Multiplex Allele-specific PCR Research Articles

Abstract 5703: An ultra-sensitive multiplex allele-specific real-time PCR (Udx-PCR) assay for detection of ESR1 mutations in metastatic breast cancer

Abstract Activating mutations of estrogen receptor α (ESR1) are attributed to acquired resistance to estrogen-deprivation therapy in patients with metastatic breast cancer (MBC). Thus, detection of these mutations is clinically critical for monitoring early progression and effective therapeutic options in treatment of BC patients under hormonal therapy. However, current investigations for detection ESR1 mutations mainly focus on digital PCR technology due to low abundance of the cfDNA in plasma samples, which is not a currently feasible method for clinical diagnosis. Herein, we developed a multiplex allele-specific real-time (ARMS) PCR assay for detection of ESR1 four mutations (Y537S, Y537C, Y537N, and D538G) in a single tube reaction. In this real-time PCR system, the wild-type ESR1 DNA is completely blocked by a modified probe with a higher annealing temperature, and the mutant gene is selectively amplified by the modified ARMS primers. The assay was found to be highly specific and sensitive. With this assay, as low as 0.1% mutant DNA template in the background of a total of 10ng wild-type genomic DNA could be detected. By using this assay, we analyzed the ESR1 mutations in 50 Chinese MBC FFPE and plasma samples. The ESR1 mutations were detected in 3 FFPE and 6 plasma samples, which were confirmed by pyrophosphate sequencing. The multiplex allele-specific real-time PCR assay provides a rapid and reliable diagnostic tool for accurate detection of ESR1 mutations with potential for clinical application. Citation Format: Jiasu Liu, Yaohuai Wang, Shengrong Sun, Dehua Derek Yu. An ultra-sensitive multiplex allele-specific real-time PCR (Udx-PCR) assay for detection of ESR1 mutations in metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5703. doi:10.1158/1538-7445.AM2017-5703

Association between the Prevalence of Somatic Mutations in PIK3CA Gene in Tumors and Clinical and Morphological Characteristics of Breast Cancer Patients.

The presence of activating somatic mutations in codons 542 and 545 of exon 9 (p.E542K c.1624G>A and p.E545K c.1633G>A) and in codon 1047 of exon 20 (p.H1047R c.3140A>G and p.H1047L c.3140A>T) of PIK3CA gene encoding catalytic p110α-subunit of phosphatidylinositol-3-kinase was studied in tumors of 473 breast cancer patients by multiplex allele-specific real-time PCR. Fifty-eight (12.3%) different mutations were found. An increase in the frequency of PIK3CA gene mutations with disease progression (from 2.4 to 28.7% with tumor progression from I-IIa to III-IV stage; p=0.0001) and a trend towards its increase in the tumors with unfavorable prognostic characteristics (high histological grade, triple negative phenotype) were demonstrated. The presence of the studied PIK3CA gene mutations in tumors significantly reduces relapse-free survival in the total group and in stage III cancer patients.

Molecular detection of drug resistance to ofloxacin and kanamycin in Mycobacterium tuberculosis by using multiplex allele-specific PCR

Drug resistance in tuberculosis (TB) is the biggest global health challenge as it hinders the tuberculosis control program and makes the disease more worsen. Molecular methods interrupt the spread of drug resistance by facilitating the appropriate anti- tuberculosis therapy at correct time through rapid diagnosis of multi drug resistant (MDR) and extensively drug resistant tuberculosis (XDR-TB). In this study we standardized and evaluated the diagnostic utility of multiplex allele specific PCR (MAS-PCR) targeting gyrA D94G and rrs A1401G mutations for detection of resistance against two key drugs (ofloxacin and kanamycin) of second line anti tuberculosis treatment. MAS-PCR assays targeting gyrA D94G and rrs A1401G for ofloxacin (OFL) and kanamycin (KAN) resistance respectively were carried out on 150 multidrug resistant isolates of Mycobacterium tuberculosis. The results were compared with phenotypic drug susceptibility test against ofloxacin and kanamycin by using proportion method on MGIT 960. Of 150 MDR isolates 50 were resistant to both ofloxacin and kanamycin, 36 were resistant to ofloxacin only, 8 were resistant to kanamycin only and 56 were susceptible to both the drugs. MAS-PCR correctly identified gyrA D94G and rrs A1401G mutations in phenotypically resistant isolates with a specificity of 100%. The sensitivity of MAS-PCR was 88.66%, 93.55% and 86% for OFL, KAN and XDR-TB respectively. There was no mutation detected at gyrA D94G region of 12.86% (11 of 86) OFL resistant isolates while 6.89% (4 of 58) of KAN resistant isolates did not carry rrs A1401G substitution. MAS-PCR proves to be a rapid tool for detection of drug resistance which could also be used as an initial marker for screening of XDR-TB.

