Analytic validity of genetic tests to identify factor V Leiden and prothrombin G20210A

Laboratory Diagnosis of Activated Protein C Resistance and Factor V Leiden

The factor V Leiden (FVL) polymorphism is known as the most common inherited risk factor for venous thrombosis. In turn, FVL is the leading cause of an activated protein C resistance (APCR) phenotype, in which the addition of exogenous activated protein C to plasma does not result in the expected anticoagulant effect. In the routine laboratory approach to the formal diagnosis of FVL, an initial positive screening plasma-based method for APCR is often performed, and only if needed, this is followed by a confirmatory DNA-based assay for FVL. Multiple methods with accepted sensitivity and specificity for determining an APCR/FVL phenotype are commonly categorized into two separate groups: (1) screening plasma-based assays, including qualitative functional clot-based assays, for APCR, and (2) confirmatory DNA-based molecular assays, entailing several tests and platforms, including polymerase chain reaction-based and non-PCR-based techniques, for FVL. This review will describe the methodological aspects of each laboratory test and prepare suggestions on the indication of APCR and FVL testing and method selection.

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.

ARMS TaqMan real-time PCR for genotyping factor V Leiden mutation in Han Chinese

Factor V Leiden (FV_Leiden ) is a missense mutation of 1691 position (G1691A) in exon 10 of FV gene, and being a genetic risk for venous thrombosis. Currently, there are several PCR-based methods for detecting FV_Leiden mutation; however, these methods have disadvantages such as time-consuming, cumbersome steps and potentially hazardous gels. The aims of present study were to develop a simple, time-saving, accurate, and gel-free method, called amplification refractory mutation system (ARMS) TaqMan real-time PCR, for detecting FV_Leiden mutation. We severally designed two specific reverse primers for mutant and wild-type through intentional introduction of mismatched nucleotide at the penultimate 3' position. Although target amplicon amplification efficiency is reduced, but another corresponding amplicon is almost completely inhibited. Then, specific TaqMan-probe was designed to detect target amplicon. Established method was used to detect 500 unselected samples in Han Chinese, the results showed 499 cases of wild-type and one heterozygote. Afterward, 50 randomly picked wild-type cases and one heterozygote were reexamined by bidirectional DNA sequencing, which is considered as "Gold standard method." Exhilaratingly, the results detected by the two methods were completely consistent. At last, allelic frequency of FV_Leiden was calculated the in Han Chinese. Given the above results, A FV_Leiden heterozygote has been found in 500 random samples in Han Chinese, and the allelic frequency was 0.1%. In conclusion, the ARMS TaqMan real-time PCR is an ideal detecting system for genotyping FV_Leiden mutation in clinical application, and FV_Leiden mutation exists in Han Chinese despite extremely low prevalence.

Direct blood PCR: TaqMan-probe based detection of the venous thromboembolism associated mutations factor V Leiden and prothrombin c.20210G>A without DNA extraction

BACKGROUND

Practically, the initial step of genetic analysis is the extraction of DNA from blood or other cells, which is often time consuming and cost-intensive. We aimed at establishing a real-time PCR protocol for the detection of the venous thromboembolism associated mutations factor V Leiden (F5 c.1691G>A; p.R506Q) and prothrombin (F2) c.20210G>A from whole blood, without DNA extraction.

METHODS

F5 c.1691G>A (p.R506Q) and F2 c.20210G>A mutations were determined in 205 EDTA anti-coagulated whole blood samples from patients who underwent routine clinical genotyping using the DirectBlood Genotyping PCR Kit (myPOLS Biotec, Konstanz, Germany) together with in-house developed TaqMan primer-probe assays.

RESULTS

Validity score values of genotype calls using whole blood were similar and did not significantly differ compared to those using genomic DNA as substrate in PCR. Mutation analysis of 205 whole blood samples showed a negligible PCR dropout rate (one in 410 reactions) and were in 100% concordance with results obtained by conventional genotyping.

CONCLUSION

We successfully established a robust and valid real-time PCR protocol for the detection of the venous thromboembolism associated mutations F5 c.1691G>A (p.R506Q) and F2 c.20210G>A directly from whole blood.

Multiplex testing for Factor II and Factor V mutations in thrombophilia: technical verification and clinical validation of the cobas® Factor II and Factor V test

Laboratory testing for thrombophilia is complicated but essential for diagnosis. In 2017, the cobas® Factor II and Factor V Test (cobas F2F5 test) was launched for use with the cobas z 480 analyzer. This qualitative polymerase chain reaction test enables multiplex Factor II and Factor V testing with flexible reporting and workflow efficiency. Here, we report the results from studies investigating the performance of the cobas F2F5 test. Technical performance verification, clinical validation, external laboratory performance, and workflow comparison studies were performed. Fresh and frozen whole-blood and genomic DNA (gDNA) samples were tested, and several manual and automated DNA isolation methods were used. Bidirectional Sanger sequencing was used to verify genotypes identified by the cobas F2F5 test. One hundred percent agreement between the cobas F2F5 test and Sanger sequencing was observed for all genotypes. An external laboratory using remnant clinical samples also yielded 100% agreement between cobas F2F5 test results and their routine testing method. The cobas F2F5 test reduced the total sample processing time compared with the LightCycler® 1.2 platform (98.6 vs 420.2 min; 96 samples). Hemoglobin, extraction buffer, and ethanol contamination of the gDNA sample can lead to invalid results. The cobas F2F5 test has a high degree of accuracy for identification of Factor II and Factor V genotypes. This multiplex testing with short sample processing time can reduce handling errors and increase efficiency. Both manual and automated DNA isolation methods can be used with the cobas F2F5 test.

Specificity of SNP detection with molecular beacons is improved by stem and loop separation with spacers

Dissection of stem and loop regions in molecular beacons by nucleotide or non-nucleotide linkers minimizes nonspecific recognition in SNP discrimination.

Molecular markers for resistance against infectious diseases of economic importance

Huge livestock population of India is under threat by a large number of endemic infectious (bacterial, viral, and parasitic) diseases. These diseases are associated with high rates of morbidity and mortality, particularly in exotic and crossbred cattle. Beside morbidity and mortality, economic losses by these diseases occur through reduced fertility, production losses, etc. Some of the major infectious diseases which have great economic impact on Indian dairy industries are tuberculosis (TB), Johne's disease (JD), mastitis, tick and tick-borne diseases (TTBDs), foot and mouth disease, etc. The development of effective strategies for the assessment and control of infectious diseases requires a better understanding of pathogen biology, host immune response, and diseases pathogenesis as well as the identification of the associated biomarkers. Indigenous cattle (Bos indicus) are reported to be comparatively less affected than exotic and crossbred cattle. However, genetic basis of resistance in indigenous cattle is not well documented. The association studies of few of the genes associated with various diseases, namely, solute carrier family 11 member 1, Toll-like receptors 1, with TB; Caspase associated recruitment domain 15, SP110 with JD; CACNA2D1, CD14 with mastitis and interferon gamma, BoLA--DRB3.2 alleles with TTBDs, etc., are presented. Breeding for genetic resistance is one of the promising ways to control the infectious diseases. High host resistance is the most important method for controlling such diseases, but till today no breed is total immune. Therefore, work may be undertaken under the hypothesis that the different susceptibility to these diseases are exhibited by indigenous and crossbred cattle is due to breed-specific differences in the dealing of infected cells with other immune cells, which ultimately influence the immune response responded against infections. Achieving maximum resistance to these diseases is the ultimate goal, is technically possible to achieve, and is permanent. Progress could be enhanced through introgression of resistance genes to breeds with low resistance. The quest for knowledge of the genetic basis for infectious diseases in indigenous livestock is strongly warranted.

Diagnosis and management of factor V Leiden

INTRODUCTION

The discovery of the factor V Leiden (FVL) missense mutation (Arg506Gln) causing factor V resistance to the anticoagulant action of activated protein C was a landmark that allowed a better understanding of the basis of inherited thrombotic risk. FVL mutation is currently the most common known hereditary defect predisposing to venous thrombosis. Areas covered: Novel data-driven FVL diagnosis and therapeutic approaches in the management of FVL carriers in various clinical settings. Brief conclusions on topics of direct clinical relevance including currently available indications for primary and secondary prophylaxis, the management of female, pediatric carriers and asymptomatic relatives. Latest evidence on the association between FVL and cancer, as well as the possible use of direct oral anticoagulant therapy. Expert commentary: Although FVL diagnosis nowadays is highly accurate, many doubts remain regarding the best management and therapeutic protocols. The main role of clinicians is to tailor therapeutic strategies to carriers and their relatives. High familial penetrance, distinctive aspects of the first thrombotic event (provoked/unprovoked, age, etc.) and laboratory biomarkers can guide the optimal management of secondary antithrombotic prophylaxis, primary prophylaxis in asymptomatic individuals, and whether to screen relatives.

Can Factor V Leiden and prothrombin G20210A testing in women with recurrent pregnancy loss result in improved pregnancy outcomes?: Results from a targeted evidence-based review

Women with recurrent pregnancy loss are offered Factor V Leiden (F5) and/or prothrombin G20210A (F2) testing to identify candidates for anticoagulation to improve outcomes. A systematic literature review was performed to estimate test performance, effect sizes, and treatment effectiveness. Electronic searches were performed through April 2011, with review of references from included articles. English-language studies addressed analytic validity, clinical validity, and/or clinical utility and satisfied predefined inclusion criteria. Adequate evidence showed high analytic sensitivity and specificity for F5 and F2 testing. Evidence for clinical validity was adequate. The summary odds ratio for association of recurrent pregnancy loss with F5 in case-controlled studies was 2.02 (95% confidence interval, 1.60-2.55), with moderate heterogeneity and suggestion of publication bias. Longitudinal studies in women with recurrent pregnancy loss or unselected cohorts showed F5 carriers were more likely to have a subsequent loss than noncarriers (odds ratios: 1.93 and 2.03, respectively). Results for F2 testing were similar. For clinical utility, evidence was adequate that anticoagulation treatments were ineffective (except in antiphospholipid antibody syndrome) and had treatment-associated harms. The certainty of evidence is moderate (high, moderate, and low) that anticoagulation of women with recurrent pregnancy loss and F5/F2 variants would currently lead to net harms.

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.

Thrombophilia screening--at the right time, for the right patient, with a good reason

Thrombophilia can be identified in about half of all patients presenting with venous thromboembolism (VTE). Thrombophilia screening for various indications has increased tremendously, but whether the results of such tests help in the clinical management of patients is uncertain. Here, current recommendations for thrombophilia screening in selected groups of patients, and considerations whether other high-risk subjects should be tested are reviewed. The methods for determination of the most common thrombophilic defects (antithrombin, protein C, protein S deficiencies, Factor V Leiden and prothrombin G20210A) associated with strong to moderate risk of VTE are described, indicating the timing and location of thrombophilia screening. Circumstances when a positive result of thrombophilia screening helps clinicians decide if adjustments of the anticoagulant regime are needed are discussed. Finally, psychological, social and ethical dilemmas associated with thrombophilia screening are indicated.