Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping Research Articles

Genotyping of toxoplasma gondii isolates from México reveals non-archetypal and potentially virulent strains for mice.

Genotyping and virulence studies of Toxoplasma gondii are essential to investigate the pathogenesis of strains circulating worldwide. In this study, eight T. gondii isolates obtained from a congenitally infected newborn, a calf, two cats, three dogs, and a wallaby from five states of México were genotyped by Mn-PCR-RFLP with 11 typing markers (SAG1, SAG2 5'3', altSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico), five virulence markers (CS3, ROP16, ROP17, ROP18 and ROP5), 15 microsatellite markers (TUB-2, W35, TgM-A, B18, B17, M33, IV.1, XI.1, M48, M102, N60, N82, AA, N61, N83), and sequencing. A phylogenetic network was built to determine the relationship between Mexican isolates and those reported worldwide. Six different genotypes were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), ToxoDB #8, #10, #28 (n = 3), #48, #116, and #282. Genotyping by microsatellite analysis differentiated the three PCR-RFLP genotype #28 isolates into two strains, revealing a total of seven microsatellite genotypes. Three different allele combinations of ROP18/ROP5 virulence markers were also found, 3/3, 1/1, and 4/1. The last two combinations are predicted to be highly virulent in the murine model. According to the phylogenetic network, the T. gondii strains studied here are related to archetypal strains I and III, but none are related to the strains previously reported in México. The genotypes identified in this study in different species of animals demonstrate the great genetic diversity of T. gondii in México. The ToxoDB-PCR-RFLP #28 genotype was found in three isolates from different hosts and states. Additionally, four of the isolates are predicted to be highly virulent in mice. The next step will be to perform in vitro and in vivo assays to determine the phenotype of these T. gondii isolates in murine models.

Exploring the genetic diversity of Eimeria acervulina: A polymerase chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) approach

Eimeria, protozoan parasites that can cause the disease coccidiosis, pose a persistent challenge to poultry production and welfare. Control is commonly achieved using good husbandry supplemented with routine chemoprophylaxis and/or live parasite vaccination, although widespread drug resistance and challenges to vaccine supply or cost can prove limiting. Extensive effort has been applied to develop subunit anticoccidial vaccines as scalable, cost-effective alternatives, but translation to the field will require a robust understanding of parasite diversity. Using a new Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) panel we begin to describe the genetic diversity of Eimeria acervulina populations in Africa and Europe. PCR-RFLP genotyping E. acervulina populations sampled from commercial broiler and layer chickens reared in Nigeria or the United Kingdom (UK) and Republic of Ireland (RoI) revealed comparable levels of haplotype diversity, in direct contrast to previous descriptions from the close relative E. tenella. Here, 25 distinct PCR-RFLP haplotypes were detected from a panel of 42 E. acervulina samples, including 0.7 and 0.5 haplotypes per sample in Nigeria (n = 20) and the UK/RoI (n = 14), respectively. All but six haplotypes were found to be country-specific. The PCR-RFLP markers immune mapped protein 1 (IMP1) and heat shock protein 90 (HSP90) were most informative for Nigerian E. acervulina, while microneme protein 3 (MIC3) and HSP90 were most informative in UK/RoI populations. High haplotype diversity within E. acervulina populations may indicate frequent genetic exchange and potential for rapid dissemination of genetic material associated with escape from selective barriers such as anticoccidial drugs and future subunit vaccines.

Pharmacogenetic Study of the Impact of ABCB1 Single Nucleotide Polymorphisms on the Response to Cyclosporine in Psoriasis Patients.

