1
|
Cereja-Pantoja KBC, de Brito Azevedo TC, Vinagre LWMS, de Moraes FCA, da Costa Nunes GG, Monte N, de Alcântara AL, Cohen-Paes A, Fernandes MR, Batista Dos Santos SE, de Assumpção PP, Ribeiro Dos Santos ÂK, Burbano RMR, Guerrero RC, Carracedo Á, Carneiro Dos Santos NP. Alterations in pharmacogenetic genes and their implications for imatinib resistance in Chronic Myeloid Leukemia patients from an admixed population. Cancer Chemother Pharmacol 2024:10.1007/s00280-024-04689-x. [PMID: 38888766 DOI: 10.1007/s00280-024-04689-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
Imatinib is the tyrosine kinase inhibitor used as the gold standard for the treatment of Chronic Myeloid Leukemia. However, about 30% of patients do not respond well to this therapy. Variants in drug administration, distribution, metabolism and excretion (ADME) genes play an important role in drug resistance especially in admixed populations. We investigated 129 patients diagnosed with Chronic Myeloid Leukemia treated with imatinib as first choice therapy. The participants of the study are highly admixed, populations that exhibit genetic diversity and complexity due to the contributions of multiple ancestral groups. Thus, the aim of this work was to investigate the association of 30 SNVs in genes related to response to treatment with Imatinibe in CML. Our results indicated that for the rs2290573 of the ULK3 gene, patients with the recessive AA genotype are three times more likely to develop resistance over time (secondary resistance) (p = 0.019, OR = 3.19, IC 95%= 1.21-8.36). Finally, we performed interaction analysis between the investigated variants and found several associations between SNVs and secondary resistance. We concluded that the variant rs2290573 of the ULK3 gene may be relevant for predicting treatment response of CML with imatinib, as well as possible treatment resistance. The use of predictive biomarkers is an important tool for therapeutic choice of patients, improving their quality of life and treatment efficacy.
Collapse
Affiliation(s)
| | | | | | | | | | - Natasha Monte
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, 66073-005, Brazil
| | | | - Amanda Cohen-Paes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, 66073-005, Brazil
| | | | | | | | | | | | - Raquel Cruz Guerrero
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas - CiMUS, Universidad de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Ángel Carracedo
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas - CiMUS, Universidad de Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | | |
Collapse
|
2
|
Liu Z, Zhao J, Cui K, Guo H, Li Z, Zhou Z. Detection accuracy and clinical applications of DP-TOF mass spectrometry. J Int Med Res 2024; 52:3000605241255568. [PMID: 38819085 PMCID: PMC11143829 DOI: 10.1177/03000605241255568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Abstract
OBJECTIVE Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently used in clinical microbiology laboratories. This study aimed to determine whether dual-polarity time-of-flight mass spectrometry (DP-TOF MS) could be applied to clinical nucleotide detection. METHODS This prospective study included 40 healthy individuals and 110 patients diagnosed with cardiovascular diseases. We used DP-TOF MS and Sanger sequencing to evaluate 17 loci across 11 genes associated with cardiovascular drug responses. In addition, we used DP-TOF MS to test 998 retrospectively collected clinical DNA samples with known results. RESULTS A, T, and G nucleotide detection by DP-TOF MS and Sanger sequencing revealed 100% concordance, whereas the C nucleotide concordance was 99.86%. Genotyping based on the results of the two methods showed 99.96% concordance. Regarding clinical applications, DP-TOF MS yielded a 99.91% concordance rate for known loci. The minimum detection limit for DNA was 0.4 ng; the inter-assay and intra-assay precision rates were both 100%. Anti-interference analysis showed that aerosol contamination greater than 1013 copies/µL in the laboratory environment could influence the results of DP-TOF MS. CONCLUSIONS The DP-TOF MS platform displayed good detection performance, as demonstrated by its 99.96% concordance rate with Sanger sequencing. Thus, it may be applied to clinical nucleotide detection.
