| 1. |
- Andersson, Daniel, 1979, et al.
(författare)
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Properties of targeted preamplification in DNA and cDNA quantification
- 2015
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 15:8, s. 1085-1100
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Forskningsöversikt (refereegranskat)abstract
- Objective: Quantification of small molecule numbers often requires preamplification to generate enough copies for accurate downstream enumerations. Here, we studied experimental parameters in targeted preamplification and their effects on downstream quantitative real-time PCR (qPCR). Methods: To evaluate different strategies, we monitored the preamplification reaction in real-time using SYBR Green detection chemistry followed by melting curve analysis. Furthermore, individual targets were evaluated by qPCR. Result: The preamplification reaction performed best when a large number of primer pairs was included in the primer pool. In addition, preamplification efficiency, reproducibility and specificity were found to depend on the number of template molecules present, primer concentration, annealing time and annealing temperature. The amount of nonspecific PCR products could also be reduced about 1000-fold using bovine serum albumin, glycerol and formamide in the preamplification. Conclusion: On the basis of our findings, we provide recommendations how to perform robust and highly accurate targeted preamplification in combination with qPCR or next-generation sequencing.
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| 2. |
- Andersson, Daniel, 1979, et al.
(författare)
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Ultrasensitive circulating tumor DNA analysis enables precision medicine: experimental workflow considerations
- 2021
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 21:3, s. 299-310
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Circulating tumor DNA (ctDNA) has become a relevant biomarker in cancer management, allowing tumor assessment through analysis of minimally invasive liquid biopsies. Applications include screening, diagnostics, monitoring of treatment efficacy and detection of minimal residual disease as well as relapse. The potential of ctDNA analysis is significant, but several biological and technical challenges need to be addressed before widespread clinical implementation. Areas covered: Several clinical applications where ctDNA analysis may be beneficial require detection of individual DNA molecules. Consequently, to acquire accurate and informative data the entire workflow from sampling to final data interpretation needs to be optimized. In this review, we discuss the biological and technical challenges of ctDNA analysis and how preanalytical and analytical approaches affect different cancer applications. Expert opinion: While numerous studies have demonstrated the potential of using ctDNA in cancer applications, yet few reports about true clinical utility exist. Despite encouraging data, the sensitivity of ctDNA analyses, i.e. the probability to detect presence of cancer in liquid biopsies, is still an issue. Analysis of multiple mutations in combination with simultaneous assessment of other analytes is one solution. Improved standardization and guidelines will also facilitate the introduction of ctDNA analysis into clinical routine.
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| 3. |
- Belak, Sandor, et al.
(författare)
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Advances in viral disease diagnostic and molecular epidemiological technologies
- 2009
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Ingår i: Expert Review of Molecular Diagnostics. - 1473-7159 .- 1744-8352. ; 9, s. 367-381
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Forskningsöversikt (refereegranskat)abstract
- The early and rapid detection and characterization of specific nucleic acids of medico-veterinary pathogens have proven invaluable for diagnostic purposes. The integration of amplification and signal detection systems, including online real-time devices, have increased speed and sensitivity and greatly facilitated the quantification of target nucleic acids. They have also allowed for sequence characterization using melting or hybridization curves. The newer-generation molecular diagnostic technologies offer, hitherto, unparalleled detection and discrimination methodologies, which are vital for the positive detection and identification of pathogenic agents, as well as the effects of the pathogens on the production of antibodies. The development phase of the novel technologies entails a thorough understanding of accurate diagnosis and discrimination of present and emerging diseases. The development of novel technologies can only be successful if they are transferred and used in the field with a sustainable quality-assured application to allow for the optimal detection and effective control of diseases. The aim of these new tools is to detect the presence of a pathogen agent before the onset of disease. This manuscript focuses mainly on the experiences of two World Organisation for Animal Health collaborating centers in context to molecular diagnosis and molecular epidemiology of transboundary and endemic animal diseases of viral origin, food safety and zoonoses.
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| 4. |
- Blennow, Kaj, 1958
(författare)
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CSF biomarkers for Alzheimer's disease: use in early diagnosis and evaluation of drug treatment.
- 2005
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Ingår i: Expert review of molecular diagnostics. - : Informa UK Limited. - 1744-8352 .- 1473-7159. ; 5:5, s. 661-72
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Tidskriftsartikel (refereegranskat)abstract
- Early diagnosis of Alzheimer's disease is important in initiating symptomatic treatment with acetylcholine esterase inhibitors, and will be of even greater significance if drugs with a potential to slow down the degenerative process, such as beta-secretase inhibitors and beta-amyloid vaccination, prove to have a clinical effect. During the last decade, research efforts have focused on developing cerebrospinal fluid (CSF) biomarkers for Alzheimer's disease. In this review, the background and principles for, and the diagnostic performance of, the CSF biomarkers total tau, phosphorylated tau and the 42-amino acid form of beta-amyloid, are reviewed. New candidate CSF biomarkers and new strategies, including multiparameter immunoassays and CSF proteomics techniques, in the search of additional CSF biomarkers are also reviewed. Finally, the rationale for the use of CSF biomarkers to identify and monitor the biochemical effect of new drug candidates is reviewed.
