (TDT) and conditional logistic regression models (CLRMs). Minor allele frequency, heterozygosity, chi2 test for Hardy-Weinberg equilibrium, and pairwise linkage disequilibrium (LD) at each SNP were computed. The family- and haplotype-based association test programs were used to perform allelic and genotypic TDTs for individual SNPs and to fabricate sliding windows of haplotypes. Genotypic odds ratios (GORs) were obtained from CLRMs using R software. Although the family-based TDT indicated a meaningful association for rs3821949 (P = 0.028), the haplotype analysis did not reveal any significant association with rs3821949, rs12532, or rs4464513. The A allele at rs3821949 had a significant increased risk of NS-CL +/- P (GOR, 1.64; 95% confidence interval,1.03-2.63; P = 0.038, additive model). A positive association is suggested between MSX1 rs3821949 and NS-CL +/- P in the Korean population.

Análisis molecular de Sonic hedgehog (Shh) en la etiología de la fisura labiopalatina no sindrómica en tríos caso-progenitores chilenos / Molecular analysis of Sonic hedgehog (Shh) in the etiology of nonsyndromic cleft lip and palate in Chilean case-parent trios

introducción: la fisura labio palatina no sindrómica, NSCLP (del inglés Nonsyndromic cleft lip and palate) es una de las malformaciones congénitas más frecuentes tanto en Chile como en el resto del mundo. Presenta un modo de herencia multifactorial, en la que interactúan varios genes y el medio ambiente. Evidencias experimentales han demostrado la participación de Sonic hedgedhog (Shh) en la migración de las células de la cresta neural, en la transformación epitelio-mesénquima y en la formación de las estructurasmedias craneofaciales durante el desarrollo embrionario, es probable una asociación entre variantes de Shh y la NSCLP. Métodos: el objetivo de este trabajo fue evaluar las regiones exónicas e intrónicas adyacentes de Shh, en una muestra de 150 tríos caso-progenitores para hallar la asociación con NSCLP. Se utilizó el método PCR-RFLP para determinar la presencia de heterodúplex. Luego, se utilizó la técnica de Conformation Sensitive Gel Electrophoresis (CSGE) para ver la distorsión del ADN en los heterodúplex. Como método alternativo, se hizo un análisis de polimorfismos de un solo nucleótido (del inglés single-nucleotide polymorphism SNP) para determinar asociación entre NSCLP y Shh, para lo cual se utilizaron los SNP: rs1233555 y rs1233556, ubicados en el primer intrón de Shh. Resultados:no se observaron heterodúplex en ninguno de los segmentos de Shh analizados en 150 tríos, el análisis de SNP tampoco mostró asociación con Shh y FLPNS. conclusión: la no asociación puede deberse a que la frecuencia de distribución de los SNP en la población chilena es diferente a la de las poblaciones referidas, o a que el número de SNP analizados fue insuficiente, o la no inclusión para el análisis de otras regiones de Shh.

introduction: nonsyndromic cleft lip and palate (NSCLP) is one of the most common congenital malformations not only in Chile but also worldwide. It has a multifactorial inheritance pattern with interaction of several genes and the environment. Several experimental studies have proven the participation of Sonic hedgedhog (Shh) in the migration process of cells from the neural crest,in the epithelium-mesenchyme transformation, and in the formation of middle craniofacial structures during embryo development; an association between Shh variants and NSCLP is probable. Methods: the goal of this study was to evaluate both exonic and intronic regions adjacent to Shh, in a sample of 150 case-parent trios in order to find possible associations with NSCLP. The PCR-RFLP method was used to determine the presence of heteroduplex. Afterwards, the Conformation Sensitive Gel Electrophoresis (CSGE) technique wasused to visualize DNA distortion at the heteroduplexes. As an alternative method, a single-nucleotide polymorphism (SNP) analysis wasperformed in order to determine NSCLP-Shh associations, by means of these SNPs: rs1233555 and rs1233556, located at the first Shhintron. Results: no heteroduplexes were found in any of the analyzed Shh segments in 150 trios; SNP analysis did not show associations between Shh and NSCLP either. conclusions: this lack of association may be due to the fact that SNP distribution frequency among Chilean population is different to that of reference populations, or because the number of SNPs analyzed was not sufficient, or even because this study did not include other Shh regions.