Collapse
Affiliation(s)
- Zhaohui Liu
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Center of Laboratory Medicine, Fuwai Yunnan Cardiovascular Hospital, Kunming, Yunnan, China
| | - Juan Zhao
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Cui
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huimin Guo
- Zhejiang Digena Diagnosis Technology Co., Ltd., Hangzhou, Zhejiang, China
| | - Zhikai Li
- Zhejiang Digena Diagnosis Technology Co., Ltd., Hangzhou, Zhejiang, China
| | - Zhou Zhou
- State Key Laboratory of Cardiovascular Disease, Beijing Key Laboratory for Molecular Diagnostics of Cardiovascular Diseases, Center of Laboratory Medicine, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
3
|
Zhu Y, Liu Z, Peng L, Liu B, Wu K, Zhang M, Wang X, Pan J. Evaluation of nucleotide MALDI-TOF-MS for the identification of Mycobacterium species. Front Cell Infect Microbiol 2024; 14:1335104. [PMID: 38379773 PMCID: PMC10876993 DOI: 10.3389/fcimb.2024.1335104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Background The accurate identification of the Mycobacterium tuberculosis complex (MTBC) and different nontuberculous mycobacteria (NTM) species is crucial for the timely diagnosis of NTM infections and for reducing poor prognoses. Nucleotide matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been extensively used for microbial identification with high accuracy and throughput. However, its efficacy for Mycobacterium species identification has been less studied. The objective of this study was to evaluate the performance of nucleotide MALDI-TOF-MS for Mycobacterium species identification. Methods A total of 933 clinical Mycobacterium isolates were preliminarily identified as NTM by the MPB64 test. These isolates were identified by nucleotide MALDI-TOF-MS and Sanger sequencing. The performance of nucleotide MALDI-TOF MS for identifying various Mycobacterium species was analyzed based on Sanger sequencing as the gold standard. Results The total correct detection rate of all 933 clinical Mycobacterium isolates using nucleotide MALDI-TOF-MS was 91.64% (855/933), and mixed infections were detected in 18.65% (174/933) of the samples. The correct detection rates for Mycobacterium intracellulare, Mycobacterium abscessus, Mycobacterium kansasii, Mycobacterium avium, MTBC, Mycobacterium gordonae, and Mycobacterium massiliense were 99.32% (585/589), 100% (86/86), 98.46% (64/65), 94.59% (35/37), 100.00% (34/34), 95.65% (22/23), and 100% (19/19), respectively. For the identification of the MTBC, M. intracellulare, M. abscessus, M. kansasii, M. avium, M. gordonae, and M. massiliense, nucleotide MALDI-TOF-MS and Sanger sequencing results were in good agreement (k > 0.7). Conclusion In conclusion, nucleotide MALDI-TOF-MS is a promising approach for identifying MTBC and the most common clinical NTM species.
Collapse
Affiliation(s)
- Yelei Zhu
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhengwei Liu
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Lina Peng
- Department of Service and Support, Agena Bioscience, Shanghai, China
| | - Bin Liu
- Department of Service and Support, Agena Bioscience, Shanghai, China
| | - Kunyang Wu
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Mingwu Zhang
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaomeng Wang
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Junhang Pan
- Department of Tuberculosis Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| |
Collapse
|
4
|
Fung AWS, Sugumar V, Ren AH, Kulasingam V. Emerging role of clinical mass spectrometry in pathology. J Clin Pathol 2019; 73:61-69. [PMID: 31690564 DOI: 10.1136/jclinpath-2019-206269] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022]
Abstract
Mass spectrometry-based assays have been increasingly implemented in various disciplines in clinical diagnostic laboratories for their combined advantages in multiplexing capacity and high analytical specificity and sensitivity. It is now routinely used in areas including reference methods development, therapeutic drug monitoring, toxicology, endocrinology, paediatrics, immunology and microbiology to identify and quantify biomolecules in a variety of biological specimens. As new ionisation methods, instrumentation and techniques are continuously being improved and developed, novel mass spectrometry-based clinical applications will emerge for areas such as proteomics, metabolomics, haematology and anatomical pathology. This review will summarise the general principles of mass spectrometry and specifically highlight current and future clinical applications in anatomical pathology.
