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

Neela, Praveen Kumar; Gosla, Srinivas Reddy; Husain, Akhter; Mohan, Vasavi; Thumoju, Sravya; Rajeshwari, Rajeshwari

doi:10.18585/inabj.v13i1.1239

Cited by 2 publications

(2 citation statements)

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“… 24 25 26 A family study by Neela et al reported that several genes on the locus 13q33.1–34 were not associated with NSCL/P in the Indian population. 27 Case-parent trio studies are rare in India, and there are no reported case-parent trio studies to evaluate the possible association between the PAX7 gene and the risk of NSCL/P.…”

Section: Discussionmentioning

confidence: 99%

Maternal Transmission of the PAX7 Single Nucleotide Polymorphisms among Indian Cleft Trios

Khan

Cs²,

Mustak

et al. 2023

Glob Med Genet

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Cleft lip and/or cleft palate (CL/P) is one of the most common congenital anomalies of the human face with a complex etiology involving multiple genetic and environmental factors. Several studies have shown the association of the paired box 7 (PAX7) gene with CL/P in different populations worldwide. However, the current literature reveals no reported case-parent trio studies to evaluate the association between the PAX7 gene and the risk of nonsyndromic cleft lip and/or palate (NSCL/P) in the Indian population. Hence, the purpose of this study was to assess the PAX7 gene single nucleotide polymorphisms (SNPs) in the etiology of NSCL/P among the Indian cleft trios. Forty Indian case-parent trios of NSCL/P were included. The cases and their parents' genomic DNA were extracted. The SNPs rs9439714, rs1339062, rs6695765, rs742071, and rs618941of the PAX7 gene were genotyped using the Agena Bio MassARRAY analysis. The allelic transmission disequilibrium test was performed using PLINK software while pair-wise linkage disequilibrium by the Haploview program. The SNP rs9439714 showed evidence of association (p-value = 0.02, odds ratio = 3) with NSCL/P. Considering the parent-of-origin effects, the SNPs rs9439714 and rs618941 showed an excess maternal transmission of allele C at rs9439714 (p-value = 0.05) and G allele at rs618941 (p-value = 0.04). The results of the present study suggested that the SNPs rs9439714 and rs618941 showed an excess maternal transmission of alleles suggestive of the possible role of the PAX7 gene involvement in the etiology of NSCL/P in the Indian population.

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Section: Discussionmentioning

confidence: 99%

Maternal Transmission of the PAX7 Single Nucleotide Polymorphisms among Indian Cleft Trios

Khan

Cs²,

Mustak

et al. 2023

Glob Med Genet

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“…( 7) Several studies have reported the use of different genotyping methods to detect SNV. (12)(13)(14)(15) Despite that, each method has different advantages and disadvantage to consider. Sequencing and genotyping array are a high-throughput genotyping technique but they need expensive machineries and reagents.…”

Section: Discussionmentioning

confidence: 99%

Development of Tetra-primer Amplification Refractory Mutation System (ARMS) PCR for Detection of CHRNA3 rs8040868

2021

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BACKGROUND: Single nucleotide variations (SNV) have been mapped to be associated with several human conditions and diseases. To validate the association between SNV to certain human traits or diseases, a large number of subjects must be included. Thus, in need of a fast, relatively economic, and reliable genotyping method. This can be achieved through the use of tetra-primer amplification refractory mutation system polymerase chain reaction (Tetra-primer ARMS PCR). This study reports strategy to develop Tetra-primer ARMS PCR-based genotyping of CHRNA3 rs8040868.METHODS: The optimization of Tetra-primer ARMS PCR was done through these steps: identification of gene sequence and position of single mutation; designing outer and inner PCR primers; amplification of target gene fragments through PCR by using outer primer; confirming genotype of the PCR product by using sequencing; determining an optimum ratio of outer and inner primer; and determining optimum annealing temperature and cycles for the PCR program. The PCR products were run in 2% gel agarose electrophoresis and visualized under UV illumination.RESULTS: Outer and inner primer ratio of 1:3 with annealing temperature of 64.4°C and 40x cycles was found to be the most optimum condition. Tetra-primer ARMS PCR was able to confirm the results of the DNA sequence of 2 samples, confirming wild-type variants (TT allele) and the heterozygous mutant (CT allele).CONCLUSION: Tetra-primer ARMS PCR was able to genotype rs8040868 of the CHRNA3 gene.KEYWORDS: tetra-primer ARMS PCR, CHRNA3, rs8040868, genotyping

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

Cited by 2 publications

References 17 publications

Maternal Transmission of the PAX7 Single Nucleotide Polymorphisms among Indian Cleft Trios

Maternal Transmission of the PAX7 Single Nucleotide Polymorphisms among Indian Cleft Trios

Development of Tetra-primer Amplification Refractory Mutation System (ARMS) PCR for Detection of CHRNA3 rs8040868

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