Novel Artificial Restriction Fragment Length Polymorphism Methods for Genotyping Immunity-related GTPase M Promoter Polymorphisms

An artificial-restriction fragment length polymorphism (A-RFLP) method for genotyping intronic SNP rs7587633 C/T of ATG16L1

SNPs could either cause a disorder or directly alter the efficacy of a particular treatment and act as biological markers. The SNP rs7587633 C/T present in the intronic region of the ATG16L1 gene has been studied for its role in psoriasis vulgaris and Palmoplantar pustulosis. To genotype rs7587633 C/T using PCR-RFLP no restriction site is present for any of the restriction enzymes at the SNP position. To develop an artificial-RFLP method for genotyping rs7587633 C/T, the forward primer was designed in such a way that it resulted in the creation of an EcoRI restriction site in the amplified product which could further be digested with EcoRI to find the genotype of the individual. The newly developed A-RFLP method was applied to genotype the SNP rs7587633 C/T in DNA samples of 100 healthy control individuals. The allelic and genotypic frequencies of the SNPs were 0.80(C), 0.20(T) and 65%(CC), 31%(CT) and 4%(TT), respectively. In conclusion, we developed an A-RFLP method to genotype the SNP rs7587633 C/T which is not present in any of the natural restriction sites and this method could be applied to genotype this SNP in various populations/diseases to find its role.

Mutagenic primer-based novel multiplex PCR-RFLP technique to genotype BECN1 SNPs rs10512488 and rs11552192

BACKGROUND

Single Nucleotide Polymorphisms (SNPs) in candidate autophagy gene BECN1 could influence its functions thereby autophagy process. BECN1 noncoding SNPs were found to be significantly associated with neurodegenerative disease and type 2 diabetes mellitus. This study aimed to develop a simultaneous genotyping technique for two BECN1 SNPs (rs10512488 and rs11552192).

METHODS

A mutagenic primer-based approach was used to introduce a NdeI restriction site to genotype rs10512488 by Artificial-Restriction Fragment Length Polymorphism (A-RFLP) along with rs11552192 by Polymerase Chain Reaction (PCR)-RFLP. Multiplexing PCR and restriction digestion reactions were set up for simultaneous genotyping of both SNPs in 100 healthy individuals. Genotypic and allele frequencies were manually calculated, and the Hardy-Weinberg Equilibrium was assessed using the chi-square test.

RESULTS

We successfully developed PCR and RFLP conditions for the amplification and restriction digestion of both SNPs within the same tube for genotyping. The results of genotyping by newly developed multiplexing PCR-RFLP technique were concordant with the genotypes obtained by Sanger sequencing of samples. Allelic frequencies of rs10512488 obtained were 0.15 (A) and 0.85 (G), whereas allelic frequencies of rs11552192 were 0.16 (T) and 0.84 (A).

CONCLUSION

The newly developed technique is rapid, cost-effective and time-saving for large-scale applications compared to sequencing methods and would play an important role in low-income settings. For the first time, allelic frequencies of rs10512488 and rs11552192 were reported among the North Indian population.

Association of IRGM gene promoter polymorphisms with Hepatitis B Virus infection

BACKGROUND

In response to intracellular pathogens the autophagy gene IRGM plays an essential role in the innate immune response. Various identified IRGM gene risk loci are associated with several diseases, but so far no study is available which shows the association of IRGM with HBV infection.

METHODS

We genotyped promoter variants (rs4958842, rs4958843, and rs4958846) of IRGM in HBV infected patients (551) and healthy controls (247) for their role in HBV infection. The genotyping was done applying methods developed in our laboratory and various biochemical parameters were assessed applying commercially available kits.

RESULTS

Data analysis has shown that the mutant allele A of rs4958842 plays a role in the protection from HBV infection in various genetic models that includes allelic, co-dominant and dominant models with the respective statistical data (OR=0.61; 95%CI=0.48-0.78; p=0.0003), (OR=0.52; 95%CI=0.38-0.71; p=0.0008) and (OR=0.51; 95%CI=0.38-0.70, p=0.0004). In CHB, protective association was observed in allelic (OR=0.48; 95%CI=0.35-0.65, p=0.0004), co-dominant (OR=0.38; 95%CI=0.26-0.54, p=0.0004) and dominant models (OR=0.38; 95%CI=0.26-0.54, p=0.0002). Mutant allele C of rs49598843 was associated with the risk of CHB in co-dominant (OR=1.52; 95%CI=1.07-2.16, p=0.04) and dominant models (OR=1.41; 95%CI=1.00-2.00, p=0.04). The mutant allele C of rs4958846 decreased the risk of HBV infection in allelic (OR=0.74; 95%CI=0.59-0.92, p=0.01), dominant (OR=0.72; 95%CI=0.53-0.98, p=0.05), homozygous (OR=0.42; 95%CI=0.24-0.74, p=0.01) and recessive (OR=0.42; 95%CI=0.24-0.74, p=0.0004) models. However, in asymptomatic group it was associated with the increased chance of HBV infection. Haplotypes, ATT (OR=0.47; 95%CI=0.33-0.68, p=0.001), GTC (OR=0.68; 95%CI=0.51-0.92, p=0.01) protect while GTT (OR=2.01; 95%CI=(1.55-2.60), p<0.0001) predisposes the individuals to HBV infection. All of these p-values mentioned here were obtained after performing Bonferroni correction.