Psoriasis is a chronic, T cell-mediated skin disease affecting 2-3% of the Caucasian population. Cyclosporine A is a calcineurin inhibitor that acts selectively on T cells. The cyclosporine A treatment response has been suggested to be modulated by single-nucleotide polymorphisms (SNPs) in the ABCB1 gene. The aim of this research was to evaluate the effect of ABCB1 genetic variants that could affect the response to a cyclosporine treatment in Russian psoriasis patients with the ABCB1 genotype status. The ABCB1 T-129C, G1199A, C1236T, G2677T/A and C3435T SNPs in the 168 patients with psoriasis were genotyped by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) and TaqMan SNP genotyping assays. The ABCB1 C1236T, G2677T/A and C3435T SNPs were significantly associated with a negative response to cyclosporine therapy. A very strong association was evident for the C3435T SNP in the ABCB1 gene in the allele, dominant and recessive models (OR = 2.58, OR = 4.01, OR = 2.50, respectively). ABCB1 C1236T and G2677T/A polymorphisms were significantly associated with a negative response to the cyclosporine therapy in the codominant, dominant and recessive models (p ˂ 0.05). Additionally, the haplotype analysis identified that the TGC haplotype is significantly associated with a negative response to cyclosporine therapy in psoriasis patients (p ˂ 0.05). The current study to the best of our knowledge is the first of its kind to be performed in the Russian population. In conclusion, the present results suggest an association between the ABCB1 genetic variants and unresponsiveness to cyclosporine in the Russian population. Further, larger studies are necessary to confirm our findings and replicate them in various ethnic populations before its implementation in the clinical practice.

PCR-RFLP genotyping analysis of TP53 Arg72Pro polymorphism and susceptibility to esophageal cancer in Pakistani population

Background and objectiveTumor suppressor gene TP53 is necessary for prevention of inappropriate cell proliferation and maintenance of genome integrity. TP53 Arg72Pro is the most studied single nucleotide polymorphism (SNP) associated with different cancers including esophageal cancer (EC). The study was established to investigate relationship between Arg72Pro polymorphism and EC susceptibility. Materials and methodsDNA from a total of 200 individuals (100 EC patients and 100 controls) were genotyped for TP53 codon 72 (Arg72Pro) polymorphism by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Logistic regression was used to estimate odds ratios and 95% confidence interval. ResultsSignificant differences in genotypes of Arg72Pro polymorphism between cases and controls were observed (P < 0.05). The patients represented 34% Pro/Pro, 44% Arg/Pro and 22% Arg/Arg whereas controls had 19% Pro/Pro, 42% Arg/Pro and 39% Arg/Arg genotypes. Pro/Pro variant showed 3.17-fold (95% CI: 1.47–6.83, P = 0.003) and Arg/Pro 1.71-fold (95% CI: 0.85–3.45, P = 0.071) increased EC risk compared with Arg/Arg. The Pro/Pro genotype was found to be significantly, whereas Arg/Pro was non-significantly associated with the esophageal cancer risk. Both males and females with Pro/Pro genotype were highly susceptible to cancer. Preserved meat consumers with Pro/Pro genotype were 4.8 fold (95% CI: 1.7–13.8) and subjects aged >50 with Pro/Pro were 4.6 fold (95% CI: 1.8–11.8) at increased risk of esophageal cancer. ConclusionsOur study suggests that Pro72 variant of TP53 polymorphism is highly correlated with increased EC. Further, the interaction between this polymorphism and tobacco consumption significantly affected EC development in Pakistani population.

Toxoplasma gondii prevalence in carnivorous wild birds in the eastern United States.

Toxoplasma gondii is an important zoonotic protozoan parasite that can infect all warm-blooded animals including mammals and birds. Raptors can be intermediate hosts for T. gondii and the infection may be dependent on their feeding habits. In this study, we investigated the seroprevalence of T. gondii in ten raptor species from Florida, Pennsylvania, and Tennessee followed by a parasite bioassay on select seropositive samples. From a total of 155 raptors, we detected T. gondii antibodies using a modified agglutination test (cutoff 1:25) in 32 (20.6%) birds. The T. gondii seroprevalence was 44.8% in Falconiformes (13/29), 75% in Strigiformes (15/20), and 3.8% in Ciconiiformes (4/106). All Ciconiiformes samples (hearts and sera) were collected from Pennsylvania during nuisance wildlife removal projects and all birds were apparently healthy. Falconiform and Strigiform samples were collected from an exotics clinic in Tennessee and a rehabilitation center in Florida. All sampled birds were dead or euthanatized due to failure of rehabilitation or treatment. There was no statistically significant difference in T. gondii seroprevalence between Tennessee and Florida in the tested raptors. There was also no statistically significant difference in T. gondii exposure between males and females or adults and subadults. Mice bioassay attempts using fresh brain and/or heart tissue were performed on four seropositive birds. We isolated viable T. gondii tachyzoites from one red-shouldered hawk (Buteo lineatus) and genotyped the isolate using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of ten genetic markers. The isolated strain was designated as TgHawkFL1, which is ToxoDB PCR-RFLP genotype #28. Further research is needed to investigate the prevalence of T. gondii in raptors in the United States to obtain a better understanding of the life cycle, wildlife population impacts, and transmission dynamics of the parasite.

A facile PCR-RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms.

Inosine triphosphate pyrophosphatase (ITPA) gene single nucleotide polymorphisms (SNPs), rs1127354 and rs7270101, may cause a functional impairment in ITPase enzyme, resulting anemia protection in patients with chronic hepatitis C virus (HCV) infection undergoing ribavirin (RBV)-dependent regimens. The main purpose of this study was to provide and validate a simple, rapid, and inexpensive polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique for genotyping of ITPA rs1127354 and rs7270101 polymorphisms in chronic HCV-infected patients. In the current study, 100 Iranian patients with chronic hepatitis C were examined and genotyped for ITPA rs1127354 and rs7270101 gene polymorphisms. To genotype rs1127354 and rs7270101 polymorphisms, PCR-RFLP technique and sequencing technique were performed on these samples. To validate the PCR-RFLP method, the PCR-RFLP genotyping results should be 100% concordant with the PCR-sequencing results. The rs1127354 and rs7270101 polymorphisms of ITPA gene were genotyped by PCR-RFLP technique and sequencing simultaneously, and the results of both techniques were 100% concordant in all 100 patients. Both PCR-RFLP and sequencing techniques indicated that the genotypic frequency of rs7270101 was 80% AA, 19% AC and 1% CC, and for rs1127354 was 79% CC, 20% CA and 1% AA, respectively. We developed and validated a rapid and inexpensive PCR-RFLP technique for the detection of ITPA rs1127354 and rs7270101 gene polymorphisms.

Toxoplasma gondii seroprevalence and genotype diversity in select wildlife species from the southeastern United States

BackgroundToxoplasma gondii is a widespread protozoan parasite that infects humans and other animals. Previous studies indicate some genotypes of T. gondii are more frequently isolated in wildlife than agricultural animals, suggesting a wild/feral animal diversity model. To determine seroprevalence and genetic diversity of T. gondii in southeastern US wildlife, we collected sera from 471 wild animals, including 453 mammals and 18 birds, between 2011 and 2014. These serum samples were assayed for T. gondii infection using the modified agglutination test (MAT). Heart or tongue tissues from 66 seropositive animals were bioassayed in mice and 19 isolates were obtained. The isolated parasites were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method employing 10 genetic markers.ResultsOne hundred and ninety-six of 471 samples (41.6%) had a titer ≥1:32 and were considered positive for T. gondii infection. Of 453 mammals, 195 (43%) were seropositive, whereas only one (5.6%) of 18 birds was seropositive. The seroprevalence in mammals was significantly higher than in the birds. Mammalian hosts with adequate samples size (≥ 20) comprised white-tailed deer (n = 241), feral hogs (n = 100), raccoons (n = 34) and coyotes (n = 22), with seroprevalences of 41.0%, 51.0%, 50.0% and 72.7%, respectively. Coyotes had significantly higher seroprevalence than the white-tailed deer. Genotyping revealed five distinct genotypes, including the ToxoDB PCR-RFLP genotype #5 (a.k.a type 12) for 15 isolates, genotype #3 (a.k.a. type II) for 1 isolate, and genotypes #154, #167 and #216, each for 1 isolate. The results showed moderate to high infection rates of T. gondii in white-tailed deer, feral hogs, raccoons and coyotes. Genotyping results indicated limited genetic diversity and a dominance of genotype #5, which has been reported as a major type in wildlife in North America.ConclusionsWe conclude that T. gondii infection is common in game animals (white-tailed deer and feral hogs) in the southeastern US, which may pose a food safety risk to humans. Further research is necessary to understand T. gondii transmission from wildlife to farm animals and humans.

Molecular Detection and Genetic Characterization of Toxoplasma gondii in Farmed Minks (Neovison vison) in Northern China by PCR-RFLP.

Toxoplasma gondii is a worldwide prevalent parasite, affecting a wide range of mammals and human beings. Little information is available about the distribution of genetic diversity of T. gondii infection in minks (Neovison vison). This study was conducted to estimate the prevalence and genetic characterization of T. gondii isolates from minks in China. A total of 418 minks brain tissue samples were collected from Jilin and Hebei provinces, northern China. Genomic DNA were extracted and assayed for T. gondii infection by semi-nested PCR of B1 gene. The positive DNA samples were typed at 10 genetic markers (SAG1, SAG2 (5'+3' SAG2, alter.SAG2), SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. 36 (8.6%) of 418 DNA samples were overall positive for T. gondii. Among them, 5 samples were genotyped at all loci, and 1 sample was genotyped for 9 loci. In total, five samples belong to ToxoDB PCR-RFLP genotype#9, one belong to ToxoDB genotye#3. To our knowledge, this is the first report of genetic characterization of T. gondii in minks in China. Meanwhile, these results revealed a distribution of T. gondii infection in minks in China. These data provided base-line information for controlling T. gondii infection in minks.

Toxoplasmosis in geese and detection of two new atypical Toxoplasma gondii strains from naturally infected Canada geese (Branta canadensis).

Wild birds are important in the epidemiology of toxoplasmosis because they can serve as reservoir hosts, and vectors of zoonotic pathogens including Toxoplasma gondii. Canada goose (Branta canadensis) is the most widespread geese in North America. Little is known concerning T. gondii infection in both migratory, and local resident populations of Canada geese. Here, we evaluated the seroprevalence, isolation, and genetic characterization of viable T. gondii isolates from a migratory population of Canada geese. Antibodies against T. gondii were detected in 12 of 169 Canada geese using the modified agglutination test (MAT, cutoff 1:25). The hearts of 12 seropositive geese were bioassayed in mice for isolation of T. gondii. Viable parasites were isolated from eight. One isolate was obtained from a seropositive goose by both bioassays in mice, and in a cat; the cat fed infected heart excreted T. gondii oocysts. Additionally, one isolate was obtained from a pool of four seronegative (<1:25) geese by bioassay in a cat. The T. gondii isolates were further propagated in cell culture, and DNA extracted from cell culture-derived tachyzoites were characterized using 10 polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) genetic markers (SAG1, 5' and 3'SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). The results revealed five different genotypes. ToxoDB PCR-RFLP genotype #1 (type II) in one isolate, genotype #2 (type III) in four isolates, genotype #4 in two isolates, and two new genotypes (ToxoDB PCR-RFLP genotype #266 in one isolate and #267 in one isolate) were identified. These results indicate genetic diversity of T. gondii strains in the Canada geese, and this migratory bird might provide a mechanism of T. gondii transmission at great distances from where an infection was acquired.

Polymorphisms in methylenetetrahydrofolate reductase and cystathionine beta-synthase in oral cancer – a case–control study in southeastern Brazilians

IntroductionOral squamous cell carcinoma (OSCC) is a serious public health problem, due to its high mortality rate and worldwide rising incidence. OSCC susceptibility is mediated by interactions between genetic and environmental factors. Studies suggest that genetic variants encoding enzymes involved in folate metabolism may modulate OSCC risk by altering DNA synthesis/repair and methylation process. ObjectiveThe goals of this study were to evaluate the association of three genotypic polymorphism (MTHFR C677T, MTHFR A1298C and CBS 844ins68) and oral cancer risk in southeastern Brazilians and evaluate the interactions between polymorphisms and clinical histopathological parameters. MethodsThis case–control study included 101 cases and 102 controls in the state of Espírito Santo, Brazil. MTHFR genotyping was done by PCR-RFLP (polymerase chain reaction – restriction fragment length polymorphism) and CBS genotyping by PCR (polymerase chain reaction) analysis. ResultsMTHFR C677T polymorphism was associated with lymph node involvement. Genotype CT+TT acted as a protective factor. MTHFR A1298C AC+CC genotype was associated with tumor differentiation, and possibly with a better prognosis. In risk analysis, no correlation was observed between genotypes and OSCC. ConclusionWe concluded that MTHFR C677T, MTHFR A1298C and CBS 844ins68 polymorphisms were not associated with OSCC risk in southeastern Brazilians; however, we suggest a prognosis effect associated with MTHFR C677T and A1298C polymorphisms in OSCC.

Genetic characterization of Toxoplasma gondii in Yunnan black goats (Capra hircus) in southwest China by PCR-RFLP.

BackgroundToxoplasma gondii is a protozoan parasite that infects almost all warm-blooded animals and human beings. Goats are one of the susceptible animals to T. gondii. However, little is known of genetic diversity of T. gondii in Yunnan black goats in China. The objective of this present study was to determine the genotypes of T. gondii isolates from black goats in Yunnan province, southwest China.MethodsGenomic DNA was extracted from liver (n = 403), lung (n = 403) and lymph nodes (n = 250) of Yunnan black goats and assayed for T. gondii infection by semi-nested PCR of B1 gene. Then, the positive DNA samples were typed at 10 genetic markers using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. These markers include 9 nuclear loci, namely, SAG1, SAG2 (5’-SAG2 and 3’-SAG2, alternative SAG2), SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and an apicoplast locus Apico.ResultsOut of 403 tested samples, 20 (4.96%) DNA samples were T. gondii positive by amplification of B1 gene. Among them, 2 isolates were genotyped at all loci, and 6 isolates were genotyped for 8 or more loci. In total, seven samples belong to ToxoDB PCR-RFLP genotype#10 (Type I), and one belongs to genotype ToxoDB #9.ConclusionsTo our knowledge, this is the first report of ToxoDB#9 and ToxoDB#10 T. gondii in Yunnan black goats in China. These results revealed a wide distribution of these T. gondii in Yunnan black goats in China, which has important implications for public health.

Analysing diversity and community structures usingPCR‐RFLP: a new software application

Restriction fragment length polymorphism tools is an R application which supports a complete workflow of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), dealing with the problems which accompany analysis when PCR-RFLP is used in diversity studies. Large numbers of different RFLP samples obtained from multiple electrophoresis runs might lead to limitations or misidentifications due to the need for band matching in most existing software applications. Due to the common problem of variation in the density of bands (i.e. distances between bands or visual intensity) in the electropherograms, it is desirable to have options for handling samples with uncertain or faint bands. As a further step in the workflow, scientists often use DNA sequencing to identify individual genotypes, so that the use of specific software to combine these tasks might be helpful. With this background, we here present an application that supports a complete workflow, starting with the analysis of single species samples by PCR-RFLP, to PCR-RFLP genotype identification based on a reference data set and DNA sequencing followed by similarity analysis. RFLPtools is a freely available, platform-independent application which provides analysis functions for DNA fragment molecular weights (e.g. by RFLP analysis), including similarity calculations without the need for band matching. As it is written for the statistical software R, other statistical analyses might also be easily applied.

PCR-RFLP genotyping of Toxoplasma gondii from chickens from Espírito Santo state, Southeast region, Brazil: New genotypes and a new SAG3 marker allele

Brazil is one of the regions with the highest prevalences of Toxoplasma gondii in humans and animals. Because free-range chickens become infected by feeding from ground contaminated with oocysts, the prevalence of T. gondii in this host has been widely used as an indicator of the strains prevalent in the environment. The genetic variability among T. gondii isolates from different healthy and sick hosts all over the world has been recently studied. Three clonal genetic lineages (Types I, II and III) were initially recognised as predominant in Western Europe and the United States. T. gondii strains are genetically diverse in South America. In Brazil, recombination plays an important role in strain diversification. The objective of this study was to genetically characterise T. gondii isolates from free-range chickens from Espírito Santo state, Southeast region, Brazil, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). A total of 44 isolates among 47 previously described isolates (TgCkBr234-281) from free-range chickens were included in this study. Strain typing was performed using 12 PCR-RFLP markers: SAG1, SAG2, alt. SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, Apico and CS3. Eleven genotypes were identified. Ten isolates (23%) were grouped into four novel genotypes. Four isolates, distributed in four counties, corresponded to the Type BrI lineage, the genotype found most frequently in Brazil. No clonal Types I, II or III lineages were found. Two novel genotypes were represented by single isolates. Unique alleles were identified for the markers SAG1, c22-8 and CS3, and for the first time, a unique allele was found for the marker SAG3. Although a large number of T. gondii genotypes have already been identified from a variety of animal hosts in Brazil, new genotypes are continuously identified from different animal species. This study confirmed the diversity of T. gondii in Brazil and demonstrates clonal Type I, II and III lineages are rare in this country.