Characteristics of MSX1 gene in Korean nonsyndromic cleft lip and palate individuals / 대한치과교정학회지

OBJECTIVE: This study was performed to identify the characteristics of the MSX1 gene (locus chromosome 4p16) in Korean nonsyndromic cleft lip and palate (CL/P), which is assumed to be a major candidate gene acting as a causal factor in nonsyndromic CL/P and missing teeth. METHODS: The 36 individuals (23 males and 13 females) who had visited the department of orthodontics at from 1998 to 2002 and who had nonsyndromic CL/P were included in the study. Using a PCR-based assay, the MSX1 gene was amplified, sequenced, and searched for inferred protein products (Reference: Homo sapiens MSX1, accession number AF426432 and NP_002439). The common single nucleotide polymorphisms were observed. RESULTS: In exon 1, nucleotide "A" of the 253 basepair (bp) region was substituted for "G", and in the 255 bp region, nucleotide "G" was inserted. In exon 2, nucleotide "C" of the 11 bp region was substituted for "A", and "T" or "G" was inserted into the 351 bp region whereas "T" or "A" was inserted into the 352 bp region. In protein analysis, "Thr85Ala" missense mutation was found. The "Thr85Ala" missense mutation in this study is different from those of studies using subjects of other races. CONCLUSIONS: The results suggest that there is specific mutation of MSX1 in Korean and it plays an important role in Korean nonsyndromic CL/P. However, any distinct genetic polymorphisms between CL/P with missing teeth in the cleft region and CL/P without missing teeth could not be found.

Association between TGF-α gene BaraH Ⅰ polymorphism and nonsyndromic cleft lip with or without cleft palate / 中华医学美学美容杂志

Objective Nonsyndromic cleft lip with or without cleft palate(NSCL/P)is a common craniofacial birth defect which results in lifelong medical and social consequences.Although Asians have the highest birth prevalence of oral-facial clefts,the majority of gene mapping studies of cleft lip with or without cleft palate(CL/P)have been in European or Ameriean Caucasians.Therefore,the obiective of this study was to evaluate association between transforming growth factor alpha(TGF-α)gene BamH Ⅰ polymorphism and NSCL/P in Chinese.Methods 107 patients with NSCL/P and 136 healthy controls were examined for TGF-α/BamH Ⅰ genotypes.TGF-α/BamH Ⅰ typing was carried out by digesting the locus specific polymerase chain reaction amplified products with alleles specific BamH Ⅰ restriction enzyme(PCR-RELP).Resuits A1 allele frequency was 0.06 and A2 allele frequency was 0.94 in the controls.A1 allele frequency was 0.14 and A2 allele frequency was 0.86 in patients with NSCL/P(x2=8.27,df=1,P＜0.05).A1 allele frequency was 0.17 and A2 allele frequency was 0.83 in the bilateral cleft lip with or without cleft palate.A1 allele frequency was 0.13 and A2 allele frequency was 0.87 in the unilateral cleft lip with or without cleft palate(x2=0.36,df=1,P＞0.05).There was no statistically significant between the case with family history and the case without family history(x2=0.34,df=1,P＞0.05).Conclusions The above data demonstrate that there is evidence for the association of TGF-α polymorphism with development of NSCL/P in Chinese.

Assessment of the association between SMAD1 and HHIP gene variation and non-syndromic cleft-lip palate in Chilean case-parent trios

Nonsyndromic cleft lip/palate (NSCLP) is a congenital malformation with features of a complex genetic trait. Several studies have reported positive association and linkage between NSCLP and microsatellite markers in the 4q28-4q33 region particularly with the D4S192 (4q31) marker. We hypothesized that the candidate genes SMAD1 and HHIP (4q31) could be involved in the etiology of NSCLP based on previous positive linkage results and their important role in maxillofacial development. We evaluated the possible association between microsatellite markers located at less than 1 cM from these genes and NSCLP using a sample of 58 Chilean case-parent trios. Microsatellite markers were analyzed using the polymerase chain reaction (PCR) with fluorescent labeled primers. Electrophoresis of the PCR products was performed on a laser-fluorescent automatic DNA sequencer. The extended transmission disequilibrium test (ETDT) was used to analyze allelic transmissions from the parents to their affected progeny. No significant association due to linkage disequilibrium was detected between both markers and NSCLP.