Identification of Panax ginseng, P. notoginseng and P. quinquefolius admixture by multiplex allele-specific polymerase chain reaction

To achieve a molecular method to identify Panax ginseng, P. notoginseng,P. quinquefolius and their admixture. The ITS,18S and matK sequences of Panax genus were analyzed to develop species-specific SNP marker. Three pairs of species-specific primers were designed to establish a multiplex allele-specific polymerase chain reaction (MAS-PCR) and the samples from different region were tested. The results showed that when the annealing temperature was 60 ℃ and the cycle number was 35, approximately 250, 500,1 000 bp specific band were obtained from P. ginseng, P. notoginseng and P. quinquefolius obtain, respectively. This method could also be used to authentificate admixture samples and could detect 0.5% percent of P. notoginseng or P. quinquefolius adulterated in P. ginseng, or 0.5% percent of P. ginseng or P. quinquefolius adulterated in P. notoginseng. The detect limit of P. ginseng in P. quinquefolius was 0.5% and P. notoginseng in P. quinquefolius was 1%. This results showed that the present method could be used as a promise method to identify Panax ginseng, P. notoginseng, P. quinquefolius and their admixture.

Epidemiology and Molecular Basis of Resistance to Fluconazole Among Clinical Candida parapsilosis Isolates in Kuwait.

Fluconazole resistance among clinical Candida parapsilosis isolates is an emerging problem in many countries, including Kuwait. Resistance to fluconazole is mediated by amino acid substitutions in ERG11 and/or by overexpression of efflux pumps MDR1 and CDR1. Clinical C. parapsilosis sensu stricto isolates (n = 442) were tested for susceptibility to fluconazole by Etest, Vitek II, and broth microdilution methods. ERG11 was analyzed from fluconazole-resistant, fluconazole-susceptible dose-dependent, and selected fluconazole-susceptible isolates. Of 442 C. parapsilosis isolates, 425, 2, and 15 were identified as susceptible, susceptible dose-dependent, and resistant to fluconazole, respectively. PCR sequencing of ERG11 identified Y132F mutation in 5 of 11 fluconazole-resistant isolates available for analysis. This mutation was absent in 46 fluconazole-susceptible and 2 fluconazole-susceptible dose-dependent isolates. A multiplex allele-specific PCR was developed for detection of Y132F mutation in ERG11, and results correlated perfectly with PCR sequencing data for ERG11 codon 132 for all isolates analyzed. Detection of resistance in 15 and reduced susceptibility in 2 among 442 C. parapsilosis isolates highlights emerging resistance to fluconazole in Kuwait. The Y132F mutation in ERG11 was found in 5 of 11 (45%) fluconazole-resistant isolates only. Detection of fluconazole resistance in C. parapsilosis will help in proper management of patients infected with this species.

Hematological Characterizations and Molecular Diagnostic Aspects of Hb Wiangpapao [α44(CE2)Pro→Ser (α1), CCG>TCG; HBA1: c.133C>T], a New α-Globin Variant Found in a Pregnant Thai Woman

We report the hematological parameters and provide a rapid molecular analysis method for detection of Hb Wiangpapao [α44(CE2)Pro→Ser, CCG>TCG; HBA1: c.133C>T], a new α-globin variant found in a pregnant Thai woman. Her red cell indices were measured by an automated blood counter. The results were: red blood cell (RBC) count 4.03 × 1012/L, Hb 13.1 (g/dL), packed cell volume (PCV) 0.39 L/L, mean corpuscular volume (MCV) 97.0 fL, mean corpuscular hemoglobin (Hb) (MCH) 32.5 pg, mean corpuscular Hb concentration (MCHC) 33.4 g/dL, and RBC distribution width (RDW) 9.4%. The Hb typing by high performance liquid chromatography (HPLC) showed 13.6% abnormal Hb at a retention time of 2.20 min. that was difficult to distinguish from Hb A. On the capillary electrophoresis (CE) electropherogram, this hemoglobinopathy peak did not separate from the Hb A peak. DNA sequencing showed a C>T transition at the first position of codon 44 (CCG>TCG) of the α1-globin gene that led to a substitution of proline for serine. This mutation has not been recorded in the public databases. Therefore, we named it Hb Wiangpapao as it was first discovered in the Wiangpapao District, Chiang Rai, Thailand. The multiplex allele-specific polymerase chain reaction (ASPCR) for detection of Hb Wiangpapao was developed and revealed a 510 bp specifically amplified fragment. The better understanding of hematological characterizations and the newly developed multiplex ASPCR for diagnosis of Hb Wiangpapao are useful for genetic counseling and family education.

Specific authentication of Hippocampus based on SNP markers

Seahorses, which are used as traditional Chinese medicine, have large market demands and premium price. Because of overfishing, many seahorse species are endangered and listed in IUCN Red List. The purpose of this study was to develop a simple, rapid and reliable molecular method for specific authentication of seahorse species. Cytochrome c oxidase subunit I (COI) sequences were analyzed for molecular authentication of seahorses in this study. Many single nucleotide polymorphism (SNP) sites were detected among COI sequences of nine seahorse species. Based on the SNP sites, four pairs of modified specific primers were designed respectively for authentication of Hippocampus kuda, Hippocampus japonicus, Hippocampus trimaculatus and Hippocampus kelloggi using allele-specific PCR. Moreover, a multiplex allele-specific PCR for simultaneous authentication of H. kuda, H. japonicus and H. trimaculatus was also developed. The study showed that allele-specific PCR required no sequencing and electrophoresis, and the only necessity is to add fluorochrome into PCR products. Hence the whole authentication procedure only takes about 1.5 h. This work provides an effective method for rapid and reliable identification of seahorse species.

Association of the IL-10 receptor A536G (S138G) loss-of-function variant with multiple sclerosis in Tunisian patients.

Interleukin-10 (IL-10), a potent anti-inflammatory T-cell cytokine, has been shown to be a regulatory cytokine that is associated with disease remission in multiple sclerosis (MS) and exerts its activity through its cognate cell surface receptor complex, IL-10 receptor 1 (IL-10R1) and IL-10R2. The purpose of this study was to investigate the IL-10R1 S138G loss-of-function polymorphism (A536G: rs3135932) for possible influence on susceptibility and outcome of MS in Tunisian patients. A total of 103 Tunisian MS patients and 160 control subjects were studied. Genomic DNA samples were extracted from leukocytes and used to investigate S138G polymorphism in IL-10R1 gene by multiplex allele-specific polymerase chain reaction. Associations between G allele [odds ratio (OR) = 5.57; 95% confidence intervals (CI) = 3.26-9.54; p = 10-7 ], GG genotypes [OR = 10.41; 95% CI = 2.28-47.58; p = 0.0007] and AG genotype [OR = 4.14; 95% CI = 2.16-7.93; p = 0.000016] with the risk development of MS were found. In contrast, the AA genotype seemed to be associated with protection against MS [OR = 0.17; 95% CI = 0.09-0.30; p = 10-7 ]. No association was found between S138G SNP and clinical features or disease activity of MS patients. In conclusion, our results suggest that S138G loss-of-function polymorphism of the IL-10R1 may be important risk factor in increasing susceptibility to MS.

Beta-2-adrenoreceptor polymorphism at position 16 determines the clinical severity of chronic obstructive pulmonary disease

The Arg/Arg homozygosity at codon 16 of the beta-2-adrenoreceptor (ADRB2) gene has been thought to predispose asthma patients to a poorer therapeutic response to beta-2-mimetics, or to worse control of the disease. In contrast, the results of the studies analysing the effect of ADRB2 polymorphisms on the response to beta-2-adrenoreceptor agonists in chronic obstructive pulmonary disease (COPD) patients are sparse and inconclusive. The aim of this research was to verify if p.Arg16Gly (c.46A > G) and p.Gly27Glu (c.79G > C) single nucleotide polymorphisms (SNPs) exert a negative effect on the selected clinical indicators of COPD.The SNPs of the ADRB2 were identified by multiplex allele-specific PCR on DNA isolated from the venous blood leukocytes of 92 patients with stable grade COPD. In addition, all of the patients were asked about the course of COPD during the 12 months preceding the study, including the frequency of exacerbations requiring hospitalisation, the number of antibiotic therapy courses given due to the lower respiratory tract infection, and the number of courses of systemic corticosteroid therapy administered due to the exacerbation of COPD.Arg/Arg homozygotes at codon 16 required at least two courses of antibiotic therapy administered as a result of a lower respiratory tract infection significantly more frequently than carriers of other polymorphic variants of the ADRB2. Moreover, they were the only ones who required three or more courses of corticosteroid therapy due to COPD exacerbation. No significant relationships were observed between the polymorphism at codon 27 and the analysed clinical indicators of COPD severity.These data suggested that Arg/Arg homozygosity at codon 16 of the ADRB2 gene predisposes patients to a clinically more severe course of COPD.

Helicobacter pylori Pathogenicity Associated cagA and vacA Genotypes Among Nigerian Dyspeptic Patients

Objective: Although Helicobacter pylori infection is endemic in Nigeria, the specific genotypes that influence treatment responses are scarcely known. We aimed to determine the specific genotypes of H. pylori virulence genes, vacA and cagA in dyspeptic patients.Subjects and methods: Gastric biopsy samples were obtained from 80 dyspeptic patients referred for endoscopy. Genomic DNA was extracted from biopsies using the ReliaPrep DNA kit. H. pylori DNA was detected by a singleplex PCR based on the genus specific 16s rRNA gene. The vacA subtypes for the s1 and s2 regions and the m1 and m2 alleles were detected by allele specific multiplex PCR. The cagA gene was amplified by a singleplex PCR.Results: Of the 80 samples, 30 (37.5%) had abnormal mucosa which were chronic gastritis. The rest (62.5%) had normal mucosa lining. Of the 30 chronic gastritis cases, 22 (73%) had H. pylori infection as detected by 16s rRNA PCR. Only 2 (4%) of the normal mucosa cases had H. pylori infection. For the vacA genotypes, 79% of the H. pylori infections were s1c/m2 genotype, followed by 8% s1b/m2 genotype. Three different genotypes: s1c/m1/m2, s1c/s2/m2 and s1c/m1 occurred at 4% each. The most virulent vacA genotype, s1/m1 was only 8% while the least virulent vacA genotype s2/m2 was 4%. The moderate virulent vacA genotype, s1/m2 was the most prevalent (83%) in the Nigerian patients. The most prevalent subtype was the s1c/m2. Only 7 cases (29%) were cagA positive.Conclusion: The pathogenicity-associated virulence genes present in Nigerian dyspeptic patients were moderate types. The endemicity of the disease may not necessarily lead to high rate of fatal outcomes or treatment failures as reported in other parts of the world.

Novel rapid PCR for the detection of Ile491Phe rpoB mutation of Mycobacterium tuberculosis, a rifampicin-resistance-conferring mutation undetected by commercial assays

ObjectivesNeither the liquid medium-based Bactec MGIT, nor commercial molecular assays such as the Xpert MTB/RIF and the MTBDRplus V2.0 assays are capable of detecting up to 30% of rifampicin-resistant Mycobacterium tuberculosis strains in Swaziland because of the large proportion of the rpoB Ile491Phe mutations. In other countries, the frequency of this mutation is thought to be low. MethodsWe designed a real-time multiplex allele-specific PCR assay to identify the rpoB Ile491Phe mutation responsible for these undetected resistant M. tuberculosis strains. ResultsThe technique showed 100% similarity with rpoB sequencing on a panel of 78 strains from Swaziland. ConclusionsWe propose that the detection of the rpoB Ile491Phe rpoB mutation should complement commercial assays for the diagnosis of rifampicin-resistant M. tuberculosis in routine conditions, particularly in countries where this specific mutation is frequent. The technique proposed in this paper is adapted for most reference laboratories.

Evaluation of Sensitivity of Molecular Methods for Detection of Rifampin-Resistant Strains Amongst Drug-resistant Mycobacterium tuberculosis Isolates