Collapse
Affiliation(s)
- Angela W S Fung
- Department of Pathology and Laboratory Medicine, St Paul's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Vijithan Sugumar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Annie He Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
5
|
de Coo A, Quintela I, Blanco J, Diz P, Carracedo Á. Assessment of genotyping tools applied in genetic susceptibility studies of periodontal disease: A systematic review. Arch Oral Biol 2018; 92:38-50. [DOI: 10.1016/j.archoralbio.2018.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/14/2022]
|
6
|
Lu Z, Chen Y, Jing X, Hu C. Diagnostic accuracy of MALDI-TOF mass spectrometry for non-small cell lung cancer: a meta-analysis. Biomarkers 2018; 23:245-252. [PMID: 29264950 DOI: 10.1080/1354750x.2017.1420822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Zhaolian Lu
- School of Graduate, Second Military Medical University, Shanghai, China
- Department of Laboratory Medicine, General Hospital of Jinan Military Command Region, Jinan, China
| | - Yingjian Chen
- Department of Laboratory Medicine, General Hospital of Jinan Military Command Region, Jinan, China
| | - Xinyan Jing
- School of Graduate, Weifang Medical University, Weifang, China
| | - Chengjin Hu
- Department of Laboratory Medicine, General Hospital of Jinan Military Command Region, Jinan, China
| |
Collapse
|
7
|
Abstract
Drug analysis represents a large field in different disciplines. Plasma is commonly considered to be the biosample of choice for that purpose. However, concentrations often do not represent the levels present within deeper compartments and therefore cannot sufficiently explain efficacy or toxicology of drugs. MALDI-MS in drug analysis is of great interest for high-throughput quantification and particularly spatially resolved tissue imaging. The current perspective article will deal with challenges and opportunities of MALDI-MS drug analysis in different biological samples. A particular focus will be on hair samples. Recent applications were included, reviewed for their instrumental setup and sample preparation and pros and cons as well as future perspectives are critically discussed.
Collapse
|
8
|
Song Z, Qiu L, Hu Z, Liu J, Liu D, Hou D. Evaluation of the Obesity Genes FTO and MC4R for Contribution to the Risk of Large Artery Atherosclerotic Stroke in a Chinese Population. Obes Facts 2016; 9:353-362. [PMID: 27701175 PMCID: PMC5644882 DOI: 10.1159/000448588] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Obesity is a well-established risk factor for large artery atherosclerotic (LAA) stroke. The aim of the study was to explore whether obesity genes, such as MC4R and FTO, contribute to LAA stroke risk in the Chinese Han population. METHODS 322 LAA stroke patients and 473 controls were recruited. Gene polymorphism of MC4R (rs17782313) and FTO (rs8050136 and rs9939609) were genotyped. RESULTS No differences were observed in genotype frequencies of variants of FTO (rs8050136 and rs9939609) or MC4R (rs17782313) between LAA stroke patients and control subjects. However, rs17782313 of the MC4R gene was associated with LAA stroke susceptibility in smokers (rs17782313: p = 0.020, OR (95% CI) = 1.55 (1.07-2.23)) in the stratified analysis. Furthermore, multifactor dimensionality reduction analysis revealed that the combination of MC4R variant (rs17782313), hypertension and smoking habit was significantly associated with increased risk of LAA stroke (p < 0.0001, OR (95% CI) = 6.57 (4.79-9.01)). CONCLUSION Our study indicated that the synergistic effects of MC4R variants, hypertension, and smoking habit contribute significantly to the risk of LAA stroke in the Chinese Han population. The finding revealed that obesity gene MC4R contribute to the risk of LAA stroke via a synergistic mechanism, which will provide new insight into the genetic architecture of LAA stroke.