Development and Validation of a Simple, Rapid and Inexpensive PCRRFLP Method for Genotyping of Common IL28B Polymorphisms: A Useful Pharmacogenetic Tool for Prediction of Hepatitis C Treatment Response

In 2009, 3 genome-wide association studies implicated IL28B single-nucleotide polymorphisms (SNPs) as the strongest genetic pretreatment predictor of sustained virological response (SVR) in hepatitis C infection. Recently, the American Association for the Study of Liver Diseases (AASLD) and the European Association for the Study of the Liver (EASL) included IL28B testing in their guidelines. The main aim of this study was to develop and validate a simple, rapid, and inexpensive polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for genotyping of common IL28B polymorphisms (rs12979860 and rs8099917). Two methods were developed to genotype common IL28B polymorphisms: 1) PCR-sequencing as a reference method and 2) PCR-RFLP as a rapid and inexpensive method. Both polymorphisms were genotyped in 104 Iranian hepatitis C patients by both methods simultaneously. To validate the PCR-RFLP method, the PCR-RFLP genotyping results should be 100% concordant with the PCR-sequencing results. Genotyping of rs12979860 and rs8099917 by PCR-RFLP was concordant with PCR-sequencing in 104 (100%) individuals. The analytical sensitivity and specificity of the PCR-RFLP method for genotyping of both SNPs are 100%. Among these 104 patients with chronic hepatitis C, the frequency of the rs12979860 CC, CT and TT genotypes were 40.4%, 47.1% and 12.5% and the frequency of the rs8099917 TT, GT and GG genotypes were 59.6%, 35.6% and 4.8%, respectively. Also, three IL28B haplotypes (rs12979860-rs8099917) were found among our patients including C-T, T-G and T-T with 63.9%, 22.6% and 13.5% frequency, respectively. C-G haplotype was absent in all of our patients. We have developed a validated, fast, and simple PCR-RFLP method for genotyping of common IL28B SNPs that is more cost-effective than sequencing.

Development and Validation of a Simple, Rapid and Inexpensive PCR-RFLP Method for Genotyping of Common IL28B Polymorphisms: A Useful Pharmacogenetic Tool for Prediction of Hepatitis C Treatment Response

: Background: In 2009, 3 genome-wide association studies implicated IL28B single-nucleotide polymorphisms (SNPs) as the strongest genetic pretreatment predictor of sustained virological response (SVR) in hepatitis C infection. Recently, the American Association for the Study of Liver Diseases (AASLD) and the European Association for the Study of the Liver (EASL) included IL28B testing in their guidelines.Objectives: The main aim of this study was to develop and validate a simple, rapid, and inexpensive polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for genotyping of common IL28B polymorphisms (rs12979860 and rs8099917).Patients and Methods: Two methods were developed to genotype common IL28B polymorphisms: 1) PCR-sequencing as a reference method and 2) PCR-RFLP as a rapid and inexpensive method. Both polymorphisms were genotyped in 104 Iranian hepatitis C patients by both methods simultaneously. To validate the PCR-RFLP method, the PCR-RFLP genotyping results should be 100% concordant with the PCR-sequencing results.Results: Genotyping of rs12979860 and rs8099917 by PCR-RFLP was concordant with PCR-sequencing in 104 (100%) individuals. The analytical sensitivity and specificity of the PCR-RFLP method for genotyping of both SNPs are 100%. Among these 104 patients with chronic hepatitis C, the frequency of the rs12979860 CC, CT and TT genotypes were 40.4%, 47.1% and 12.5% and the frequency of the rs8099917 TT, GT and GG genotypes were 59.6%, 35.6% and 4.8%, respectively. Also, three IL28B haplotypes (rs12979860-rs8099917) were found among our patients including C-T, T-G and T-T with 63.9%, 22.6% and 13.5% frequency, respectively. C-G haplotype was absent in all of our patients.Conclusions: We have developed a validated, fast, and simple PCR-RFLP method for genotyping of common IL28B SNPs that is more cost-effective than sequencing. Implication for health policy/practice/research/medical education:This article focuses on development of a simple method for genotyping of IL28B polymorphisms. This study is recommended to researchers in the field of viral hepatitis. Please cite this paper as:Sharafi H, Pouryasin A, Alavian SM, Behnava B, Keshvari M, Mehrnoush L, et al. Development and Validation of a Simple, Rapid and Inexpensive PCR-RFLP Method for Genotyping of Common IL28B Polymorphisms: A Useful Pharmacogenetic Tool for Prediction of Hepatitis C Treatment Response. Hepat Mon. 2012;12(3):190-5. DOI: 10.5812/hepatmon.849 Copyright © 2012 Kowsar Corp. All rights reserved.