Background: Resistance to rifampin in multidrug-resistant M. tuberculosis (MDR-TB) is one of the major threats to the global public health system. Objectives: The aim of the present study was to explore the molecular characterization of resistance against rifampin amongst multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates obtained from patients. Methods: In this study, we used XDR (n = 6), MDR (n = 9) and rifampin sensitive (n = 39) isolates whose drug susceptibility patterns were identified by proportion method. A simple single-step multiplex-allele specific-polymerase chain reaction (MAS-PCR) assay was optimized to detect the three most frequent mutations in rifampin resistance-determining region (RRDR) fragment of rpoB gene. Additionally, single-strand conformational polymorphism (SSCP)-PCR and Sequencing were utilized. Results: Out of nine MDR isolates, five were detected by MAS-PCR as rifampin resistant (sensitivity; 55.5). In comparison with the proportion method, the sensitivity of SSCP for XDR, MDR and rifampin sensitive isolates were 83.3, 77.7 and 97.4, respectively. The DNA sequencing revealed that three of the 6 XDR isolates had several silent mutations, one isolate had one silent mutation, one strain had no mutations and only one isolate had mutations at codon 531. Conclusions: In sum, although the molecular methods are rapid, they are not able to identify resistance against rifampin efficiently. © 2016, Pediartric Infections Research Center.

Genetic diagnosis of familial hypercholesterolaemia using a rapid biochip array assay for 40 common LDLR, APOB and PCSK9 mutations

Background and aimsFamilial hypercholesterolaemia (FH) leads to a lifelong increase in plasma LDL levels with subsequent increase in premature vascular disease. Early diagnosis and treatment is the key to effective management of this condition. This research aims to produce a simple and cost effective genetic test which could identify the majority (71%) of mutations causing FH in the UK and Ireland. MethodsThe Randox Biochip Array Technology was used to detect 40 point mutations in LDLR, APOB and PCSK9 genes, over two 5 × 5 arrays. This technology uses multiplex allele specific PCR and biochip array hybridisation, followed by a chemiluminescence detection system and software for automated mutation calling. ResultsThe FH biochip array assay was validated in the Belfast Genetics Laboratory using 199 cascade screening samples previously sequenced for known FH causing family mutations, the overall sensitivity was 98%. The assay was then used for routine testing of 663 patients with possible FH, from clinics across the UK and Ireland. A total of 49 (7.4%) mutation positive individuals were identified, however, for the clinics in England the detection rate was 12.9%. Further analysis of 120 biochip negative patients, using DNA sequencing, did not identify any false negatives. ConclusionsThe FH biochip array provides a rapid and reliable genetic test for the majority of FH causing point mutations in the UK and Ireland. A total of 32 samples can be run in 3 h. This allows clinics to evaluate additional patients for a possible diagnosis of FH such as patients with high LDL, patients with early onset coronary disease, and patients with relatives known to have FH.

Genetic variations in TCF7L2 influence therapeutic response to sulfonylureas in Indian diabetics

Sulfonylureas are widely used to treat type 2 diabetes, with considerable inter-individual variation in the hypoglycaemic response to sulfonylureas. Genetic variants in the gene encoding for transcription factor-7-like 2 (TCF7L2) have been associated with type 2 diabetes. This study aimed to study the effect of variations in TCF7L2 on therapeutic response to sulfonylureas in Type 2 diabetes mellitus patients. The effect of TCF7L2 rs12255372, rs7903146 and rs4506565 genotypes on glycaemic response was observed in 250 diabetic patients treated with sulfonylureas and sulfonylureas along with metformin. The genotyping tests were done by allele-specific multiplex PCR. Glycated haemoglobin (HbA1c) levels were used as phenotypic marker. 60% of sulfonylurea users did not achieve a target HbA1c levels of ⩽6.5% (48mmol/mol) (which denotes good control in diabetics). Genotype influenced response to sulfonylureas, with more treatment failure in the TT homozygotes in case of rs12255372 and rs4506565. The GG genotype at rs12255372 favourably influences treatment success with sulfonylurea therapy in patients with type 2 diabetes (p⩽0.05). At rs12255372, 70.5% GT or TT genotype failed to achieve therapeutic target, an absolute difference of 19% compared to GG homozygotes. Our preliminary data show that genetic variation at rs12255372 has a direct correlation with therapeutic success with sulfonylureas in type 2 diabetes, hence paving the way for better treatment outcomes in diabetics.