Collapse
Affiliation(s)
| | | | - Zhongyang Hu
- *Dr. Zhongyang Hu, Department of Neurology, Third Xiangya Hospital, Central South University, 410013 Changsha, China,
| | | | | | | |
Collapse
|
9
|
Duncan MW, Nedelkov D, Walsh R, Hattan SJ. Applications of MALDI Mass Spectrometry in Clinical Chemistry. Clin Chem 2015; 62:134-43. [PMID: 26585930 DOI: 10.1373/clinchem.2015.239491] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/02/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND MALDI-TOF mass spectrometry (MS) is set to make inroads into clinical chemistry because it offers advantages over other analytical platforms. These advantages include low acquisition and operating costs, ease of use, ruggedness, and high throughput. When coupled with innovative front-end strategies and applied to important clinical problems, it can deliver rapid, sensitive, and cost-effective assays. CONTENT This review describes the general principles of MALDI-TOF MS, highlights the unique features of the platform, and discusses some practical methods based upon it. There is substantial potential for MALDI-TOF MS to make further inroads into clinical chemistry because of the selectivity of mass detection and its ability to independently quantify proteoforms. SUMMARY MALDI-TOF MS has already transformed the practice of clinical microbiology and this review illustrates how and why it is now set to play an increasingly important role in in vitro diagnostics in particular, and clinical chemistry in general.
Collapse
Affiliation(s)
- Mark W Duncan
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO; Obesity Research Center, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia;
| | - Dobrin Nedelkov
- Molecular Biomarkers Laboratory, Biodesign Institute, Arizona State University, Tempe, AZ
| | - Ryan Walsh
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
| | | |
Collapse
|
10
|
Zhou ZY, Ji T, Luo HS. Surface-enhanced laser desorption ionization time-of-flight mass spectrometry used to screen serum diagnostic markers of colon cancer recurrence in situ following surgery. Oncol Lett 2015; 9:2313-2316. [PMID: 26137063 DOI: 10.3892/ol.2015.2987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 01/30/2015] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to identify specific serum biomarkers in patients with colon cancer recurrence in situ following surgery. The study was conducted at the Renmin Hospital of Wuhan University (Wuhan, China) between January 2012 and January 2014. Surface-enhanced laser desorption ionization time-of-flight mass spectrometry was used to compare and analyze the serum protein profiles of patients with (n=50) and patients without (n=50) recurrence in situ. Biomarker Wizard software was used to analyze and obtain the protein spectrum. In total, nine protein peaks demonstrated statistically significant differences between the recurrence and non-recurrence group (P<0.05), which included two protein peaks (7,731.3 Da and 8,266.5 Da). The two protein peaks were highly expressed in patients with colon cancer recurrence in situ following surgery, but lowly expressed in patients without recurrence. Therefore, the two protein peaks may represent potential biomarkers for the prediction of colon cancer recurrence in situ following surgical treatment.
Collapse
Affiliation(s)
- Zhong-Yin Zhou
- Department of Gastroenterology, Renmin Hospital, Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Tuo Ji
- Department of Gastroenterology, Renmin Hospital, Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - He-Sheng Luo
- Department of Gastroenterology, Renmin Hospital, Wuhan University, Wuhan, Hubei 430060, P.R. China
| |
Collapse
|
11
|
Srivastava AK, Chopra R, Ali S, Aggarwal S, Vig L, Bamezai RNK. Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering. Nucleic Acids Res 2014; 42:e122. [PMID: 25030906 PMCID: PMC4150763 DOI: 10.1093/nar/gku585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Inundation of evolutionary markers expedited in Human Genome Project and 1000 Genome Consortium has necessitated pruning of redundant and dependent variables. Various computational tools based on machine-learning and data-mining methods like feature selection/extraction have been proposed to escape the curse of dimensionality in large datasets. Incidentally, evolutionary studies, primarily based on sequentially evolved variations have remained un-facilitated by such advances till date. Here, we present a novel approach of recursive feature selection for hierarchical clustering of Y-chromosomal SNPs/haplogroups to select a minimal set of independent markers, sufficient to infer population structure as precisely as deduced by a larger number of evolutionary markers. To validate the applicability of our approach, we optimally designed MALDI-TOF mass spectrometry-based multiplex to accommodate independent Y-chromosomal markers in a single multiplex and genotyped two geographically distinct Indian populations. An analysis of 105 world-wide populations reflected that 15 independent variations/markers were optimal in defining population structure parameters, such as FST, molecular variance and correlation-based relationship. A subsequent addition of randomly selected markers had a negligible effect (close to zero, i.e. 1 × 10−3) on these parameters. The study proves efficient in tracing complex population structures and deriving relationships among world-wide populations in a cost-effective and expedient manner.
