Association of Single Nucleotide Polymorphisms on Locus 18q21.1 in the Etiology of Nonsyndromic Cleft Lip Palate (NSCLP) in Indian Multiplex Families

Abstract Background Cleft lip palate (CLP) is a common congenital anomaly with multifactorial etiology. Many polymorphisms at different loci on multiple chromosomes were reported to be involved in its etiology. Genetic research on a single multigenerational American family reported 18q21.1 locus as a high-risk locus for nonsyndromic CLP (NSCLP). However, its association in multiple multiplex families and Indian population is not analyzed for its association in NSCLP. Aim This study was aimed to evaluate whether high-risk single nucleotide polymorphisms (SNPs) on chromosome 18q21.1 are involved in the etiology of NSCLP in multiplex Indian families. Materials and Methods Twenty multigenerational families affected by NSCLP were selected for the study after following inclusion and exclusion criteria. Genomic DNA was isolated from the affected and unaffected members of these 20 multiplex families and sent for genetic analysis. High-risk polymorphisms, such as rs6507872 and rs8091995 of CTIF, rs17715416, rs17713847 and rs183559995 of MYO5B, rs78950893 of SMAD7, rs1450425 of LOXHD1, and rs6507992 of SKA1 candidate genes on the 18q21.1 locus, were analyzed. SNP genotyping was done using the MassARRAY method. Statistical analysis of the genomic data was done by PLINK. Results Polymorphisms followed the Hardy–Weinberg equilibrium. In the allelic association, all the polymorphisms had a p-value more than 0.05. The odds ratio was not more than 1.6 for all the SNPs. Conclusion High-risk polymorphisms, such as rs6507872 and rs8091995 of CTIF, rs17715416, rs17713847 and rs183559995 of MYO5B, rs78950893 of SMAD7, rs1450425 of LOXHD1, and rs6507992 of SKA1 in the locus 18q21.1, are not associated with NSCLP in Indian multiplex families.

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5,10-Methylenetetrahydrofolate reductase single nucleotide polymorphisms and gene-environment interaction analysis in non-syndromic cleft lip/palate

European Journal Of Oral Sciences ◽

10.1111/eos.12114 ◽

2014 ◽

Vol 122 (2) ◽

pp. 109-113 ◽

Cited By ~ 16

Author(s):

Bernardette Estandia-Ortega ◽

José A. Velázquez-Aragón ◽

Miguel A. Alcántara-Ortigoza ◽

Miriam E. Reyna-Fabian ◽

Sandra Villagómez-Martínez ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Cleft Lip ◽

Methylenetetrahydrofolate Reductase ◽

Interaction Analysis ◽

Environment Interaction ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Gene Environment Interaction ◽

Gene Environment ◽

Cleft Lip Palate

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Association of the GABRB3 Gene with Nonsyndromic Oral Clefts

The Cleft Palate-Craniofacial Journal ◽

10.1597/06-142 ◽

2008 ◽

Vol 45 (3) ◽

pp. 261-266 ◽

Cited By ~ 7

Author(s):

Hiroki Inoue ◽

Shuji Kayano ◽

Yoko Aoki ◽

Shigeo Kure ◽

Atsushi Yamada ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Cleft Palate ◽