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| 5. |
- Borrebaeck, Carl
(författare)
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Advanced technologies and diagnostic spin-outs: an interview with Carl Borrebaeck.
- 2015
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1744-8352 .- 1473-7159. ; 15:11, s. 1409-1410
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Tidskriftsartikel (refereegranskat)abstract
- Interview with Professor Carl Borrebaeck DSc by Claire Raison (Commissioning Editor) Professor Carl Borrebaeck DSc, is the Director of CREATE Health (Lund, Sweden), a translational cancer center, previous Vice President of Lund University and specializes in immunotechnology, diagnostics and treatments for cancer. He has had remarkable success in co-founding collaborative working groups and related spin-out companies based in Lund. Professor Borrebaeck also serves as a member of the editorial advisory board for Expert Review of Molecular Diagnostics. Here, Professor Borrebaeck talks to Expert Review of Molecular Diagnostics about his experience and what is next for cutting-edge technology in cancer diagnostics.
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| 6. |
- Borrebaeck, Carl, et al.
(författare)
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High-throughput proteomics using antibody microarrays: an update
- 2007
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1744-8352 .- 1473-7159. ; 7:5, s. 673-686
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Forskningsöversikt (refereegranskat)abstract
- Antibody-based microarrays are a rapidly emerging technology that has advanced from the first proof-of-concept studies to demanding serum protein profiling applications during recent years, displaying great promise within disease proteomics. Miniaturized micro- and nanoarrays can be fabricated with an almost infinite number of antibodies carrying the desired specificities. While consuming only minute amounts of reagents, multiplexed and ultrasensitive assays can be performed targeting high- as well as low-abundance analytes in complex nonfractionated proteomes. The microarray images generated can then be converted into protein expression profiles or protein atlases, revealing a detailed composition of the sample. The technology will provide unique opportunities for fields such as disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence and drug target discovery. This review describes an update of high-throughput proteomics, using antibody-based microarrays, focusing on key technological advances and novel applications that have emerged over the last 3 years.
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| 7. |
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| 8. |
- Donà, Valentina, et al.
(författare)
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Recent advances in the development and use of molecular tests to predict antimicrobial resistance in Neisseria gonorrhoeae
- 2017
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Ingår i: Expert Review of Molecular Diagnostics. - : Taylor & Francis Group. - 1473-7159 .- 1744-8352. ; 17:9, s. 845-859
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: The number of genetic tests, mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae is increasing. Several of these assays are promising, but there are important shortcomings and few assays have been adequately validated and quality assured.Areas covered: Recent advances, focusing on publications since 2012, in the development and use of molecular tests to predict gonococcal AMR for surveillance and for clinical use, advantages and disadvantages of these tests and of molecular AMR prediction compared with phenotypic AMR testing, and future perspectives for effective use of molecular AMR tests for different purposes.Expert commentary: Several challenges for direct testing of clinical, especially extra-genital, specimens remain. The choice of molecular assay needs to consider the assay target, quality controls, sample types, limitations intrinsic to molecular technologies, and specific to the chosen methodology, and the intended use of the test. Improved molecular- and particularly genome-sequencing-based methods will supplement AMR testing for surveillance purposes, and translate into point-of-care tests that will lead to personalized treatments, while sparing the last available empiric treatment option (ceftriaxone). However, genetic AMR prediction will never completely replace phenotypic AMR testing, which detects also AMR due to unknown AMR determinants.
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| 9. |
- Faghihi, MA, et al.
(författare)
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Genetics of neurological disorders
- 2004
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Ingår i: Expert review of molecular diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 4:3, s. 317-332
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Tidskriftsartikel (refereegranskat)
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| 10. |
- Garcia Gonzalez, Javier, et al.
(författare)
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Nuclease activity : an exploitable biomarker in bacterial infections
- 2022
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Ingår i: Expert Review of Molecular Diagnostics. - : Taylor & Francis AS. - 1473-7159 .- 1744-8352. ; 22:3, s. 265-294
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Tidskriftsartikel (refereegranskat)abstract
- Introduction In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications. Areas covered This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using the terms: nuclease, bacteria, nuclease activity or biomarker. For overview sections, original and review articles between 2000 and 2019 were searched for using the terms: infections, diagnosis, bacterial, burden, challenges. Informative articles were selected. Expert opinion Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.