Collapse
Affiliation(s)
- Amit Kumar Srivastava
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rupali Chopra
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shafat Ali
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shweta Aggarwal
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Lovekesh Vig
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rameshwar Nath Koul Bamezai
- National Centre of Applied Human Genetics, School of Life Sciences, and School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
12
|
Custodio A, Moreno-Rubio J, Aparicio J, Gallego-Plazas J, Yaya R, Maurel J, Rodríguez-Salas N, Burgos E, Ramos D, Calatrava A, Andrada E, Díaz-López E, Sánchez A, Madero R, Cejas P, Feliu J. Pharmacogenetic Predictors of Outcome in Patients with Stage II and III Colon Cancer Treated with Oxaliplatin and Fluoropyrimidine-Based Adjuvant Chemotherapy. Mol Cancer Ther 2014; 13:2226-37. [DOI: 10.1158/1535-7163.mct-13-1109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
13
|
Custodio A, Moreno-Rubio J, Aparicio J, Gallego-Plazas J, Yaya R, Maurel J, Higuera O, Burgos E, Ramos D, Calatrava A, Andrada E, López R, Moreno V, Madero R, Cejas P, Feliu J. Pharmacogenetic predictors of severe peripheral neuropathy in colon cancer patients treated with oxaliplatin-based adjuvant chemotherapy: a GEMCAD group study. Ann Oncol 2014; 25:398-403. [DOI: 10.1093/annonc/mdt546] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
14
|
CYP 450 2C19 polymorphisms in Indian patients with coronary artery disease. Indian Heart J 2013; 66:16-24. [PMID: 24581091 PMCID: PMC3946470 DOI: 10.1016/j.ihj.2013.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/15/2013] [Accepted: 10/05/2013] [Indexed: 01/02/2023] Open
Abstract
Background Dual antiplatelet therapy is the cornerstone in the management of acute coronary syndromes (ACS) and prevention of stent thrombosis (ST). Genetic polymorphisms in CYP2C19 gene involved in hepatic activation of clopidogrel leads to clopidogrel non-responsiveness and may influence clinical outcomes. These polymorphisms in CYP2C19 gene and their impact on clinical outcome in coronary artery disease (CAD) have not been studied in Indian population. Methods We studied 110 consecutive patients (mean age 55.7 ± 10.7 years; 90% male) taking clopidogrel with angiographically proven CAD for various genetic polymorphisms in CYP2C19 gene. Relationship between loss of function mutation and clinical presentation with recurrent ACS including ST was analyzed. Results Out of 110 patients, 26 (23.64%) had normal genotype, 52 (47.23%) had loss of function mutation *2 and 39 (35.45%) had a gain of function mutation *17, 7 (6.36%) patients were undefined metabolizers (*2/*17) which were excluded from analyses. Final analyses included 103 patients, with 45 (40.90%) having loss of function. Overall 51 patients had ACS, with 27 developing recurrence while on clopidogrel. The prevalence of loss of function mutation was no different between the group with recurrences and those without recurrences (55.6% vs. 50%, p = 0.7). Two patients developed ST while on clopidogrel; both had loss of function mutation. Conclusion CYP2C19 gene polymorphisms are common in Indian population. Loss of function mutation status did not affect the clinical outcomes. A larger study also considering P2Y12 receptor polymorphisms together with platelet activity testing, may be required to establish the role of CYP2C19 gene polymorphisms in clinical practice.
