A new PCR method: one primer amplification of PCR-CTPP products

Association of Variants of the NFE2L2 Gene with Metabolic and Kidney Function Parameters in Patients with Diabetes and/or Hypertension

Background: Type 2 diabetes mellitus (T2DM) and high blood pressure (HBP) are the main risk factors for chronic kidney disease (CKD). Relationships between variants within the NFE2L2 gene and the presence of risk factors for CKD, such as HBP and hyperglycemia, have been suggested; however, their role on kidney parameters remains unclear. Aim: To analyze the association of NFE2L2 variants with metabolic and kidney parameters. Materials and Methods: Six-hundred and fifty-one patients grouped according to the diagnosis of T2DM (n = 166), T2DM+HBP (n = 348), and HBP (n = 137) were included. Metabolic characteristics were evaluated to identify risk factors and presence of CKD. Genotyping was performed by polymerase chain reaction (PCR) coupled to confronting two pair primers for rs35652124 and rs6721961 and by real-time PCR for rs2364723. Logistic regression analyses, adjusted by confounding factors and correction for multiple tests, were performed. Results: Significant associations of rs35652124 (allele A) and rs2364723 (allele G) variants with low risk for presenting CKD were detected. Other variables consistently associated with these alleles were HBP, body mass index, waist circumference, uric acid, and triglycerides. Haplotypes AAC and GCG (loci order: rs35652124-rs6721961-rs2364723) showed similar trends. After adjustment for age and sex and correction for multiple tests, only rs35652124 (odds ratio [OR] = 0.5; confidence interval at 95% (CI95%), 0.3-0.9; p = 0.04) and rs2364723 (OR = 0.3; CI95%, 0.1-0.8; p = 0.009) variants remained associated with low risk for CKD in T2DM patients. Conclusion: This study showed for the first time that NFE2L2 variants were associated with low risk for CKD and with some traits related to kidney damage, such as HBP, hyperuricemia, and albuminuria, in Mexican patients with diabetes.

Confronting two biomolecular techniques to detect NRF2 gene polymorphism biomarkers

Aim:

Gene polymorphism biomarkers identify individual susceptibility to environmental and occupational hazards. The conventional approach considers polymerase chain reaction (PCR) followed by restriction fragment length polymorphism analysis (RFLP), a reliable but expensive and time-consuming two-step procedure. Therefore we evaluated the simpler method confronting two-pair primers (CTPP)–PCR for its robustness and applicability to epidemiologic studies.

Materials & methods:

We compared CTPP–PCR and PCR–RFLP techniques to detect two NRF2 polymorphisms in a set of biological samples.

Results:

CTPP–PCR produced contradictory results and required the orthogonal technique for confirming the data.

Conclusion:

In contrast to PCR-RFLP, CTPP–PCR of NRF2 polymorphisms resulted in ambiguous genotyping which strongly jeopardized heterozygosis classification. The necessity of long optimization and control procedures nullified the potential advantages of CTPP–PCR in terms of costs and time.

Confronting two-pair primers-polymerase chain reaction (CTPP–PCR) is potentially a fast, simple and cost-efficient method for the detection of gene polymorphism biomarkers. This technique was used to genotype two SNPs of NRF2 gene in a set of biological samples but resulted in ambiguous results. Therefore, it was necessary to validate the CTPP–PCR genotyping data with the orthogonal technique PCR-RFLP. Since reproducibility is a critical issue in both biomedical research and diagnostics, we advise pairing CTPP–PCR with control methods and evaluating whether the overall package is still convenient for massive genetic screening.

PCR-CTPP design for enzyme-free SNP genotyping using memetic algorithm

In recent years, many single nucleotide polymorphisms (SNPs) have been successfully genotyped by polymerase chain reaction with confronting two-pair primers (PCR-CTPP). However, computation experiments of feasible CTPP primers are still challenging. The melting temperatures between four primers must be within a very narrow range, and many primer constraints need to be conformed to. PCR-CTPP is a simple, time- and cost-effective SNP genotyping method applied in molecular biology and biomedical fields. In this study, an MA (memetic algorithm)-based method is proposed to enable the design of feasible CTPP primer sets. Overall, 288 SNPs which exclude the deletion/insertion polymorphisms (DIPs) and multi-nucleotide polymorphisms (MNPs) in the SLC6A4 gene were tested in silico. The results were compared with a GA (genetic algorithm)-based method and indicate that the proposed method provides more feasible CTPP primers than the GA-based method. The MA-based CTPP primer design method provides critical melting temperatures and all kinds of evaluation of the common primer constraints. It could conceivably assist biologists and other researchers in obtaining feasible CTTP primer sets. The MA-CTPP algorithm is implemented in JAVA and a user-friendly input interface is freely available at http://bio.kuas.edu.tw/ma-ctpp/.

