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Comparison of Direct Sequencing with Real-time PCR High Resolution Melt and PCR Restriction Fragment Length Polymorphism Analysis to Identify Clinically Important Candida Species. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2021. [DOI: 10.5812/archcid.110202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Candida albicans is the predominant yeast reported from human infection. Non-albicans Candida species have been recently developed as medically vital fungi. Therefore, it is essential to detect and identify the pathogens at the species level to prescribe appropriate treatment. Methods: This study assessed two complementary methods, including real-time polymerase chain reaction-high resolution melt (PCR-HRM) and polymerase chain reaction-restriction fragment length morphism (PCR-RFLP) with standard PCR and Sanger sequencing as the benchmark. Results: In total, 66 samples were tested, and two newly-advanced assays were more effective and displayed comprehensive concordance (66/66, 100%) with Sanger sequencing outcomes. Moreover, accurate and economical tests were positively advanced by real-time PCR-HRM for C. albicans and C. parapsilosis complexes. Conclusions: Given the number of studies performed on the comparison of sensitivity and specificity of phenotypic and genotypic methods to diagnose and identify invasive fungal pathogens and the findings of this study, it could be stated that the correlative PCR-HRM and PCR-RFLP methods were effectively advanced as substitutes for conventional Sanger sequencing for the reasonable identification. However, supplementary evaluations and confirming studies should be carried out with a broad range of samples to standardize this method for routine application in medical laboratories.
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Yao P, Qu XM, Ren S, Ren XD, Su N, Zhao N, Wang L, Cheng L, Weng BB, Sun FJ, Huang Q. Scorpion primer PCR analysis for genotyping of allele variants of thiopurine s‑methyltransferase*3. Mol Med Rep 2020; 22:1994-2002. [PMID: 32705177 PMCID: PMC7411393 DOI: 10.3892/mmr.2020.11283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/27/2020] [Indexed: 11/09/2022] Open
Abstract
Thiopurine S-methyltransferase (TPMT) plays an important role in the metabolism of thiopurines. Mutations in the TPMT gene can affect drug activity, which may have adverse effects in humans. Thus, genotyping can help elucidate genetic determinants of drug response to thiopurines and optimize the selection of drug therapies for individual patients, effectively avoiding palindromia during maintenance treatment caused by insufficient dosing and the serious side effects caused by excessive doses. The current available detection methods used for TPMT*3B and TPMT*3C are complex, costly and time-consuming. Therefore, innovative detection methods for TPMT genotyping are urgently required. The aim of the present study was to establish and optimize a simple, specific and timesaving TPMT genotyping method. Using the principles of Web-based Allele-Specific PCR and competitive real-time fluorescent allele-specific PCR (CRAS-PCR), two pairs of Scorpion primers were designed for the detection of TPMT*3B and *3C, respectively, and a mutation in TPMT*3A was inferred based on data from TPMT*3B and *3C. In total, 226 samples from volunteers living in Chongqing were used for CRAS-PCR to detect TPMT*3 mutations. Results showed that nine (3.98%) were mutant (MT) heterozygotes and none were MT homozygotes for TPMT*3C, and no TPMT*3A and TPMT*3B mutations were found. Three TPMT*3C MT heterozygotes were randomly selected for DNA sequencing, and CRAS-PCR results were consistent with the sequencing results. In conclusion, in order to improve simplicity, specificity and efficiency, the present study established and optimized CRAS-PCR assays for commonly found mutant alleles of TPMT*3A (G460A and A719G), TPMT*3B (G460A), and TPMT*3C (A719G).