Cleft Lip ◽

Case Control ◽

Dinucleotide Repeat ◽

Aminobutyric Acid ◽

P Value ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Oral Clefts

Objective: Nonsyndromic oral clefts are common craniofacial anomalies classified into two subgroups: cleft lip with or without cleft palate and isolated cleft palate. Nonsyndromic oral clefts are multifactorial diseases, with both genetic and environmental factors involved in their pathogenesis. The inhibitory neurotransmitter, γ-aminobutyric acid plays a role in normal embryonic, and particularly facial, development and γ-aminobutyric acid receptor type A β-3 subunit (GABRB3) knockout mice have been shown to have cleft palate. The GABRB3 gene is therefore a strong candidate gene for nonsyndromic oral clefts. We investigated here whether genetic variations of the GABRB3 gene affect the risk for nonsyndromic oral clefts. Method: In this case-control study, a total of 178 Japanese patients with cleft lip with or without cleft palate and 374 unrelated controls were recruited and were genotyped for six single nucleotide polymorphisms and a dinucleotide repeat marker of the GABRB3 gene. Results: None of the single nucleotide polymorphisms showed complete linkage disequilibrium with other single nucleotide polymorphisms. In a case-control association study with the six-locus haplotype of the gene, TGTGCT haplotype frequency in patients with cleft lip with or without cleft palate was significantly higher than in the controls (corrected p value = .029). None of the alleles of the dinucleotide repeat marker showed significant association with cleft lip with or without cleft palate. Conclusions: Our data suggest that the GABRB3 gene is involved in the pathogenesis of cleft lip with or without cleft palate in the Japanese population.

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Analysis of Single Nucleotide Polymorphisms on Locus 13q33.1-34 in Multigenerational Families of Cleft Lip Palate using MassArray

The Indonesian Biomedical Journal ◽

10.18585/inabj.v13i1.1239 ◽

2021 ◽

Vol 13 (1) ◽

pp. 27-33

Author(s):

Praveen Kumar Neela ◽

Srinivas Reddy Gosla ◽

Akhter Husain ◽

Vasavi Mohan ◽

Sravya Thumoju ◽

...

Keyword(s):

Cleft Lip ◽

Haplotype Analysis ◽

Statistical Significance ◽

Genetic Research ◽

Allelic Association ◽

Chromosome Polymorphism ◽

Single Nucleotide ◽

Multigenerational Families ◽

Significant Difference ◽

Cleft Lip Palate

BACKGROUND: Cleft lip palate is a common congenital anomaly with multifactorial etiology. Many high-risk markers at different loci were reported to be involved in its etiology. Advanced genetic research led to the discovery of evidence of a new linkage on 13q33.1-34 region at marker rs1830756 in two multigenerational Indian families. However, no further study was reported to confirm or validate this linkage in other families. Hence, the present study was designed.METHODS: Twenty multigenerational families affected by non-syndromic cleft lip palate were selected for the study. Polymorphisms, rs1830756, rs1323672, rs1935135 of FAM155A gene; rs1961495, rs953386, rs1411040 of COL4A1 gene; and rs726449, rs984300 of MYO16 gene were selected. Genomic DNA was isolated and sent for genetic analysis by single nucleotide polymorphism (SNP) genotyping using the MassArray method. Statistical analysis of the genomic data was done by PLINK. Bonferroni correction was applied and haplotype analysis was done using Haploview software.RESULTS: Polymorphisms followed the Hardy Weinberg Equilibrium. In the allelic association, all the polymorphisms analysed showed no statistical significance. Hence, there was no significant difference in the allelic frequencies between non-syndromic cleft lip palate patients and healthy controls. The odds ratio was not more than 1.6 for all the SNPs. Haplotype analysis showed that haplotypes were not significantly higher in non-syndromic cleft patients than in control subjects.CONCLUSION: There is no association between SNPs analysed in the locus 13q33.1-34 with cleft lip palate.KEYWORDS: cleft lip palate, chromosome, polymorphism

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Sex Differences in Circadian Clock Genes and Myocardial Infarction Susceptibility

Journal of Cardiovascular Development and Disease ◽

10.3390/jcdd8050053 ◽

2021 ◽

Vol 8 (5) ◽

pp. 53

Author(s):

Ivana Škrlec ◽

Jasminka Talapko ◽

Martina Juzbašić ◽

Robert Steiner

Keyword(s):

Myocardial Infarction ◽

Cardiovascular Disease ◽

Circadian Rhythm ◽

Single Nucleotide Polymorphisms ◽

Clock Genes ◽

P Value ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Biological Sex ◽

Significant Difference

The growing body of evidence shows a significant difference in the circadian rhythm of cardiovascular disease based on biological sex. The incidence of cardiovascular disease varies between women and men. Additionally, biological sex is vital for the timely application of therapy—chronotherapy, which benefits both sexes. This study aimed to examine the potential difference of single nucleotide polymorphisms (SNPs) of the circadian rhythm genes ARNTL, CLOCK, CRY2 and PER2 in women and men with myocardial infarction. A cross-sectional study was conducted, including 200 patients with myocardial infarction. Altogether, ten single nucleotide polymorphisms in the ARNTL, CLOCK, CRY2 and PER2 genes were analyzed. The Chi-square test yielded statistically significant differences in CLOCK gene rs11932595 polymorphism in a recessive genotype model between women and men with a p-value of 0.03 and an odds ratio 2.66, and a corresponding 95% confidence interval of 1.07 to 6.66. Other analyzed polymorphisms of the circadian rhythm genes ARNTL, CRY2, and PER2 did not significantly differ between the sexes. According to the study’s current results, the CLOCK gene’s genetic variability might affect myocardial infarction concerning biological sex.

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Association between single-nucleotide polymorphisms on chromosome 1p22 and 20q12 and nonsyndromic cleft lip with or without cleft palate: New data in Han Chinese and meta-analysis

Birth Defects Research Part A Clinical and Molecular Teratology ◽

10.1002/bdra.23013 ◽

2012 ◽

Vol 94 (6) ◽

pp. 469-476 ◽

Cited By ~ 7

Author(s):

Enmin Huang ◽

Hongqiu Cheng ◽

Mingyan Xu ◽

Shenyou Shu ◽

Shijie Tang

Keyword(s):

Single Nucleotide Polymorphisms ◽

Cleft Palate ◽

Cleft Lip ◽

Meta Analysis ◽

Han Chinese ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

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Association of single-nucleotide polymorphisms in the ESR2 and FSHR genes with poor ovarian response in infertile Jordanian women

Clinical and Experimental Reproductive Medicine ◽

10.5653/cerm.2020.03706 ◽

2021 ◽

Vol 48 (1) ◽

pp. 69-79

Author(s):

Amer Mahmoud Sindiani ◽

Osamah Batiha ◽

Esra’a Al-zoubi ◽

Sara Khadrawi ◽

Ghadeer Alsoukhni ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Statistical Significance ◽

Ovarian Response ◽

Control Group ◽

P Value ◽

Case Group ◽

Nucleotide Polymorphisms ◽

Poor Ovarian Response ◽

Single Nucleotide ◽

Number Of Patients

Objective: Poor ovarian response (POR) refers to a subnormal follicular response that leads to a decrease in the quality and quantity of the eggs retrieved after ovarian stimulation during assisted reproductive treatment (ART). The present study investigated the associations of multiple variants of the estrogen receptor 2 (ESR2) and follicle-stimulating hormone receptor (FSHR) genes with POR in infertile Jordanian women undergoing ART.Methods: Four polymorphisms, namely ESR2 rs1256049, ESR2 rs4986938, FSHR rs6165, and FSHR rs6166, were investigated in 60 infertile Jordanian women undergoing ART (the case group) and 60 age-matched fertile women (the control group), with a mean age of 33.60±6.34 years. Single-nucleotide polymorphisms (SNPs) were detected by restriction fragment length polymorphism and then validated using Sanger sequencing.Results: The p-value of the difference between the case and control groups regarding FSHR rs6166 was very close to 0.05 (p=0.054). However, no significant differences were observed between the two groups in terms of the other three SNPs, namely ESR2 rs1256049, ESR2 rs4986938, and FSHR rs6165 (p=0.561, p=0.433, and p=0.696, respectively).Conclusion: The association between FSHR rs6166 and POR was not statistically meaningful in the present study, but the near-significant result of this experiment suggests that statistical significance might be found in a future study with a larger number of patients.

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