ASSOCIATION OF OBESITY WITH JAK2 V617F GENE MUTATION IN RECURRENT PREGNANCY LOSS

Maternal obesity is one of the factors that have a role in recurrent pregnancy loss ( RPL) . Increased rate of fetal loss in obese pregnant women might be due the mutation in Janus kinase2 gene (V617F). Our aim to explore the association of obesity with JAK2 V617F mutation in recurrent pregnancy loss. The study is carried out on 250 women, the case group have history of recurrent pregnancy loss with a body mass index (BMI) of >24.9kg/m2.Control group consists of women with normal body mass index with at least one live child birth and with no history of pregnancy loss. All of the subjects were investigated for the mutations by using the allele-specific multiplex PCR. In the 250 women in the study, women who were obese and tested positive for JAK2 V617F were 14 %. The case group revealed 9.3% patients who were for JAK2 V617F and had a BMI with mean of 30.9 ±4.3 ,history of live birth were 64 out of 150 with a mean of 1.3 ±0.5. In conclusion the study was able to find a correlation between the increased risk for the occurrence of RPL in obese women and the investigated V617F mutation in the Jak2 gene exon 12 and that obesity could be a risk modifier for that somatic mutation.

A multiplex allele-specific real-time polymerase chain reaction assay for HLA-B*13:01 genotyping in four Chinese populations.

Human leukocyte antigen HLA-B*13:01 is identified currently as a marker of individual susceptibility to drug-induced hypersensitivity reaction, such as dapsone-induced hypersensitivity reactions (DIHRs) and trichloroethylene-induced dermatitis. Therefore, screening for the HLA-B*13:01 allele can assist clinics in identifying patients at risk of developing DIHRs. By combining the allele-specific primers with TaqMan probes, we established a single tube, triplex real-time PCR to detect HLA-B*13:01. The reliability of this assay was validated by the comparison of genotyping results with those by sequence-based typing (SBT). With this assay, the distribution of HLA-B*13:01 in a total of 350 blood samples from four ethnic groups: Han, Tibetan, Uighur, and Buyei were determined. A 100% concordance was observed between the results with the established real-time PCR and SBT in 100 samples. The detection limit of this assay was 0.016 ng genomic DNA. The prevalence of HLA-B*13:01 carriers were 11%, 8%, 1%, and 2% in the Buyei (n = 100), Northern Han (n = 100), Tibetan (n = 100), and Uighur (n = 50) populations, respectively. The multiplex real-time PCR assay provided a fast and reliable method for accurate detection of HLA-B*13:01 allele prior to dapsone administration in clinical practice and onset of the reaction after exposure to trichloroethylene.

Rapid Detection of Rifampicin- and Isoniazid-Resistant Mycobacterium tuberculosis Using Real-Time PCR.

BackgroundAccurate and rapid detection of drug-resistant Mycobacterium tuberculosis is fundamental for the successful treatment of tuberculosis (TB).ObjectivesThe aim of this study was to determine the frequency of common mutations leading to isoniazid (INH) and rifampicin (RMP) resistance.Patients and MethodsIn a cross-sectional study carried out in 2014, 90 patients with M. tuberculosis from five border provinces of Iran were selected. After a full clinical history and physical evaluation, real-time polymerase chain reaction (PCR) technique was performed for the detection of mutations in the patients’ katG and rpoB genes. The results were compared with results of a standard proportion method as well as a multiplex allele-specific PCR (MAS-PCR).ResultsA total of 23 mutations were found in isolates among which, codon katG 315, rpoB P1 (511 - 519 sequence) and rpoB P2 (524-533 sequence) were responsible for seven, nine and seven cases, respectively. The mean (standard deviation (SD)) of melting temperature (Tm) in katG 315 codon, rpoB P1 and P2 sequences in susceptible and mutant isolates was as follows: katG 85.4°C (0.18) and 87.54°C (0.62); rpoΒ P1 84.6°C (0.61) and 82.9°C (0.38); rpoΒ P2 83.4°C (0.18) and 85.3°C (0.19), respectively. In comparison to the standard proportion test, the sensitivity of real-time PCR in detecting INH- and RMP-resistant mutations was 75% and 83.3%, respectively. In comparison to the MAS-PCR test, 100% of katG 315 mutations and 80% of rpoB mutations were determined. Overall, 10% of the patients were diagnosed with a recurrence of TB. Age and previous history of TB treatment increased mutation odds in rpoB sequences (P = 0.046, P = 0.036, respectively).ConclusionsDetection of drug resistance associated with mutations through real-time PCR by melting analysis technique showed a high differentiating power. This technique had high concordance with the standard proportion test and MAS-PCR results.

Rapid Detection of Genomic Mutations in gyrA and parC Genes of Escherichia coli by Multiplex Allele Specific Polymerase Chain Reaction.