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Affiliation(s)
- Pu Yao
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Xue-Mei Qu
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Sai Ren
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Na Zhao
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Liu Wang
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
| | - Lin Cheng
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Bang-Bi Weng
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Feng-Jun Sun
- Department of Pharmacy, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing 400042, P.R. China
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Comparison of Direct Sequencing, Real-Time PCR-High Resolution Melt (PCR-HRM) and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Analysis for Genotyping of Common Thiopurine Intolerant Variant Alleles NUDT15 c.415C>T and TPMT c.719A>G (TPMT*3C). Diagnostics (Basel) 2017; 7:diagnostics7020027. [PMID: 28498350 PMCID: PMC5489947 DOI: 10.3390/diagnostics7020027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 11/29/2022] Open
Abstract
Thiopurine intolerance and treatment-related toxicity, such as fatal myelosuppression, is related to non-function genetic variants encoding thiopurine S-methyltransferase (TPMT) and Nudix hydrolase 15 (NUDT15). Genetic testing of the common variants NUDT15:NM_018283.2:c.415C>T (Arg139Cys, dbSNP rs116855232 T allele) and TPMT: NM_000367.4:c.719A>G (TPMT*3C, dbSNP rs1142345 G allele) in East Asians including Chinese can potentially prevent treatment-related complications. Two complementary genotyping approaches, real-time PCR-high resolution melt (PCR-HRM) and PCR-restriction fragment length morphism (PCR-RFLP) analysis were evaluated using conventional PCR and Sanger sequencing genotyping as the gold standard. Sixty patient samples were tested, revealing seven patients (11.7%) heterozygous for NUDT15 c.415C>T, one patient homozygous for the variant and one patient heterozygous for the TPMT*3C non-function allele. No patient was found to harbor both variants. In total, nine out of 60 (15%) patients tested had genotypic evidence of thiopurine intolerance, which may require dosage adjustment or alternative medication should they be started on azathioprine, mercaptopurine or thioguanine. The two newly developed assays were more efficient and showed complete concordance (60/60, 100%) compared to the Sanger sequencing results. Accurate and cost-effective genotyping assays by real-time PCR-HRM and PCR-RFLP for NUDT15 c.415C>T and TPMT*3C were successfully developed. Further studies may establish their roles in genotype-informed clinical decision-making in the prevention of morbidity and mortality due to thiopurine intolerance.
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Skrzypczak-Zielinska M, Borun P, Bartkowiak-Kaczmarek A, Zakerska-Banaszak O, Walczak M, Dobrowolska A, Kurzawski M, Waszak M, Lipinski D, Plawski A, Slomski R. A Simple Method for TPMT and ITPA Genotyping Using Multiplex HRMA for Patients Treated with Thiopurine Drugs. Mol Diagn Ther 2016; 20:493-9. [PMID: 27307154 PMCID: PMC5021755 DOI: 10.1007/s40291-016-0217-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Thiopurine methyltransferase (TPMT) and inosine triphosphatase (ITPA) are crucial enzymes involved in the metabolism of thiopurine drugs: azathioprine and 6-mercaptopurine, used in the treatment of leukemia or inflammatory bowel diseases (IBD). The activity in these enzymes correlates with the genetic polymorphism of the TPMT and ITPA genes, respectively, which determines an individual reaction and dosing of thiopurines. Three main TPMT alleles: TPMT*2 (c.238G>C), TPMT*3A (c.460G>A, c.719A>G) and TPMT*3C (c.719A>G) account for 80-95 % of inherited TPMT deficiency in different populations in the world. In the ITPA gene, a c.94C>A mutation is significantly associated with an adverse thiopurine reaction. The aim of this study was to develop a quick and highly sensitive method for determining major TPMT and ITPA alleles. Here we present the molecular test for genotyping c.238G>C, c.460G>A, c.719A>G and c.94C>A changes based on multiplex high resolution melting analysis (HRMA). We analyzed DNA samples from 100 clinically diagnosed IBD patients treated with thiopurine drugs, and a known genotype in the positions 238, 460 and 719 of the TPMT gene as well as in position 94 of the ITPA gene. Our results obtained with multiplex HRMA indicated 100 % accuracy in comparison with data from restriction fragments length polymorphism (RFLP) and standard DNA sequencing. We conclude, that multiplex HRMA can be used as a quick, sensitive and efficient alternative diagnostic method compared to conventional techniques for the determination of TPMT*2, TPMT*3A and TPMT*3C alleles and c.94C>A change in the ITPA gene.