CONCLUSION

In conclusion, our findings revealed that mutant allele A of rs4958842, mutant allele C of rs4958843 and rs4958846 were associated with hepatitis B virus infection in the North Indian population.

A novel high-resolution melting analysis-based method for Salmonella genotyping

To establish a simple and rapid high-resolution melting curve (HRM) method, 5 different strains of Salmonella were identified by adding DNA denaturants at different concentrations into the HRM system to change the characteristics of DNA melting and to obtain different Tm (dissolving temperature) values of DNA from different target bacteria. When the concentration of n-butanol was 7% (v/v), the Tm value of the melting curve of the 5 strains changed from 89 °C to 80.5 °C, 81.5 °C, 79.5 °C, 81.0 °C and 82.5 °C, respectively. The sensitivity and specificity of the proposed method were both over 90% in the detection of 270 spiked milk powder samples. In summary, the proposed method in this study has potential for application to food safety and epidemiological research on Salmonella infection.

E2F1 genetic variants and risk of cervical cancer in Indian women

Introduction:

Altered expression of many E2F family members have been reported in various human cancers. In this study, we investigated the role of non-synonymous single nucleotide polymorphisms (rs3213172 C/T, rs3213173 C/T, and rs3213176 G/A) of the gene E2F1 with cervical cancer.

Methods:

A total of 181 samples including 90 cervical cancer patients and 91 healthy controls were genotyped. The genotype frequencies of these polymorphisms in collected samples were determined by either PCR-RFLP or PCR-ARFLP methods. SHEsis software was used to analyze the haplotypes.

Results:

Statistically significant differences in the alleles and the genotypes frequencies were observed in rs3213172 (C/T) and rs3213173 (C/T) polymorphisms. The rs3213172 (C/T) polymorphism was a risk factor for cervical cancer in dominant model (odds ratio (OR) 1.96; 95% confidence interval (CI) 1.07, 3.60; P = 0.02) and heterozygous model (OR 1.90; 95% CI 1.01, 3.57; P = 0.04). The rs3213173 (C/T) polymorphism increased the risk of cervical cancer in the homozygous model (OR 2.71; 95% CI 1.11, 6.58; P = 0.02). The rs3213176 (G/A) polymorphism was not associated with cervical cancer risk in any of the genotypic models. In the haplotypes analysis, three haplotypes (CTG, TCG, and TTA) were associated with the cervical cancer risk.

Conclusions:

These findings revealed that rs3213172 (C/T) and rs3213173 (C/T) polymorphisms and haplotypes (CTG, TCG, and TTA) of the E2F1 gene might play role in the susceptibility of cervical cancer. This is the first report showing an association of these polymorphisms with the cervical cancer risk.

Mutagenic primer-based PCR-RFLP assay for genotyping IRGM gene promoter variant rs4958843 (C/T)

BACKGROUND

Single-nucleotide polymorphisms play an important role in the susceptibility of many diseases, evolutionary studies, and genetic mapping. The rs4958843 in IRGM promoter is associated with tuberculosis and Crohn's disease. As this SNP is not present in any of the restriction sites, PCR-RFLP is not possible. Therefore, we have developed artificial-RFLP method to genotype this SNP.

METHODS

We designed forward primer with mismatches that resulted in the creation of a restriction site for enzyme NheI in the amplicon. Control samples of known genotypes were obtained by sequencing. The amplified product for SNP rs4958843 was digested with NheI restriction enzyme and resolved on an agarose gel to know the genotypes of the samples.

RESULTS

Results of sequencing and A-RFLP were concordant. The developed method was applied to genotype this polymorphism in 100 samples from healthy individuals. The allelic frequencies of SNP rs4958843 were C (0.16) and T (0.84), while corresponding genotypic distribution was CC (2), CT (29), and TT (69).

CONCLUSION

The newly developed method is simple, easy, and cost-effective which could be used to genotype IRGM polymorphism -1161 C/T (rs4958843) in various populations in the replication studies and has its applicability in the clinical settings. The developed method was applied for genotyping samples from healthy individuals from North India. For the first time, we report the frequency of this polymorphism from this region.