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Turk Patoloji Dergisi 2020Biobanks are units where high quality and long-term protection of biomaterials is maintained. This system, in which biological materials and data are systematically... (Review)
Review
Biobanks are units where high quality and long-term protection of biomaterials is maintained. This system, in which biological materials and data are systematically recorded and stored, is a unique resource for the study of the pathophysiology of disease, the development of diagnostic biomarkers, and working with human tissues for the potential discovery of targeted therapeutic agents. At this point, the pathology unit plays a unifying and complementary role between the clinical and core disciplines and offers optimal management of the patients' biomaterials for diagnostic and research projects. The aim of this article is to present general information with regard to a biobank constructed for the storage of tumor tissue and blood biospecimens. Ethical issues (informed consent, protection of confidentiality and privacy, and secondary use of biospecimens) and the information technology system (collection, systematic recording, backup and protection of clinical information) are important issues in biobanking. The selection of freezers to be used in storage (mechanical freezers, liquid-vapor nitrogen tanks), and if mechanical freezers are preferred the establishment of the relevant infrastructure and support team (such as additional power units for protection from power outages), the preservation of materials by aliquoting in different freezers, ensuring financing so as to afford the cost of the infrastructure, and implementation of all these dynamics while adhering to international guidelines are of the utmost importance.
Topics: Biological Specimen Banks; Humans; Pathology
PubMed: 32189322
DOI: 10.5146/tjpath.2020.01482 -
Methods in Molecular Biology (Clifton,... 2019Cerebrospinal fluid (CSF) is a physiologically essential fluid produced by the brain that is involved in protecting the brain and in the exchange of nutrients and waste... (Review)
Review
Cerebrospinal fluid (CSF) is a physiologically essential fluid produced by the brain that is involved in protecting the brain and in the exchange of nutrients and waste products. CSF has long been utilized to confirm clinical suspicion of various infectious and inflammatory disorders, such as meningitis and multiple sclerosis. However, there has been increasing interest in collecting CSF in order to study the clinical significance of additional biomarkers. This chapter outlines the procedures necessary to collect, process, store, and utilize CSF obtained for the purposes of biobanking from both living and deceased patients.
Topics: Biological Specimen Banks; Biomarkers; Brain; Cerebrospinal Fluid; Humans; Meningitis; Multiple Sclerosis; Specimen Handling
PubMed: 30539439
DOI: 10.1007/978-1-4939-8935-5_11 -
Lab on a Chip Mar 2023Sandwich immunoassays such as the enzyme-linked immunosorbent assay (ELISA) have been miniaturized and performed in a lab-on-a-chip format, but the execution of the...
Sandwich immunoassays such as the enzyme-linked immunosorbent assay (ELISA) have been miniaturized and performed in a lab-on-a-chip format, but the execution of the multiple assay steps typically requires a computer or complex peripherals. Recently, an ELISA for detecting antibodies was encoded structurally in a chip thanks to the microfluidic chain reaction (Yafia , 2022, , 464-469), but the need for precise pipetting and intolerance to commonly used surfactant concentrations limit the potential for broader adoption. Here, we introduce the ELISA-on-a-chip with aliquoting functionality that simplifies chip loading and pipetting, accommodates higher surfactant concentrations, includes barrier channels that delay the contact between solutions and prevent undesired mixing, and that executed a quantitative, high-sensitivity assay for the SARS-CoV-2 nucleocapsid protein in 4×-diluted saliva. Upon loading the chip using disposable pipettes, capillary flow draws each reagent and the sample into a separate volumetric measuring reservoir for detection antibody (70 μL), enzyme conjugate (50 μL), substrate (80 μL), and sample (210 μL), and splits washing buffer into 4 different reservoirs of 40, 40, 60, and 20 μL. The excess volume is autonomously drained a structurally encoded capillaric aliquoting circuit, creating aliquots with an accuracy of >93%. Next, the user click-connects the assay module, comprising a nitrocellulose membrane with immobilized capture antibodies and a capillary pump, to the chip which triggers the step-by-step, timed flow of all aliquoted solutions to complete the assay in 1.5 h. A colored precipitate forming a line on a nitrocellulose strip serves as an assay readout, and upon digitization, yielded a binding curve with a limit of detection of 54 and 91 pg mL for buffer and diluted saliva respectively, vastly outperforming rapid tests. The ELISA chip is 3D-printed, modular, adaptable to other targets and assays, and could be used to automate ELISA in the lab; or as a diagnostic test at the point of care with the convenience and form factor of rapid tests while preserving the protocol and performance of central laboratory ELISA.
