Polymorphisms at 1q32, 8q24, and 17q22 loci are associated with nonsyndromic cleft lip with or without cleft palate risk in the Slovak population

Salagovic, J; Klimčáková, Lucia; Zabavnikova, Marianna; Behunova, Jana; Hudáková, T.; Fedeleś, J; Molnarova, Agata; Podracká, Ľudmila

doi:10.5507/bp.2017.009

Cited by 7 publications

(8 citation statements)

References 49 publications

(61 reference statements)

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“…In our studies with subgroup analysis, this effect was predominant in Caucasian group under every genetic model without heterogeneity, which explained the increase in variation risk of NSCLP. The present study is an updated metaanalysis for rs227731, and results were consistent with previous studies in same ethnic group (Mostowska et al, 2012;Salagovic et al, 2017). On contrary, other studies did not show positive results in Chinese, Italian, and other populations (Pan et al, 2011;Cura et al, 2016).…”

Section: Discussionsupporting

confidence: 92%

“…To identify the genes of NSCLP, studies about the multigenic disease were searched and 2 SNPs were selected because conflict. Noggin ( NOG) gene encodes for protein that functions in the process of craniofacial development (Salagovic et al, 2017). The polymorphic loci rs227731 located 100 kb downstream of NOG has been reported by GWAS and thus is important for further discussion.…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Jia

Qiao

et al. 2020

The Cleft Palate-Craniofacial Journal

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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.

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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

Wang

Jia

Qiao

et al. 2020

The Cleft Palate-Craniofacial Journal

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“… 35 Numerous reports have further confirmed the close association between the 8q24 chromosome region (where the c-Myc gene is located) and NSCLP, which can be ascribed to the variants of the tissue-specific enhancer of c-Myc or other genes. 36–38 Here, qPCR analysis of clinical samples showed significantly lower expression of c-myc in the NSCL/P group as compared to that, of the control group.…”

Section: Discussionmentioning

confidence: 60%

Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate

Wang¹,

Guo²,

Zhou³

et al. 2021

IJGM

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Background Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect. Growing evidence has demonstrated the competing endogenous RNA (ceRNA) hypothesis has played a role in the pathogenesis of NSCL/P. Here, we identified the important lncRNAs in NSCL/P and constructed a ceRNA regulatory network to predict their underlying functional mechanism. Methods Total RNA isolated from the peripheral blood samples were analyzed by the Human Clariom D Affymetrix platform and differentially expressed genes (DEGs) were identified. Using the limma package in R software, DEGs in the expression profile of GSE42589 were identified from Gene Expression Omnibus (GEO) database. Co-differentially expressed lncRNAs (co-DElncRNAs) were used to predict the microRNAs that may bind to them. Co-differentially expressed mRNAs (co-DEmRNAs) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The hub genes were screened using the cytohubba plug-in in Cytoscape. A ceRNA network was built to investigate the molecular mechanism underlying the etiology of NSCL/P. The expression levels of lncRNAs, miRNAs, and mRNAs in the network were assessed by quantitative real-time polymerase chain reaction (qRT-PCR). Results We found 116 DElncRNAs and 2955 DEmRNAs from the GSE42589 dataset, and 2626 DElncRNAs and 2771 DEmRNAs from the Human Clariom D gene chip. A network of co-DEmRNAs containing 3712 edges and 621 nodes were identified by PPI analysis. A ceRNA regulatory network comprising lncRNA USP17L6P, hsa-miR-449c-5p, and MYC was established. qRT-PCR results revealed significantly lower expression levels of lncRNA USP17L6P and c-Myc in NSCL/P tissues, while the expression level of hsa-miR-449c-5p was higher as compared to control samples ( p < 0.05). Conclusion The identified lncRNAs and the established ceRNA regulatory network provide novel insight into the pathogenesis of NSCL/P, therefore hold great promise in NSCL/P management in clinical practice.

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“…Xu, et al 32 (2016) found that rs2235371 and rs2013162 polymorphisms of IRF6 were associated with NSCP in the Chinese population. Recently, Salagovic, et al 25 (2017) reported that the IRF6 rs642961 variant significantly increased the risk of NSCL/P in the Slovakian population.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2017

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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.

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Polymorphisms at 1q32, 8q24, and 17q22 loci are associated with nonsyndromic cleft lip with or without cleft palate risk in the Slovak population

Cited by 7 publications

References 49 publications

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

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

Exploring the Molecular Mechanism of lncRNA–miRNA–mRNA Networks in Non-Syndromic Cleft Lip with or without Cleft Palate

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

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