Collapse
|
15
|
|
16
|
Ganova-Raeva LM, Khudyakov YE. Application of mass spectrometry to molecular diagnostics of viral infections. Expert Rev Mol Diagn 2013; 13:377-88. [PMID: 23638820 DOI: 10.1586/erm.13.24] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mass spectrometry (MS) has found numerous applications in life sciences. It has high accuracy, sensitivity and wide dynamic range in addition to medium- to high-throughput capabilities. These features make MS a superior platform for analysis of various biomolecules including proteins, lipids, nucleic acids and carbohydrates. Until recently, MS was applied for protein detection and characterization. During the last decade, however, MS has successfully been used for molecular diagnostics of microbial and viral infections with the most notable applications being identification of pathogens, genomic sequencing, mutation detection, DNA methylation analysis, tracking of transmissions, and characterization of genetic heterogeneity. These new developments vastly expand the MS application from experimental research to public health and clinical fields. Matching of molecular techniques with specific requirements of the major MS platforms has produced powerful technologies for molecular diagnostics, which will further benefit from coupling with computational tools for extracting clinical information from MS-derived data.
Collapse
Affiliation(s)
- Lilia M Ganova-Raeva
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, 1600 Clifton Rd. NE, MS A-33, Atlanta, GA 30329, USA.
| | | |
Collapse
|
17
|
L'Ollivier C, Cassagne C, Normand AC, Bouchara JP, Contet-Audonneau N, Hendrickx M, Fourquet P, Coulibaly O, Piarroux R, Ranque S. A MALDI-TOF MS procedure for clinical dermatophyte species identification in the routine laboratory. Med Mycol 2013; 51:713-20. [PMID: 23611419 DOI: 10.3109/13693786.2013.781691] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The conventional identification of dermatophytes requires a long turnaround time and highly skilled mycologists. We have recently developed a tandardized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) assay to routinely identify molds of potential clinical significance. This study objective was to determine if this same assay could also be employed to identify clinical dermatophytes in the routine laboratory setting. The effects of the inclusion of cycloheximide in the culture medium and incubation time were tested after building a reference spectra library that included 48 well-characterized isolates of 17 dermatophyte species. Then these same isolates were prospectively identified using this library. MALDI-TOF MS-based identification was effective regardless of the presence of cycloheximide or incubation time as 130/133 (97.8%) of the clinical isolates were appropriately identified. Two Microsporum canis isolates yielded uninformative spectra and one M. audouinii isolate was misidentified. Since one only requires a small colony for MALDI-TOF MS analysis, accurate identifications were obtained in 3-6 days and, specifically, before the appearance of their characteristic morphological features. Consequently, identification turnaround time was dramatically reduced as compared to that needed for conventional morphological identification. In conclusion, this standardized MALDI-TOF MS-based identification procedure for filamentous fungi effectively identifies clinical dermatophyte isolates and drastically reduces the response times in the routine clinical laboratory.