Genotyping of flavin-containing mono-oxygenase 3 (FMO3) gene by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and mismatch amplification mutation assay (MAMA-PCR) in chickens

2Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science, 030000, Taiyuan, China. Accepted 13 December, 2011 Fishy smelling off-flavour of chicken meat is caused by a mutation ( FMO3 c.985A>T ) in exon 7 of flavincontaining mono-oxygenase 3 (FMO3) gene. Comparative analysis of the causative mutation in FMO3 gene in different chickens using two different methods was reported. Polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) method was based on general primers, whereas another employed method was the mismatch amplification mutation assay (MAMA) primers. Seventy (22.88%) of the 306 samples were genotyped using PCR-RFLP, 194 (63.40%) of the 306 samples were genotyped using MAMA-PCR and 42 (13.72%) of the 306 samples were genotyped by both of PCR-RFLP and MAMA-PCR and genotyping data were validated by DNA sequencing. The results show that the genotyping accuracy for PCR-RFLP was 90.48% in AA, 85.42% in AT and 95.35% in TT and 100% in AA, 98% in AT and 96% in TT for MAMA-PCR. This study suggests that the MAMA-PCR is more effective, accurate, easy, fast, efficient and reliable than PCR-RFLP.

Investigation of Transforming Growth Factor-β1 Gene Polymorphisms Among Iranian Patients With Chronic Hepatitis C

: Background: Chronic hepatitis C infection is caused by the hepatitis C virus (HCV), and its clinical complications include liver cirrhosis, liver failure, and hepatocellular carcinoma. Transforming growth factor-β1 (TGF-β1) is an important cytokine in cell growth and differentiation, angiogenesis, extracellular matrix formation, immune response regulation, and cancer development and progression.Objectives: The aim of this study was to investigate the relationship between single nucleotide polymorphisms (SNPs) in TGF-β1 and chronic HCV infection among patients referred to the Taleghani Hospital, Tehran, Iran between 2008 and 2010.Patients and Methods: In this case-control study, samples were collected using a convenience sampling method. We genotyped 164 HCV patients and 169 healthy controls for 3 SNPs in the TGF-β1 gene (-509 promoter, codon 10, and codon 25). We determined the SNP genotypes by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. To confirm the PCR-RFLP genotyping results, 10% of the samples were re-genotyped using a direct sequencing method.Results: There were no significant differences in the allelic frequency distribution of SNPs at -509 C/T, +869 C/T, or +915 G/C between HCV patients and the healthy controls. Genotyping results for all three polymorphic sites were similar with no statistically significant differences between the groups.Conclusions: Most of the Iranian patients (over 85%), both healthy controls and HCV patients, had the GG genotype at the +915 G/C position, resulting in a high level of TGF-β1 production. Therefore, we concluded that the SNPs investigated by us cannot be considered as prognostic factors for HCV infection in our population, despite being reported as prognostic markers in other populations. Moreover, there is a possibility that most of the population is susceptible to HCV infection. Implication for health policy/practice/research/medical education: Transforming growth factor beta-1 (TGF-β1) is a multifunctional cytokine that acts as a regulator of proliferation and cellular differentiation.Investigation of the association of single nucleotide polymorphisms (SNPs) in TGF-β1 gene sequence with increased or decreased individual’s susceptibility to chronic diseases such as hepatitis C infection could be helpful to find appropriate and population specific genetic biomarkers. Please cite this paper as: Romani S, Azimzadeh P, Mohebbi SR, Kazemian S, Almasi S, Naghoosi H, et al. Investigation of Transforming Growth Factor–β1 Gene Polymorphisms Among Iranian Patients With Chronic Hepatitis C. Hepat Mon. 2011;11(11):901-6. DOI: 10.5812/kowsar.1735143X.776

Investigation of Transforming Growth Factor-β1 Gene Polymorphisms Among Iranian Patients With Chronic Hepatitis C