Topics: Humans; Collodion; COVID-19; SARS-CoV-2; Enzyme-Linked Immunosorbent Assay; Antibodies; Antibodies, Immobilized; Printing, Three-Dimensional; Lab-On-A-Chip Devices
PubMed: 36723136
DOI: 10.1039/d2lc00878e -
FEMS Microbiology Reviews Aug 2017First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of... (Review)
Review
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.
Topics: Cryopreservation; Cryoprotective Agents; Feces; Gastrointestinal Microbiome; Humans; Intestines
PubMed: 28830090
DOI: 10.1093/femsre/fux027 -
Micromachines Jul 2023The detection of nucleic acids as specific markers of infectious diseases is commonly implemented in molecular biology laboratories. The translation of these benchtop...
The detection of nucleic acids as specific markers of infectious diseases is commonly implemented in molecular biology laboratories. The translation of these benchtop assays to a lab-on-a-chip format demands huge efforts of integration and automation. The present work is motivated by a strong requirement often posed by molecular assays that combine isothermal amplification and CRISPR/Cas-based detection: after amplification, a 2-8 microliter aliquot of the reaction products must be taken for the subsequent reaction. In order to fulfill this technical problem, we have designed and prototyped a microfluidic device that is able to meter and aliquot in the required range during the stepped assay. The operation is achieved by integrating a porous material that retains the desired amount of liquid after removing the excess reaction products, an innovative solution that avoids valving and external actuation. The prototypes were calibrated and experimentally tested to demonstrate the overall performance (general fluidics, metering, aliquoting, mixing and reaction). The proposed aliquoting method is fully compatible with additional functions, such as sample concentration or reagent storage, and could be further employed in alternative applications beyond molecular diagnosis.
PubMed: 37512736
DOI: 10.3390/mi14071425 -
Pediatric Quality & Safety 2023Sugammadex is a medication that may have cost considerations with the potential for waste of unused product in pediatric patients due to the vial size and its single-use...
UNLABELLED
Sugammadex is a medication that may have cost considerations with the potential for waste of unused product in pediatric patients due to the vial size and its single-use limitation. Therefore, exploring the potential of vial-splitting for perioperative use may be beneficial.
METHODS
The study was a retrospective, quality improvement study using the electronic medical record to identify every sugammadex administration over the last five years in a tertiary care pediatric institution. We divided patients into groups depending on the dose of sugammadex administered. The cost of sugammadex was calculated under three scenarios: (1) only 200-mg vials available; (2) 100-mg aliquots available; and (3) 50-mg aliquots. We then calculated the total money spent per patient in the 3 scenarios.
RESULTS
31,063 patients received sugammadex over the study period, of whom 23.6% received 151-200 mg. The greatest percentage of patients received ≤50 mg (32.9%). The average cost per patient was $113.58, $81.61, and $68.83 if 200 mg, 100 mg, and 50 mg doses were available, respectively. Over the last 5 years, $1,390,110.13 could have been saved by having 50 and 100 mg aliquots available.
CONCLUSIONS
Pediatric patients generally receive lower doses of sugammadex due to weight-based dosing, leading to increased waste and cost when using only 200-mg vials. Vial-splitting into smaller aliquots can significantly cut costs for healthcare centers and patients while decreasing waste.
PubMed: 37051405
DOI: 10.1097/pq9.0000000000000646 -
Journal of Extracellular Biology Sep 2023Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach...
Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients.
Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell-free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining EV-associated RNA (EV-RNA) and cfDNA signals on = 64 healthy donors (HD) and non-metastatic BrCa patients. Specifically, we isolated EV-enriched samples by a charge-based (CB) method and investigated EV-RNA and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV-RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi-analytes liquid biopsies' clinical implementation.
PubMed: 38046436
DOI: 10.1002/jex2.108 -
Clinical Chemistry Jun 2017Clinical laboratory automation has blossomed since the 1989 AACC meeting, at which Dr. Masahide Sasaki first showed a western audience what his laboratory had... (Review)
Review
Clinical laboratory automation has blossomed since the 1989 AACC meeting, at which Dr. Masahide Sasaki first showed a western audience what his laboratory had implemented. Many diagnostics and other vendors are now offering a variety of automated options for laboratories of all sizes. Replacing manual processing and handling procedures with automation was embraced by the laboratory community because of the obvious benefits of labor savings and improvement in turnaround time and quality. Automation was also embraced by the diagnostics vendors who saw automation as a means of incorporating the analyzers purchased by their customers into larger systems in which the benefits of automation were integrated to the analyzers.This report reviews the options that are available to laboratory customers. These options include so called task-targeted automation-modules that range from single function devices that automate single tasks (e.g., decapping or aliquoting) to multifunction workstations that incorporate several of the functions of a laboratory sample processing department. The options also include total laboratory automation systems that use conveyors to link sample processing functions to analyzers and often include postanalytical features such as refrigerated storage and sample retrieval.Most importantly, this report reviews a recommended process for evaluating the need for new automation and for identifying the specific requirements of a laboratory and developing solutions that can meet those requirements. The report also discusses some of the practical considerations facing a laboratory in a new implementation and reviews the concept of machine vision to replace human inspections.
Topics: Automation, Laboratory; Clinical Laboratory Information Systems; Clinical Laboratory Services; Clinical Laboratory Techniques; Humans
PubMed: 28396562
DOI: 10.1373/clinchem.2017.272047 -
Organic & Biomolecular Chemistry Dec 2016A protocol is established for the high-yielding synthesis of F-BODIPYs involving non-anhydrous reagents and not requiring precautions to exclude moisture. This simple...
A protocol is established for the high-yielding synthesis of F-BODIPYs involving non-anhydrous reagents and not requiring precautions to exclude moisture. This simple and robust strategy simply requires a second addition of NEt and BF·OEt, midway through the reaction period. The ratio and amounts of NEt and BF·OEt used in each aliquot are critical to success (6 : 9 for each aliquot). The protocol can be completed using bench-dry apparatus, without need to achieve and maintain anhydrous conditions or solvents.
PubMed: 27883144
DOI: 10.1039/c6ob02238c -
International Journal of Laboratory... Dec 2022Established parameters for the investigation of suspected iron deficiency have recognized limitations that affect their sensitivity and specificity. Reticulocyte... (Review)
Review
INTRODUCTION
Established parameters for the investigation of suspected iron deficiency have recognized limitations that affect their sensitivity and specificity. Reticulocyte haemoglobin content (RHC) is an early biomarker of iron deficiency or restriction, which also demonstrates response to iron therapy. RHC parameters are offered on all major automated haematology analysers. There is no external quality assessment (EQA) for RHC in the UK, restricting its wider clinical application. The UK National External Quality Assessment Scheme (UKNEQAS) for Haematology has completed a pilot study on the use of stabilized blood for RHC EQA.
METHODS
Blood was obtained from two JAK2 V617F mutation-positive, polycythaemia vera patients undergoing regular venesection, and from a healthy volunteer donor. Aliquots of each donation were distributed to users of Abbott, Horiba, Siemens and Sysmex automated analysers for RHC analysis on days 1, 3, 5 and 7.
RESULTS
Results were received from 20 laboratories using four different platforms. The daily mean and standard deviation (SD) were calculated for each aliquot, by day of analysis and platform. With RHC there was no significant within-platform difference (p > 0.5) between testing days, although there were statistically significant differences (p < 0.001) between different platforms. The greatest difference was seen between Abbott MCHr and Horiba RhCc (-6.14 ± 1.25 pg). Despite inter-platform differences, it was possible to define iron deficient, borderline, and normal cut-offs to classify 95% of results correctly.
CONCLUSIONS
The results demonstrate that it is possible to provide RHC EQA material using UKNEQAS standard procedures. The results are clinically relevant but indicate a requirement for inter-user comparison.
Topics: Humans; Reticulocytes; Pilot Projects; