Dideoxy single allele-specific PCR - DSASP new method to discrimination allelic

Lima, Eleonidas Moura; Lopes, Otávio Sérgio; Soares, Leonardo Ferreira; Arruda, Talitta Dantas de; Gigek, Carolina Oliveira; Melo, Cynthia Germoglio Farias de; Smith, Marı́lia de Arruda Cardoso; Oliveira, João Ricardo Gonçalves de; Medeiros, Arnaldo Correia de; Delatorre, P.; Burbano, Rommel Rodrı́guez

doi:10.1590/s1516-8913201500434

Cited by 5 publications

(3 citation statements)

References 27 publications

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“…The DSASP method is based on chainterminating inhibitors, dideoxynucleotide, established by the method of Sanger et.al. DSASP was previously validated by the Allele Specific PCR-ASP method as described by Lima et al [22]. The DSASP is a method of genotyping and comprises four stages: I -selection of SNPs of interest, design of the oligonucleotides (primer and complementary sequence) and determination of the dideoxynucleotide to be incorporated; II -asymmetric PCR as dideoxynucleotide of interest; III hybridization reaction between complementary sequence and asymmetric PCR product; IV -analysis by melting curve by qPCR and was validated and developed by Lima et al [22].…”

Section: Methods Dideoxy Single Allele-specific Pcr-dsaspmentioning

confidence: 99%

Association of Single-Nucleotide Polymorphisms of Gene XPC with Susceptibility to Basal Cell Carcinoma in Brazilian Population

Maia

Lopes²,

Calixto³

et al. 2023

J of Skin

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Background: Basal cell carcinoma (BCC) is the common neoplasm in humans and its main etiological factor is exposure to solar radiation. Mutations in repair genes can lead to tumor progression and loss of cell integrity leading to the onset of cancer. Nucleotide excision repair (NER) is an important mechanism primarily used to repair injuries caused by UV. Objective: To evaluate and describe for the first time the single nucleotide polymorphisms rs745769173, rs761106780 and rs535425175 and risk of developing BCC. Methods: The present study analyzed 100 samples of paraffin-embedded tissue from patients with histopathological diagnosis of BCC and 100 control samples. The results were obtained by genotyping method, Dideoxy Unique Allele Specific – PCR (DSASP) and molecular modeling. Results: The SNP rs535425175 of the XPC gene showed a significant association with the BCC in the analyzed samples (P <0.005) and molecular docking showed different binding energy of the complex between the XPC region 99-156 and the PH domain of TFIIH p62, being more negative, -710.53 kcal/mol, with the Asn residue at position 108 and less negative, -611.10 kcal/mol, with Lys residue related to the polymorphism. Conclusion: The results suggest that the SNP rs535425175 of the XPC gene, which causes mutation at codon 108 of the XPC protein, which consists of replacing the Ans residue with the Lys, may be considered a risk factor associated with the development of BCC.

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Section: Methods Dideoxy Single Allele-specific Pcr-dsaspmentioning

confidence: 99%

Association of Single-Nucleotide Polymorphisms of Gene XPC with Susceptibility to Basal Cell Carcinoma in Brazilian Population

Maia

Lopes²,

Calixto³

et al. 2023

J of Skin

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“…The DSASP method is based on chain termination inhibitors, dideoxynucleoside, established by the method of Sanger et al The DSASP was previously validated by the Allele-Specific PCR-ASP method, as described by Lima et al (Lima et al, 2015). This genotyping method comprises four specific stages: I -SNP selection; oligonucleotide delineation (primer and complementary sequence); choice of the specific dideoxynucleoside to be incorporated into the SNP allele position; II -Asymmetric PCR of the chosen dideoxynucleoside; III -Hybridization reaction between the complementary sequence and the asymmetric PCR product; IV -Melting curve analysis by qPCR, developed and validated by Lima et al, (2015).…”

Section: Dideoxy Single Allele-specific Pcr (Dsasp) Methodsmentioning

confidence: 99%

Association between PSCA, TNF-α, PARP1 and TP53 Gene Polymorphisms and Gastric Cancer Susceptibility in the Brazilian Population