Chronic hepatitis C infection is caused by the hepatitis C virus (HCV), and its clinical complications include liver cirrhosis, liver failure, and hepatocellular carcinoma.Transforming growth factor-β1 (TGF-β1) is an important cytokine in cell growthand differentiation, angiogenesis, extracellular matrix formation, immune responseregulation, and cancer development and progression. The aim of this study was to investigate the relationship between single nucleotide polymorphisms (SNPs) in TGF-β1 and chronic HCV infection among patients referred to the Taleghani Hospital, Tehran, Iran between 2008 and 2010. In this case-control study, samples were collected using a convenience sampling method. We genotyped 164 HCV patients and 169 healthy controls for 3 SNPs in the TGF-β1 gene (-509 promoter, codon 10, and codon 25). We determined the SNP genotypes by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. To confirm the PCR-RFLP genotyping results, 10% of the samples were re-genotyped using a direct sequencing method. There were no significant differences in the allelic frequency distribution of SNPs at -509 C/T, +869 C/T, or +915 G/C between HCV patients and the healthy controls. Genotyping results for all three polymorphic sites were similar with no statistically significant differences between the groups. Most of the Iranian patients (over 85%), both healthy controls and HCV patients, had the GG genotype at the +915 G/C position, resulting in a high level of TGF-β1 production. Therefore, we concluded that the SNPs investigated by us cannot be considered as prognostic factors for HCV infection in our population, despite being reported as prognostic markers in other populations. Moreover, there is a possibility that most of the population is susceptible to HCV infection.

SUBSPECIES CHARACTERIZATION OF UREASE-POSITIVE THERMOPHILIC CAMPYLOBACTER (UPTC) ISOLATED FROM SHELLFISH EMPLOYING MODIFIED FLAGELLIN (flaA) RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) TYPING

Shellfish including oysters (Crassostrea gigas), cockles (Cerastoderma edule) and mussels (Mytilus edulis), have previously been described as an important source of thermophilic campylobacters, with the potential of causing acute bacterial gastroenteritis in humans. Previous genotyping studies employing the polymerase chain reaction—restriction fragment length polymorphism (PCR-RFLP) typing, based on the flagellin (flaA) gene have been unable to generate an amplicon for the urease-positive thermophilic Campylobacter (UPTC), which are the predominant taxa associated with shellfish, largely caused by sequence diversity between the UPTC group and C. jejuni. Hence the aim of this study was to develop a modified PCR-RFLP genotyping assay, employing polymorphisms within the flagellin (flaA) gene of UPTC organisms, which would now allow the successful amplification and typing of previously nontypable UPTC isolates obtained from natural marine environments. A novel primer pair (UPTC flaF/UPTC flaR) was designed based on conserved regions within the flaA gene locus of UPTC organisms to generate a 1,358 bp amplicon for all UPTC organisms tested. RFLP analysis with DdeI in combination with computational analysis of genetic relatedness using BioNumerics software demonstrated the presence of four distinct flaA genotypes, among the seven UPTC isolates. In conclusion, this study describes a PCR-RFLP method, based on modified primers from UPTC flaA gene sequences that may be successfully applied to examine subspecies relatedness of UPTC organisms from natural environments, including shellfish.

Genotyping of single nucleotide polymorphisms in cytokine genes using real-time PCR allelic discrimination technology

Single nucleotide polymorphisms (SNPs), particularly those within regulatory regions of genes that code for cytokines often impact expression levels and can be disease modifiers. Investigating associations between cytokine genotype and disease outcome provides valuable insight into disease etiology and potential therapeutic intervention. Traditionally, genotyping for cytokine SNPs has been conducted using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), a low throughput technique not amenable for use in large-scale cytokine SNP association studies. Recently, Taqman ® real-time PCR chemistry has been adapted for use in allelic discrimination assays. The present study validated the accuracy and utility of real-time PCR technology for a number of commonly studied cytokine polymorphisms known to influence chronic inflammatory diseases. We show that this technique is amenable to high-throughput genotyping and overcomes many of the problematic features associated with PCR-RFLP including post-PCR manipulation, non-standardized assay conditions, manual allelic identification and false allelic identification due to incomplete enzyme digestion. The real-time PCR assays are highly accurate with an error rate in the present study of <1% and concordance rate with PCR-RFLP genotyping of 99.4%. The public databases of cytokine polymorphisms and validated genotyping assays highlighted in the present study will greatly benefit this important field of research.