ICAM-1 molecular mechanism and genome wide SNP's association studies

Macrophages transformed foam cell formation occurs as a result of leukocyte accumulation mediated through intercellular adhesion molecule 1 (ICAM1), vascular cell adhesion molecule 1 (VCAM1), and E-selectin, secreted by inflamed or damaged endothelium. The key molecule is the ICAM-1, member of the adhesion immunoglobulin super family that maps to chromosome 19 p13.2-p13.3 codes for 505 amino acids have five extracellular domains including circulatory leukocytes binding site (primarily monocytes) for recruiting it at the sites of inflammation and the tight adhesion with vascular endothelium for the above mentioned pathogenesis as an initial step. Hence the objective of the current paper is to review the Genome Wide Association (GWA) studies and summarizes its understanding of functional Single Nucleotide Polymorphism (SNP's) of ICAM-1 clinical association to provide better guidance for the clinicians and researchers of the merits, demerits of the current results and direct them to do research on larger number of population for better prospective.

A PCR method for VKORC1 G-1639A and CYP2C9 A1075C genotyping useful to warfarin therapy among Japanese

Warfarin is widely prescribed for patients with the risk of thromboembolism around the world. The inter-individual and inter-racial differences in appropriate dosage depend highly on age, body weight, and genetic factors. A lot of studies including genome-wide association studies revealed that vitamin K epoxide reductase complex, subunit 1 (VKORC1) G-1639A and Cytochrome P450 (CYP) 2C9 A1075C are the most strong genetic factors for determining warfarin effects in Asians and Africans. Since we developed a quick and inexpensive genotyping method, polymerase chain reaction with confronting two-pair primers (PCR-CTPP), the method was applied for these genotypes to examine the possibility to clinical use. Subjects were 436 examinees (117 males and 319 females, aged 32 to 85 years) who attended a health checkup program in Japan. The PCR-CTPP for VKORC1 G-1639A and CYP2C9 A1075C was conducted for the subjects, as well as the samples genotyped by DigiTag2 method. The allele frequencies of VKORC1 G-1639A were 0.085 for G and 0.915 for A, and those of CYP2C9 A1075C were 0.979 for A and 0.021 for C, being in Hardy-Weinberg equilibrium (p = 0.658 and p = 0.514, respectively). These frequencies were similar to those reported in the HapMap project. Genotyping for both SNPs by PCR-CTPP was replicated by DigiTag2 method. Our results indicated that the PCR-CTPP could be one of the alternative methods for genotyping VKORC1 G-1639A and CYP2C9 A1075C for Asians and Africans with similar allele frequencies to Japanese.

Betaine significantly improves multiplex tetra-primer ARMS-PCR methods

The tetra-primer ARMS-PCR method offers significant advantages over the commonly used methods to genotype single nucleotide polymorphisms. It offers fast and cost-effective detection and requires minimum level of expertise and basic instrumentation. The benefits of TP-ARMS-PCR increase exponentially upon multiplexing. However, several complications preclude the common use of multiplex TP-ARMS-PCR methods, primarily the lack of robustness and the difficulty of optimization. We have previously developed triplex and quadruplex TP-ARMS-PCR methods involving the simultaneous detection of up to three SNPs in a single reaction and utilized Betaine, a PCR additive used to enable amplification of GC-rich templates with strong secondary structures, in an attempt to facilitate method development and optimization. In the present communication, we introduced experimental data demonstrating the important effects of Betaine on our previous methods and its potential to overcome the ruggedness and robustness issues commonly found in TP-ARMS-PCR methods, and highlighted the general benefits of Betaine with respect to TP-ARMS-PCR. Our data support the routine inclusion of Betaine in all TP-ARMS-PCR methods, especially when multiplexing is concerned.