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| 11. |
- Golparian, Daniel, 1984-, et al.
(författare)
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Antimicrobial resistance prediction in Neisseria gonorrhoeae : Current status and future prospects
- 2022
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Ingår i: Expert Review of Molecular Diagnostics. - : Expert Reviews Ltd.. - 1473-7159 .- 1744-8352. ; 22:1, s. 29-48
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Forskningsöversikt (refereegranskat)abstract
- Introduction: Several nucleic acid amplification tests (NAATs), mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae are promising, and some may be ready to apply at the point-of-care (POC), but important limitations remain with most NAATs. Next-generation sequencing (NGS) can overcome many of these limitations.Areas covered: Recent advances, with main focus on publications since 2017, in the development and use of NAATs and NGS to predict gonococcal AMR for surveillance and clinical use, and pros and cons of these tests as well as future perspectives for appropriate use of molecular AMR prediction for N. gonorrhoeae.Expert Commentary: NAATs and/or NGS for AMR prediction should supplement culture-based AMR surveillance, which will remain because it detects also AMR due to unknown AMR determinants, and translation into POC tests is imperative for the end-goal of individualized treatment, sparing ceftriaxone±azithromycin. Several challenges for direct testing of clinical, especially pharyngeal, specimens and for accurate prediction of cephalosporins and azithromycin resistance, especially using NAATs, remain. The choice of AMR prediction assay needs to carefully consider the intended use of the assay; limitations intrinsic to the AMR prediction technology, algorithms and specific to chosen methodology; specimen types analyzed; and cost-effectiveness.
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| 12. |
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| 13. |
- Hoglund, K, et al.
(författare)
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Molecular biomarkers of neurodegeneration
- 2013
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Ingår i: Expert review of molecular diagnostics. - : Informa UK Limited. - 1744-8352 .- 1473-7159. ; 13:8, s. 845-861
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Tidskriftsartikel (refereegranskat)
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| 14. |
- Hyötyläinen, Tuulia, 1971-
(författare)
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Novel methodologies in metabolic profiling with a focus on molecular diagnostic applications
- 2012
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Ingår i: Expert Review of Molecular Diagnostics. - : Taylor & Francis. - 1473-7159 .- 1744-8352. ; 12:5, s. 527-538
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Tidskriftsartikel (refereegranskat)abstract
- The metabolome contains all the biological end points of genomic, transcriptomic and proteomic perturbations, also including the influence of gut microbiota and the environment, giving a direct picture of an organism's ongoing metabolic state. Metabolomics thus has the potential to be an effective tool for early diagnosis of disease, and also to be a predictor of treatment response and survival. In recent years, the development of instrumental systems has enabled more comprehensive coverage of the metabolome. Advances in mass spectrometry and chromatography have particularly improved both the efficiency of nontargeted metabolic profiling as well as the sensitivity and reliability of targeted analyses. Mass spectrometric techniques are also increasingly becoming accepted as a routine diagnostic tool in clinical laboratories. This review summarizes the most recent advances and current challenges in metabolomics, with a focus on mass spectrometric methods utilized in biomarker research, highlighted with selected examples.
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| 15. |
- Jevtusevskaja, Jekaterina, et al.
(författare)
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The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification
- 2017
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 17:4, s. 403-410
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Forskningsöversikt (refereegranskat)abstract
- Background: The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assaysMethods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplificationResults: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases.Conclusion: These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.
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| 16. |
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| 17. |
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| 18. |
- Krõlov, Katrin, et al.
(författare)
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Implementation of antimicrobial peptides for sample preparation prior to nucleic acid amplification in point-of-care settings
- 2017
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 17:12, s. 1117-1125
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Tidskriftsartikel (refereegranskat)abstract
- Background: A variety of sample preparation techniques are used prior to nucleic acid amplification. However, their efficiency is not always sufficient and nucleic acid purification remains the preferred method for template preparation. Purification is difficult and costly to apply in point-of-care (POC) settings and there is a strong need for more robust, rapid, and efficient biological sample preparation techniques in molecular diagnostics. Methods: Here, the authors applied antimicrobial peptides (AMPs) for urine sample preparation prior to isothermal loop-mediated amplification (LAMP). AMPs bind to many microorganisms such as bacteria, fungi, protozoa and viruses causing disruption of their membrane integrity and facilitate nucleic acid release. Results: The authors show that incubation of E. coli with antimicrobial peptide cecropin P1 for 5 min had a significant effect on the availability of template DNA compared with untreated or even heat treated samples resulting in up to six times increase of the amplification efficiency. Conclusion: These results show that AMPs treatment is a very efficient sample preparation technique that is suitable for application prior to nucleic acid amplification directly within biological samples. Furthermore, the entire process of AMPs treatment was performed at room temperature for 5 min thereby making it a good candidate for use in POC applications.
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| 19. |
- Käller, Max, et al.
(författare)
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Arrayed identification of DNA signatures
- 2007
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 7:1, s. 65-76
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Forskningsöversikt (refereegranskat)abstract
- Over the last few years, several initiatives have described efforts to combine previously invented techniques in molecular biology with parallel detection principles to sequence or genotype DNA signatures. The Infinium (R) system from Illumina and the Affymetrix GeneChips (R) are two systems suitable for whole-genome scoring of variable positions. However, directed candidate-gene approaches are more cost effective and several academic groups and the private sector provide techniques with moderate typing throughput combined with large sample capacity suiting these needs. Recently, whole-genome sequencing platforms based on the sequencing-by-synthesis principle were presented by 454 Life Sciences and Solexa, showing great potential as alternatives to conventional genotyping approaches. In addition to these sequencing initiatives, many efforts are pursuing novel ideas to facilitate fast and cost-effective whole genome sequencing, such as ligation-based sequencing. Reliable methods for routine resequencing of human genomes as a tool for personalized medicine, however, remain to be developed.
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| 20. |
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| 21. |
- Lindskog, Cecilia, et al.
(författare)
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Immunohistochemistry-based prognostic biomarkers in NSCLC : novel findings on the road to clinical use?
- 2015
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Ingår i: Expert Review of Molecular Diagnostics. - : Informa UK Limited. - 1473-7159 .- 1744-8352. ; 15:4, s. 471-490
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Forskningsöversikt (refereegranskat)abstract
- Prognostication of non-small cell lung cancer is principally based on stage, age and performance status. This review provides an overview of 342 potential prognostic biomarkers in non-small cell lung cancer described between January 2008 and June 2013, evaluating the association between immunohistochemical protein expression and survival endpoint. Numerous studies proposed prognostic biomarkers, but many were only evaluated in a single patient cohort, and a large number of biomarkers revealed inconclusive findings when analyzed in more than one study. Only 26 proteins first described after 2008 (ALDH1A1, ANXA1, BCAR1, CLDN1, EIF4E, EZH2, FOLR1, FOXM1, IL7R, IL12RB2, KIAA1524, CRMP1, LOX, MCM7, MTA1, MTDH, NCOA3, NDRG2, NEDD9, NES, PBK, PPM1D, SIRT1, SLC7A5, SQSTM1 and WNT1) demonstrated a consistent prognostic association in two or more independent patient cohorts, thus qualifying as promising candidates for diagnostic use. Raised quality standards for study design and antibody validation, and integration of preclinical findings with clinical needs are clearly warranted.
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| 22. |
- Ludvigsson, Johnny
(författare)
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The clinical potential of low-level C-peptide secretion
- 2016
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Ingår i: Expert Review of Molecular Diagnostics. - : TAYLOR & FRANCIS LTD. - 1473-7159 .- 1744-8352. ; 16:9, s. 933-940
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Forskningsöversikt (refereegranskat)abstract
- Introduction: In all forms of diabetes, especially so in Type 1 diabetes (T1D), beta cell function is crucial for the course. The interest for residual beta cell function has been meagre, but increased in recent years with interventions to preserve function.Areas covered: Importance and clinical use of C-peptide in Type 1 diabetes. Data for this review were identified by searches of PubMed, and references from relevant articles using the search terms: type 1 diabetes, C-peptide, beta cell function, HbA1c, quality of life, complications. Abstracts and reports from meetings were not included.Expert commentary: C-peptide may help to get a correct diagnosis, and it is of practical clinical value to know degree of residual insulin secretion to diminish the risk of severe hypoglycaemia and ketoacidosis. Evidence shows that even a quite reduced beta cell function may play an important role for quality of life, for metabolic balance/control, possibility to avoid complications and even for long-term survival. Furthermore, the evidence is increasing for C-peptide being a hormone per se.
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| 23. |
- Oresic, Matej, 1967-, et al.
(författare)
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Metabolomic approaches to phenotype characterization and applications to complex diseases
- 2006
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Ingår i: Expert Review of Molecular Diagnostics. - : Expert Reviews Ltd.. - 1473-7159 .- 1744-8352. ; 6:4, s. 575-585
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Tidskriftsartikel (refereegranskat)abstract
- Metabolites are the key regulators of systems homeostasis. As such, concentration changes of specific groups of metabolites may reflect systemic responses to environmental, therapeutic or genetic interventions. Thus, the study of metabolites is a powerful tool for the characterization of complex phenotypes as well as for the development of biomarkers for specific physiological responses. Therefore, metabolomics is a valuable platform for studies of complex diseases and the development of new therapies, both in nonclinical disease model characterization and clinical settings.
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