scholarly journals PharmFrag: An Easy and Fast Multiplex Pharmacogenetics Assay to Simultaneously Analyze 9 Genetic Polymorphisms Involved in Response Variability of Anticancer Drugs

2020 ◽  
Vol 21 (24) ◽  
pp. 9650
Author(s):  
Régis Bouvet ◽  
Marie-Clémence Verdier ◽  
Yahya El Baroudi ◽  
Marie-Dominique Galibert ◽  
Véronique David ◽  
...  
Keyword(s):  
Genetic Polymorphisms ◽  
Anticancer Drugs ◽  
Reference Method ◽  
Cost Effective ◽  
Cytotoxic Agents ◽  
Individual Response ◽  
Specific Pcr ◽  
Genes Encoding ◽  
Specific Pcr Assay ◽  
Widespread Access

Regarding several cytotoxic agents, it was evidenced that genetic polymorphisms in genes encoding enzymes involved in their metabolism are associated with higher risk of toxicity. Genotyping these genes before treatment is a valuable strategy to prevent side effects and to predict individual response to drug therapy. This pharmacogenetic approach is recommended for chemotherapies such as thiopurines (azathioprine, 6-mercaptopurine, thioguanine), irinotecan, and fluoropyrimidines (capecitabine and 5-fluorouracil). In this study, we aimed at developing and validating a fast, cost-effective, and easily implementable multiplex genotyping method suitable for analyzing a panel of nine variants involved in the pharmacogenetics of widely prescribed anticancer drugs. We designed a multiplex-specific PCR assay where fragments were labeled by two different fluorescent dye markers (HEX/FAM) identifiable by fragment analysis. These two labels were used to discriminate bi-allelic variants, while the size of the fragment allowed the identification of a particular polymorphism location. Variants of interest were TPMT (rs1800462, rs1142345, rs1800460), NUDT15 (rs116855232), DPYD (rs55886062, rs3918290, rs67376798, rs75017182), and UGT1A1 (rs8175347). The assay was repeatable, and genotypes could be determined when DNA sample amounts ranged from 25 to 100 ng. Primers and dye remained stable in a ready-to-use mixture solution after five freeze–thaw cycles. Accuracy was evidenced by the consistency of 187 genotyping results obtained with our multiplex assay and a reference method. The developed method is fast and cost-effective in simultaneously identifying nine variants involved in the pharmacological response of anticancer drugs. This assay can be easily implemented in laboratories for widespread access to pharmacogenetics in clinical practice.

scholarly journals Occurrence of methicillin-resistant strains of Staphylococcus aureus at a goat breeding farm

2009 ◽  
Vol 54 (No. 9) ◽  
pp. 419-426 ◽  
Author(s):  
Z. Stastkova ◽  
S. Karpiskova ◽  
R. Karpiskova
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistant ◽  
Specific Pcr ◽  
Type Iv ◽  
Genes Encoding ◽  
Pcr Method ◽  
Specific Pcr Assay ◽  
Mrsa Strains ◽  
Phenotypic Methods ◽  
Species Specific

The aim of this study was to report the detection of methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) strains at a veterinary university goat breeding farm and their characteristics. A total of 278 samples collected from animals, milk, environment and farm personnel between June 2006 and March 2008 were examined. The identification of <i>S. aureus</i> isolates was performed by a species specific PCR assay. All detected isolates were tested for resistance to oxacillin and other antimicrobials by phenotypic methods and for the <i>mecA</i> gene by PCR method. Eight MRSA were detected in this study. Five of them originated from goat’s milk and three were recovered from one human carrier of the farm personnel. All obtained MRSA isolates were clonally consistent and were characterized as: <i>SCCmec</i> type IV, spa type t064, seb positive and for genes encoding TSST-1, PVL and exfoliative toxins A and B negative.

scholarly journals Development and validation of an allele-specific PCR assay for genotyping a promoter and exonic single nucleotide polymorphisms of MGMT gene

2018 ◽  
Vol 5 (2) ◽  
pp. e92
Author(s):  
Anuj Kumar Tyagi ◽  
Mary Boudal Khoshbeen ◽  
Patricia Huezo-Diaz Curtis ◽  
Chakradhara Rao S. Uppugunduri ◽  
Marc Ansari
Keyword(s):  
Dna Methyltransferase ◽  
Cost Effective ◽  
Nucleotide Polymorphisms ◽  
Pcr Assay ◽  
Mgmt Gene ◽  
Methylguanine Dna Methyltransferase ◽  
Specific Pcr ◽  
Allele Specific ◽  
Specific Pcr Assay ◽  
Allele Specific Pcr

DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) specifically remove the methyl/alkyl group from the O6-position of guanine and restore the guanine to its normal form without causing DNA strand breaks. Relationship between MGMT activity and resistance to alkylating therapeutic agents is well established. Non-availability of simple, cost-effective and efficient methods of genotyping may hinder investigations on genotype-phenotype associations. No simple genotyping procedures such as allele-discrimination Taqman Assays were available for two genetic variations in MGMT gene that had previously demonstrated to be affecting its function and expression.These two variants were included to genotype in a clinical study (Clinicaltrail.gov ID: NCT01257854). Hence, the present study is aimed at developing,   validating a rapid and simple allele-specific PCR method that genotypes exonic variant rs2308321 (c.520A>G) and a promoter variant rs113813075 (c.-459C>A) with standard PCR instruments.Web-based allele-specific (AS) primer design application called web-based allele-specific primer was used to design primers. Genomic DNA of lymphoblastoid cell line obtained from the Coriell repository with known genotypes were used to standardize the genotyping procedure. The PCR products were analyzed by 3% Agarose gel electrophoresis and by DNA Screen Tape assay with the Agilent 4200 TapeStation. The allele-specific PCR assay described here is a suitable strategy for efficient and reliable genotyping for difficult variants. This method offers cost-effective strategy for genotyping in clinical cohort studies provided positive controls established by Sanger sequencing are available for the variant. 

scholarly journals Wart Immunotherapies: A Short Review

2017 ◽  
Vol 11 (1) ◽  
pp. 30-34
Author(s):  
Ryan S. Sefcik ◽  
Craig G. Burkhart
Keyword(s):  
Target Location ◽  
Treatment Options ◽  
Cost Effective ◽  
Complete Response ◽  
Short Review ◽  
Skin Lesions ◽  
The Body ◽  
Cytotoxic Agents ◽  
Individual Response ◽  
Contact Allergens

Objective: To review the efficacy and costs of various contact immunotherapies, contact allergens, intralesional immunotherapies, and intralesional cytotoxic agents for the treatment of recalcitrant warts. Background: Cutaneous warts are common viral skin lesions caused by human papillomavirus that can be challenging to treat and frustrating for physicians and patients. Although several treatment options exist, there is no single treatment that can ensure a complete response with lack of lesion recurrence. Immunotherapies for recalcitrant warts present as a cost-effective, efficient therapy option for patients. Intralesional approaches have the added benefit of affecting warts at locations distant to the target location by inducing a systemic T-cell mediated response in the body. Results: Various contact immunotherapies, contact allergens, intralesional immunotherapies, and intralesional cytotoxic agents have shown to be effective in treating warts. The costs of each treatment varies drastically from around $10 US to over $1000 US to achieve a complete response. Several antigens were found to be both efficacious and cost effective. Conclusion: Although efficacy of several antigens has been confirmed by randomized studies, more randomized comparative studies will need to be performed in order to determine the best antigen and correct standardized doses for the treatment of warts in individual patients. It is important to note that individual response to antigen type and dose may vary among patients. Therefore, further studies may play an important role in the use of immunotherapies in a clinical setting.

Application of Machine Learning Approaches for the Design and Study of Anticancer Drugs

2019 ◽  
Vol 20 (5) ◽  
pp. 488-500 ◽  
Author(s):  
Yan Hu ◽  
Yi Lu ◽  
Shuo Wang ◽  
Mengying Zhang ◽  
Xiaosheng Qu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Design ◽  
Anticancer Drugs ◽  
Nearest Neighbor ◽  
Cost Effective ◽  
Support Vector ◽  
Learning Approaches ◽  
K Nearest Neighbor ◽  
Activity Prediction ◽  
Linear Discriminant

Background: Globally the number of cancer patients and deaths are continuing to increase yearly, and cancer has, therefore, become one of the world&#039;s highest causes of morbidity and mortality. In recent years, the study of anticancer drugs has become one of the most popular medical topics. </P><P> Objective: In this review, in order to study the application of machine learning in predicting anticancer drugs activity, some machine learning approaches such as Linear Discriminant Analysis (LDA), Principal components analysis (PCA), Support Vector Machine (SVM), Random forest (RF), k-Nearest Neighbor (kNN), and Naïve Bayes (NB) were selected, and the examples of their applications in anticancer drugs design are listed. </P><P> Results: Machine learning contributes a lot to anticancer drugs design and helps researchers by saving time and is cost effective. However, it can only be an assisting tool for drug design. </P><P> Conclusion: This paper introduces the application of machine learning approaches in anticancer drug design. Many examples of success in identification and prediction in the area of anticancer drugs activity prediction are discussed, and the anticancer drugs research is still in active progress. Moreover, the merits of some web servers related to anticancer drugs are mentioned.

Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in Mycobacterium tuberculosis complex clinical isolates

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 967-978 ◽  
Author(s):  
C. Viana-Niero ◽  
P. E. de Haas ◽  
D. van Soolingen ◽  
S. C. Leão
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Phospholipase C ◽  
Genetic Polymorphisms ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Clinical Isolates ◽  
Significant Similarity ◽  
Genomic Deletions ◽  
Genes Encoding ◽  
Mycobacterium Africanum

The Mycobacterium tuberculosis genome contains four highly related genes which present significant similarity to Pseudomonas aeruginosa genes encoding phospholipase C enzymes. Three of these genes, plcA, plcB and plcC, are organized in tandem (locus plcABC). The fourth gene, plcD, is located in a different region. This study investigates variations in plcABC and plcD genes in clinical isolates of M. tuberculosis, Mycobacterium africanum and ‘Mycobacterium canettii’. Genetic polymorphisms were examined by PCR, Southern blot hybridization, sequence analysis and RT-PCR. Seven M. tuberculosis isolates contain insertions of IS6110 elements within plcA, plcC or plcD. In 19 of 25 M. tuberculosis isolates examined, genomic deletions were identified, resulting in loss of parts of genes or complete genes from the plcABC and/or plcD loci. Partial plcD deletion was observed in one M. africanum isolate. In each case, deletions were associated with the presence of a copy of the IS6110 element and in all occurrences IS6110 was transposed in the same orientation. A mechanism of deletion resulting from homologous recombination of two copies of IS6110 was recognized in a group of genetically related M. tuberculosis isolates. Five M. tuberculosis isolates presented major polymorphisms in the plcABC and plcD regions, along with loss of expression competence that affected all four plc genes. Phospholipase C is a well-known bacterial virulence factor. The precise role of phospholipase C in the pathogenicity of M. tuberculosis is unknown, but considering the potential importance that the plc genes may have in the virulence of the tubercle bacillus, the study of isolates cultured from patients with active tuberculosis bearing genetic variations affecting these genes may provide insights into the significance of phospholipase C enzymes for tuberculosis pathogenicity.

Identification of Klebsiella oxytoca using a specific PCR assay targeting the polygalacturonase pehX gene

2003 ◽  
Vol 154 (8) ◽  
pp. 587-592 ◽  
Author(s):  
Gennadiy Kovtunovych ◽  
Tetyana Lytvynenko ◽  
Valentyna Negrutska ◽  
Olena Lar ◽  
Sylvain Brisse ◽  
...  
Keyword(s):  
Klebsiella Oxytoca ◽  
Pcr Assay ◽  
Specific Pcr ◽  
Specific Pcr Assay

scholarly journals Synchronous fluorescence as a green and selective tool for simultaneous determination of bambuterol and its main degradation product, terbutaline

2018 ◽  
Vol 5 (10) ◽  
pp. 181359 ◽  
Author(s):  
Samah Abo El Abass ◽  
Heba Elmansi
Keyword(s):  
Degradation Product ◽  
Low Cost ◽  
Reference Method ◽  
Cost Effective ◽  
Zero Crossing ◽  
Cost Effective Method ◽  
Validation Parameters ◽  
Main Degradation Product ◽  
20 Nm

A green, sensitive and cost-effective method is introduced in this research for the determination of bambuterol and its main degradation product, terbutaline, simultaneously, relying on the synchronous spectrofluorimetric technique. First derivative synchronous spectrofluorimetric amplitude is measured at Δ λ = 20 nm, so bambuterol can be quantitated at 260 nm, and terbutaline can be measured at 290 nm, each at the zero crossing point of the other. The amplitude–concentration plots were linear over the concentration ranges of 0.2–6.0 µg ml −1 and 0.2–4.0 µg ml −1 for both bambuterol and terbutaline, respectively. Official guidelines were followed to calculate the validation parameters of the proposed method. The low values of limits of detection of 0.023, 0.056 µg ml −1 and limits of quantitation of 0.071, 0.169 µg ml −1 for bambuterol and terbutaline, respectively, point to the sensitivity of the method. Bambuterol is a prodrug for terbutaline, and the latter is considered its degradation product so the established method could be regarded as a stability-indicating one. Moreover, the proposed method was used for the analysis of bambuterol and terbutaline in their single ingredient preparations and the results revealed statistical agreement with the reference method. The suggested method, being a simple and low-cost procedure, is superior to the previously published methods which need more sophisticated techniques, longer analysis time and highly toxic solvents and reagents. It could be considered as an eco-friendly analytical procedure.

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