Sequencing analysis of the OFC1 gene on the nonsyndromic cleft lip and palate patient in Korean / 대한치과교정학회지

This study was performed to identify the characteristics of the OFC1 gene (locus: chromosome 6p24.3) in Korean patients, which is assumed to be the major gene behind the nonsyndromic cleft lip and palate. The sample consisted of 80 subjects: 40 nonsyndromic cleft lip and palate patients (proband, 20 males and females, mean age 14.2 years); and 40 normal adults (20 males and 20 females, mean age 25.6 years). Using PCR-based assay, the OFC1 gene was amplified, sequenced, and then searched for similar protein structures. Results were as follows: 1. The OFC1 gene contains the microsatellite marker 'CA' repeats. The number of the reference 'CA' repeats was 21 times, and formed as TA(CA)11TA(CA)10. But,in Koreans, the number of tandem 'CA' repeats was varied from 17 to 26 except 18, and 'CA' repeats consisted of TA(CA)n. 2. Nine allelic variants were found. Distribution of the OFC1 allele was similar between the patients and control group. 3. There was a replacement of the base 'T' to 'C' after 11 tandem 'CA' repeats in Koreans compared with Weissenbach's report. However, the difference did not seem to be the ORF prediction results between Koreans and Weissenbach's report. 4. The BLAST search results showed the Telomerase reverse transcriptase (TERT) and the Nucleotide binding protein 2 (NBP2) as similar proteins. The TERT was a protein product by the hTERT gene in the locus 5p15.33 (NCBI Genome Annotation; NT023089). The NBP2 was a protein product by the ABCC3 (ATP-binding cassette, sub-family C) gene in the locus 17q22 (NCBI Genome Annotation; NT010783). 5. In the Pedant-Pro database analysis, the predictable protein structure of the OFC1 gene had at least one transmembrane region and one non-globular region.

Association of some SNP in TGFA,IRF6 and nonsyndromic cleft lip with or without cleft palate by DNA microarray technology / 中华检验医学杂志

Objective To explore the relationship between some single nucleotide polymorphisms (SNP)loci of interferon regulatory factor 6(IRF6)gene,transforming growth faetor-?(TGFA)gene and nonsyndromic cleft lip with or without cleft palate(NSCL/P)in nuclear families consisting of fathers, mothers and affected offspring with NSCL/P from southeast China.Methods Some SNloci of IRF6 and TGFA were detected by applying microarray technology in nuclear families,and then haplotype relative risk (HRR)and transmission disequilibrium test(TDT)were performed.Results There were no significant difference in genotypes and alleles distribution between patients and their parents.The SNP locus——V274I of IRF6 was associated with NSCL/P(HRR:?~2=4.5816,P

Association of TGF? and TGF?3 polymorphisms with nonsyndromic cleft lip and cleft palate / 实用口腔医学杂志

Objective:To study TGF? and TGF?3 polymorphisms in patients with nonsyndromic cleft lip with or without cleft palate(NSCLP,CLP or CL)and cleft palate only(CPO).Methods:TGF? and TGF?3 DNA was extracted and amplified from peripheral leukocytes of 56 cases of NSCLP(40 of CLP and 16 of CL),26 of CPO and 28 of unrelated controls.The primers were designed according to the 3'untranslated region of TGF? and 5th exon of TGF?3 published in the Internet.The PCR products were analyzed by single-stranded conformation polymorphism(SSCP).The aim fragments were further conformed by DNA sequencing after being cloned into pGEM-T vector.Results:The 345 bp fragment of TGF? and 193 bp of TGF?3 were amplified from NSCLP,CPO and control samples.In SSCP analysis,three alleles of TGF? and two of TGF?3 were found.Sequencing results showed three DNA polymorphic sites in TGF? and one in TGF?3 which were all base shifts.There was no difference of each genome between patients and controls.Conclusion:There are no direct association between 3'UTR of TGF? or 5th exon of TGF?3 and NSCLP or CPO in Chinese.

The expression and significance of CTGF,TGF?3 and their receptors in fissure tissues of the patients with NSCLP / 重庆医科大学学报

0.05),but the expression of CTGF receptor(LRP6)decreased in experimental group,compared with that in control group(P0.05).Conclusion:CTGF receptor(LRP6)and TGF?3 might have relationship with the generation of NSCLP