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Affiliation(s)
| | - Pawel Borun
- Institute of Human Genetics, Polish Academy of Sciences, ul. Strzeszynska 32, 60-479, Poznan, Poland
| | - Anna Bartkowiak-Kaczmarek
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Oliwia Zakerska-Banaszak
- Institute of Human Genetics, Polish Academy of Sciences, ul. Strzeszynska 32, 60-479, Poznan, Poland
| | - Michal Walczak
- Institute of Human Genetics, Polish Academy of Sciences, ul. Strzeszynska 32, 60-479, Poznan, Poland
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Human Nutrition and Internal Diseases, University of Medical Sciences, Poznan, Poland
| | - Mateusz Kurzawski
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland
| | - Malgorzata Waszak
- Department of Functional Anatomy, University School of Physical Education, Poznan, Poland
| | - Daniel Lipinski
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan, Poland
| | - Andrzej Plawski
- Institute of Human Genetics, Polish Academy of Sciences, ul. Strzeszynska 32, 60-479, Poznan, Poland
| | - Ryszard Slomski
- Institute of Human Genetics, Polish Academy of Sciences, ul. Strzeszynska 32, 60-479, Poznan, Poland
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan, Poland
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Roy LM, Zur RM, Uleryk E, Carew C, Ito S, Ungar WJ. Thiopurine S-methyltransferase testing for averting drug toxicity in patients receiving thiopurines: a systematic review. Pharmacogenomics 2016; 17:633-56. [PMID: 27020704 PMCID: PMC4931919 DOI: 10.2217/pgs.16.12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIM Thiopurine S-methyltransferase (TPMT) testing is used in patients receiving thiopurines to identify enzyme deficiencies and risk for adverse drug reactions. It is uncertain whether genotyping is superior to phenotyping. The objectives were to conduct a systematic review of TPMT-test performance studies. MATERIALS & METHODS Electronic and grey literature sources were searched for studies reporting test performance compared with a reference standard. Sixty-six eligible studies were appraised for quality. RESULTS Thirty phenotype-genotype and six phenotype-phenotype comparisons were of high quality. The calculated sensitivity and specificity for genotyping to identify a homozygous mutation ranged from 0.0-100.0% and from 97.8-100.0%, respectively. CONCLUSION Clinical decision-makers require high-quality evidence of clinical validity and clinical utility of TPMT genotyping to ensure appropriate use in patients.
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Affiliation(s)
- Lilla M Roy
- Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Richard M Zur
- Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Elizabeth Uleryk
- Library Services, The Hospital for Sick Children, Toronto, Canada
| | - Chris Carew
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Shinya Ito
- Division of Clinical Pharmacology & Toxicology, The Hospital for Sick Children, Toronto, Canada
- Departments of Pharmacology & Pharmacy, Faculty of Medicine Department of Paediatrics, University of Toronto, Canada
| | - Wendy J Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Canada
- Institute for Health Policy, Management & Evaluation, University of Toronto, Canada
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Burchard PR, Abou Tayoun AN, Lefferts JA, Lewis LD, Tsongalis GJ, Cervinski MA. Development of a rapid clinical TPMT genotyping assay. Clin Biochem 2014; 47:126-9. [PMID: 25093923 DOI: 10.1016/j.clinbiochem.2014.07.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Thiopurine compounds are commonly used in the treatment of childhood acute lymphoblastic leukemia, and as immunosuppressants following organ transplantation or for treatment of various autoimmune disorders. Thiopurine S-methyltransferase (TPMT) is required for detoxification, through S-methylation, of 6-thioguanine nucleotides (TGNs), a byproduct of thiopurine metabolism. Single nucleotide polymorphisms (SNPs) in the TPMT gene have been shown to affect its function, with some variants associated with serious clinical manifestations including severe to fatal myelosuppression and organ transplant rejection following treatment with standard thiopurine doses. In this study, we describe a TaqMan real time PCR allelic discrimination assay requiring minimal DNA input for TPMT genotyping. DESIGN AND METHODS We designed controls for the homozygous wild type and allelic variants of TPMT*2, *3B, and *3C. Genomic DNA was extracted from an additional 412 human blood samples. The samples were tested for the TPMT*2, *3B, *3C, and *3A polymorphisms by TaqMan genotyping assays using the AB 7500 FAST Real-Time PCR instrument. Allelic discrimination plots were used to identify each mutation. RESULTS The TaqMan assay correctly genotyped all custom control DNA samples. Of the 412 tested samples, our assay identified 375 samples as wild-type *1/*1 (91.02%), 3 as *1/*2 (0.73%), 1 as *1/*3B (0.24%), 3 as *1/*3C (0.73%), 27 presumed to be *1/*3A (6.55%), and 3 as *3B/*3A (0.73%). CONCLUSIONS The clinical implications of TPMT genotyping, along with the simplicity and specificity of the TaqMan genotyping assays make this test highly suitable for use in a clinical laboratory.
