Comparison of three methods for genotyping of prothrombotic polymorphisms

Testing for Factor V Leiden (FVL) and Prothrombin G20210A Genetic Variants

Laboratory testing for Factor V Leiden and Prothrombin G20210A genetic variants permits defining the increased relative risk for venous thromboembolism in selected patients. Laboratory DNA testing for these variants may be undertaken by a variety of methods, including fluorescence-based quantitative real-time PCR (qPCR). This is a rapid, simple, robust, and reliable method to identify genotypes of interest. This chapter describes the method that employs PCR amplification of the patient DNA region of interest and genotyping by allele-specific discrimination technology on a quantitative real-time PCR (qPCR) instrument.

Annexin A5 haplotype M2 is not a risk factor for recurrent spontaneous abortion in Northern Europe: is there sufficient evidence?

The M2 haplotype of the annexin A5 gene is a well-recognized predisposition factor for recurrent spontaneous abortion (RSA). A recent publication by Nagirnaja et al. (2015) in PLoS One discusses the risk role of the M2 haplotype for RSA in cases compared with controls of North European extraction and arrives at a negative result. As a number of previous and fairly recent studies have supported the proposed involvement of the M2 haplotype in the cause of idiopathic RSA, this commentary aims to highlight problematic issues in the above publication. It is the opinion of the authors that the study by Nagirnaja et al. (2015) does not generate adequate proof of the absence of RSA risk, attributable to carriage of the M2 haplotype.

Accuracy of polymerase chain reaction-restriction fragment length polymorphism for RET rs2435357 genotyping as Hirschsprung risk

BACKGROUND

Recently, the common RET rs2435357 variant has been shown to be strongly related to Hirschsprung disease (HSCR) in the Indonesian population. This association study was conducted in developed areas using high-throughput TaqMan polymerase chain reaction (PCR) assay. Although the TaqMan method is less time-consuming, it requires a special more expensive PCR machine and a highly skilled analyst. In this study, we analyzed the usefulness of the PCR-restriction fragment length polymorphism (RFLP) method for genotyping RET rs2435357 polymorphism in Indonesian HSCR patients given the limitation of resource allocation for more expensive technologies.

MATERIALS AND METHODS

We compared our previous genotyping results of RET rs2435357 in 53 HSCR patients and 86 controls using the TaqMan PCR assay with the PCR-RFLP technique. Furthermore, we included an additional 40 HSCR patients and 50 controls and subsequently genotyped all subjects using the PCR-RFLP method.

RESULTS

Compared with our previous genotyping data of RET rs2435357 using the TaqMan PCR assay, the PCR-RFLP method indicated 100% concordant results. The overall accuracy of the PCR-RFLP for RET rs2435357 genotyping was 100%. In addition, case-control analysis demonstrated that RET rs2435357 is significantly correlated with HSCR (P = 2.2 × 10(-13)) with an odds ratio of 5.1 (95% confidence interval = 3.2-8.1). The transmission disequilibrium test revealed that risk allele (T) at rs2435357 is significantly overtransmitted to probands at a transmission rate (τ) of 0.87 (P = 1.5 × 10(-6)).

CONCLUSIONS

The PCR-RFLP method is reliable and affordable for genotyping of RET rs2435357 polymorphism in developing countries. Our results strengthen the proof that the RET rs2435357 variant is a genetic risk for HSCR in Indonesia.

Evaluation of the GeneXpert assay in the detection of Factor V Leiden and prothrombin 20210 in stored, previously classified samples

BACKGROUND

In this study, we evaluated the GeneXpert HemosIL Factor II and Factor V assay, an innovative assay for the detection of Factor V Leiden (FVL) and prothrombin G20210A mutation (GPRO).

PATIENTS AND METHODS

We evaluated 132 patients that were previously classified (with a concordant result) using two commercial real-time PCR assays supplied, by Applied Biosystems and Roche Molecular Biochemicals. The cohort comprised 75 normal subjects, 10 FVL homozygous, 35 FVL heterozygous, 7 GPRO heterozygous, 2 GPRO homozygous and 3 double heterozygous FVL and GPRO subjects. All of the samples were evaluated using the GeneXpert HemosIL Factor II and Factor V assay.

RESULTS

All of the samples were correctly identified using the GeneXpert HemosIL Factor II and Factor V assay; therefore, in this patient series, the specificity and sensitivity of the test under evaluation was 1.00.

DISCUSSION

We have shown that the GeneXpert HemosIL Factor II and Factor V assay, a rapid fully automated assay, can accurately characterise the presence of FV G1691A and FII G20210A polymorphisms with specificity and sensitivity that are comparable to other current real-time PCR-based methods. The theoretical advantages of such an assay include improved standardisation across varying healthcare environments, more thorough sample manipulation and reduced human error.

Factor V Leiden and FII 20210 testing in thromboembolic disorders

Factor V Leiden and prothrombin (F2) c.20210G>A mutation detection are very important in order to define the increased relative risk for venous thromboembolism in selected patients. Use of DNA-based methods to detect both mutations has become widely available in clinical diagnostic laboratories, including fluorescence-based quantitative real-time PCR (qPCR). The latter is a rapid, simple, robust and reliable method to identify genotypes of interest. There are several chemistries used for qPCR; this article describes their principles and applicability for Factor V Leiden and prothrombin (F2) c.20210G>A mutation detection.