Dantas

Souza

Herrero

et al. 2020

Asian Pac J Cancer Prev

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Objectives: To evaluate the association of allelic and genotypic frequencies of PSCA (rs2976392), TNF-α (rs1800629), PARP1 (rs1136410) and TP53 (rs368771578) SNPs with GC susceptibility in a Brazilian population. Materials and Methods: This is a retrospective study, which included 102 paraffin-embedded adenocarcinoma tissue samples > 5 years of obtention, with 204 alleles for each studied SNP. Other 102 healthy tissue samples were included as controls. For analysis, the genotyping method Dideoxy Single Allele-Specific -PCR was used. Statistical analysis was performed with the Bioestat software 5.3, determining Hardy-Weinberg's equilibrium for the genotypic frequencies p-values < 0.05 were considered significant. Results: PSCA (rs2976392) and TNF-α (rs1800629) SNPs were associated with GC in the analyzed samples (X 2 =10.3/102 and p<0.001/0.00001, respectively). TNF-α (rs1800629) SNP presented also a statistically significant relationship between its genotypes and the morphological pattern (intestinal/diffuse) (p<0.032). However, PARP1 (rs1136410) and TP53 (rs368771578) SNPs were in Hardy-Weinberg's equilibrium and, therefore, were not significantly associated with GC in these samples (X 2 =0.73/2.89 and p<0.39/0.08). Conclusions: PSCA (rs2976392) and TNF-α (rs1800629) SNPs are potential molecular markers of susceptibility to GC development. PARP1 (rs1136410) and TP53 (rs368771578) SNPs were not associated with the risk of GC development.

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“…The Dideoxy single allele-specific PCR (DSASP) method is based on chain-terminating inhibitors, dideoxynucleotide, established by the method of Sanger et.al. DSASP was previously validated by the Allele Specific PCR-ASP method as described by Lima et al, (2015). It is a method of genotyping and comprises four stages: I -selection of target SNPs, oligonucleotides (primer and complementary sequence) design and determination of the dideoxynucleotide to be incorporated; II -asymmetric PCR of target dideoxynucleotide; III -hybridization reaction between the complementary sequence and athe symmetric PCR product; IV -analysis by melting curve by qPCR, validated and developed by Lima et al (2015).…”

Section: Dideoxy Single Allele-specific Pcr Methodsmentioning

confidence: 99%

Association between SNPs and Loss of Methylation Site on the CpG island of the Promoter Region of the Smoothened Gene, Potential Molecular Markers for Susceptibility to the Development of Basal Cell Carcinoma in the Brazilian Population

Souza

Lopes

Liberato

et al. 2020

Asian Pac J Cancer Prev

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Objective: Perform genotyping of SNPs in the promoter region of the SMO gene in BCC samples from patients from northeastern Brazil, and to determine if there is an association of these SNPs of the gene in question with the susceptibility to the development of the BCC. Methods: 100 samples of paraffined tissue from patients with histopathological diagnosis of BCC and 100 control samples were analyzed for each polymorphism by a newly developed genotyping method, the Dideoxy Single Allele Specific -PCR. The software Bioestat -version 5.3 and Haploview 4.2 were used for the statistical analysis. For all tests a P-value <0.05 was considered significant. Results: The SNP rs538312246 is the Hardy-Weinberg equilibrium, therefore, it did not present significant association with the BCC (X² =2.343 and P<0.158). However, the CpG-SNPs rs375350898 and rs75827493 were significantly associated to the BCC in the analyzed samples (X 2 = 27,740/21,500 and P <0001), the SNP rs75827493 showed a significant association with the BCC of the nodular subtype (P <0.0069). Therefore, our results suggest that SNPs rs375350898 and rs75827493 are potential molecular markers for susceptibility to BCC. Conclusion: The ability to detect SNP in a population, especially in promoter regions, has profoundly changed human genetic studies. This study allowed the understanding of the relationship between the presence of SNPs in CpG islands of the promoter region of the SMO gene can modify the methylation pattern and provide susceptibility to BCC in the population.

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Dideoxy single allele-specific PCR - DSASP new method to discrimination allelic

Abstract: Gastric cancer (GC) is a multifactorial disease with a high mortality rate in

Cited by 5 publications

References 27 publications

Association of Single-Nucleotide Polymorphisms of Gene XPC with Susceptibility to Basal Cell Carcinoma in Brazilian Population

Association of Single-Nucleotide Polymorphisms of Gene XPC with Susceptibility to Basal Cell Carcinoma in Brazilian Population

Association between PSCA, TNF-α, PARP1 and TP53 Gene Polymorphisms and Gastric Cancer Susceptibility in the Brazilian Population

Association between SNPs and Loss of Methylation Site on the CpG island of the Promoter Region of the Smoothened Gene, Potential Molecular Markers for Susceptibility to the Development of Basal Cell Carcinoma in the Brazilian Population

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