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Affiliation(s)
- Paul R Burchard
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Ahmad N Abou Tayoun
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Joel A Lefferts
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Lionel D Lewis
- Department of Medicine, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Mark A Cervinski
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.
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Kim JY, Cheong HS, Park TJ, Shin HJ, Seo DW, Na HS, Chung MW, Shin HD. Screening for 392 polymorphisms in 141 pharmacogenes. Biomed Rep 2014; 2:463-476. [PMID: 24944790 DOI: 10.3892/br.2014.272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/28/2014] [Indexed: 11/05/2022] Open
Abstract
Pharmacogenomics is the study of the association between inter-individual genetic differences and drug responses. Researches in pharmacogenomics have been performed in compliance with the use of several genotyping technologies. In this study, a total of 392 single-nucleotide polymorphisms (SNPs) located in 141 pharmacogenes, including 21 phase I, 13 phase II, 18 transporter and 5 modifier genes, were selected and genotyped in 150 subjects using the GoldenGate assay or the SNaPshot technique. These variants were in Hardy-Weinberg equilibrium (HWE) (P>0.05), except for 22 SNPs. Genotyping of the 392 SNPs revealed that the minor allele frequencies of 47 SNPs were <0.05, 105 SNPs were monomorphic and 22 variants were not in HWE. Also, based on previous studies, we predicted the association between the polymorphisms of certain pharmacogenes, such as cytochrome P450 2D6, cytochrome P450 2C9, vitamin K epoxide reductase complex, subunit 1, cytochrome P450 2C19, human leukocyte antigen, class I, B and thiopurine S-methyltransferase, and drug efficacy. In conclusion, our study demonstrated the allele distribution of SNPs in 141 pharmacogenes as determined by high-throughput screening. Our results may be helpful in developing personalized medicines by using pharmacogene polymorphisms.
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Affiliation(s)
- Jason Yongha Kim
- Department of Life Science, Sogang University, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Tae-Joon Park
- Department of Life Science, Sogang University, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Hee Jung Shin
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Doo Won Seo
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Han Sung Na
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Myeon Woo Chung
- Division of Clinical Reaserch, Department of Toxicological Evaluation and Research, National Institute of Food and Drug Safety Evaluation, Osong Health Technology Administration Complex, Osong, Chungcheongbuk 363-700, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, SNP Genetics, Inc., Seoul 121-742, Republic of Korea ; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
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Demlova R, Mrkvicova M, Sterba J, Bernatikova H, Stary J, Sukova M, Mikuskova A, Chocholova A, Mladosievicova B, Soltysova A, Behulova D, Pilatova K, Zdrazilova-Dubska L, Valik D. Augmenting Clinical Interpretability of Thiopurine Methyltransferase Laboratory Evaluation. Oncology 2014; 86:152-8. [DOI: 10.1159/000357407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/08/2013] [Indexed: 11/19/2022]
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