Fluoroquinolone (FR) resistant Escherichia coli infection has become a global problem. The FR resistance usually occurs mainly due to specific point of mutations within the quinolone resistance-determining regions (QRDRs) at the gyrA codon of Ser83 and Asp87 and the parC codon of Ser80 and Glu84. Here, we appraised type and frequency of the QRDR mutations in FR-resistant E. coli isolates, and developed multiplex allele specific PCR (MAS-PCR) for the detection of "hot spot" mutations. A total of 111 ciprofloxacin-resistant E. coli from Ramathibodi Hospital in Bangkok, Thailand, were performed Minimum Inhibitory Concentration (MIC) by Etest® and investigated for gyrA and parC genes' mutations by MAS-PCR. Sensitivity and specificity of MAS-PCR were compared to the sequencing method's. Ninety-nine of 111 (89.19%) E. coli isolates had mutation at least one point in the QRDRs. Six usual amino acid substitutes were reported, including Ser83-Lue, Asp87-Asn, Asp87-Tyr, Ser80-Ile, Glu84-Gly, and Glu84-Val. MAS-PCR detected codons 83 and 87 in gyrA and codons 80 and 84 in parC mutations, yielding 96.97%, 100%, 100%, and 93.33% sensitivity, respectively, and 100%, 100%, 100%, and 98.48% specificity, respectively. MAS-PCR may be used for rapid detection of FR resistance in routine laboratory as well as in epidemiology study.

Evaluation of efficiency of nested multiplex allele-specific PCR assay for detection of multidrug resistant tuberculosis directly from sputum samples.

For an effective control of tuberculosis, rapid detection of multidrug resistant tuberculosis (MDR-TB) is necessary. Therefore, we developed a modified nested multiplex allele-specific polymerase chain reaction (MAS-PCR) method that enables rapid MDR-TB detection directly from sputum samples. The efficacy of this method was evaluated using 79 sputum samples collected from suspected tuberculosis patients. The performance of nested MAS-PCR method was compared with other MDR-TB detection methods like drug susceptibility testing (DST) and DNA sequencing. As rifampicin (RIF) resistance conforms to MDR-TB in greater than 90% cases, only the presence of RIF-associated mutations in rpoB gene was determined by DNA sequencing and nested MAS-PCR to detect MDR-TB. The concordance between nested MAS-PCR and DNA sequencing results was found to be 96·3%. When compared with DST, the sensitivity and specificity of nested MAS-PCR for RIF-resistance detection were determined to be 92·9 and 100% respectively. For developing- and high-TB burden countries, molecular-based tests have been recommended by the World Health Organization for rapid detection of MDR-TB. The results of this study indicate that, nested MAS-PCR assay might be a practical and relatively cost effective molecular method for rapid detection of MDR-TB from suspected sputum samples in developing countries with resource poor settings.

Genetic determinants of lipid-lowering response to atorvastatin therapy in an Indian population.

Statins form the backbone of lipid-lowering therapy for the prevention of cardiovascular disease. However, there is large interindividual variability in clinical response to statin treatment. Several gene variants that can be aligned to either the pharmacokinetics or pharmacodynamics of statin have been proposed as potentially important determinants of statin response. We aimed to study the association of known variations in SLCO1B1, CYP3A4, ABCB1, CYP3A5, ABCG5 and CYP7A1 genes with lipid levels in response to atorvastatin therapy. Genotypes were determined using multiplex allele-specific polymerase chain reaction in 177 Indian patients, treated with 10 mg of atorvastatin for 8 weeks. Low-density lipoprotein-cholesterol (LDL-C) levels were recorded at baseline and after 8 weeks of atorvastatin treatment. A total of 177 hypercholesterolaemic patients were genotyped to study genetic determinants of atorvastatin response. The genotype distribution for all polymorphisms investigated was in Hardy-Weinberg equilibrium. In our study, patients with wild-type genotypes of CYP7A1 (rs3808607), CYP3A4 (rs2740574), SLCO1B1 (rs2306283) and variant allele-carrying genotype of ABCB1 (rs2032582, rs1045642) showed significantly greater LDL-cholesterol reductions in response to atorvastatin therapy. The variable response to atorvastatin therapy in terms of LDL-cholesterol lowering due to genetic variations in CYP7A1, CYP3A4, SLCO1B1 and ABCB1 is a promising finding. Further validation in large Indian cohorts is required before it can be assessed for clinical utility.