Collapse
Affiliation(s)
- Coralie L'Ollivier
- * Laboratoire de Parasitologie-Mycologie, Aix-Marseille Univ. , Marseille; AP-HM, CHU Timone , Marseille cedex 05
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Gassner C, Meyer S, Frey BM, Vollmert C. Matrix-Assisted Laser Desorption/Ionisation, Time-of-Flight Mass Spectrometry–Based Blood Group Genotyping—The Alternative Approach. Transfus Med Rev 2013; 27:2-9. [DOI: 10.1016/j.tmrv.2012.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/15/2012] [Accepted: 10/15/2012] [Indexed: 01/05/2023]
|
19
|
Pastoret S, Ameels H, Bossiroy F, Decreux A, De Longueville F, Thomas A, Desmecht D. Detection of disease resistance and susceptibility alleles in pigs using oligonucleotide microarray hybridization. J Vet Diagn Invest 2012; 24:479-88. [DOI: 10.1177/1040638712442878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A multiplex DNA microarray chip aimed at the identification of allelic polymorphisms was developed for simultaneous detection of swine disease resistance genes underlying malignant hyperthermia ( RYR), postweaning diarrhea, edema disease ( FUT1), neonatal diarrhea ( MUC4), and influenza ( MX1). The on-chip detection was performed with fragmented polymerase chain reaction (PCR)–amplified products. Particular emphasis was placed on the reduction of the number of PCR reactions required. The targets were biotin labeled during the PCR reaction, and the arrays were detected using a colorimetric methodology. Target recognition was provided by specific capture probes designed for each susceptible or resistant allelic variant. Sequencing was chosen as the gold standard to assess chip accuracy. All genotypes retrieved from the microarray (476) fit with sequencing data despite the fact that each pig was heterozygote for at least 1 target gene.
Collapse
Affiliation(s)
- Soumya Pastoret
- Unité de Recherche en Biologie Cellulaire, Facultés universitaires Notre-Dame de la Paix, Namur, Belgium (Pastoret, Ameels, Bossiroy)
- Service de Pathologie systémique, University of Liège, Liège, Belgium (Decreux, Thomas, Desmecht)
- Eppendorf Array Technology, Namur, Belgium (De Longueville, Remacle)
| | - Hélène Ameels
- Unité de Recherche en Biologie Cellulaire, Facultés universitaires Notre-Dame de la Paix, Namur, Belgium (Pastoret, Ameels, Bossiroy)
- Service de Pathologie systémique, University of Liège, Liège, Belgium (Decreux, Thomas, Desmecht)
- Eppendorf Array Technology, Namur, Belgium (De Longueville, Remacle)
| | - Frédérique Bossiroy
- Unité de Recherche en Biologie Cellulaire, Facultés universitaires Notre-Dame de la Paix, Namur, Belgium (Pastoret, Ameels, Bossiroy)
- Service de Pathologie systémique, University of Liège, Liège, Belgium (Decreux, Thomas, Desmecht)
- Eppendorf Array Technology, Namur, Belgium (De Longueville, Remacle)
| | - Annabelle Decreux
- Unité de Recherche en Biologie Cellulaire, Facultés universitaires Notre-Dame de la Paix, Namur, Belgium (Pastoret, Ameels, Bossiroy)
- Service de Pathologie systémique, University of Liège, Liège, Belgium (Decreux, Thomas, Desmecht)
- Eppendorf Array Technology, Namur, Belgium (De Longueville, Remacle)
| | - Françoise De Longueville
- Unité de Recherche en Biologie Cellulaire, Facultés universitaires Notre-Dame de la Paix, Namur, Belgium (Pastoret, Ameels, Bossiroy)
- Service de Pathologie systémique, University of Liège, Liège, Belgium (Decreux, Thomas, Desmecht)
- Eppendorf Array Technology, Namur, Belgium (De Longueville, Remacle)
| | - Anne Thomas
- Unité de Recherche en Biologie Cellulaire, Facultés universitaires Notre-Dame de la Paix, Namur, Belgium (Pastoret, Ameels, Bossiroy)
- Service de Pathologie systémique, University of Liège, Liège, Belgium (Decreux, Thomas, Desmecht)
- Eppendorf Array Technology, Namur, Belgium (De Longueville, Remacle)
| | - Daniel Desmecht
- Unité de Recherche en Biologie Cellulaire, Facultés universitaires Notre-Dame de la Paix, Namur, Belgium (Pastoret, Ameels, Bossiroy)
- Service de Pathologie systémique, University of Liège, Liège, Belgium (Decreux, Thomas, Desmecht)
- Eppendorf Array Technology, Namur, Belgium (De Longueville, Remacle)
| |
Collapse
|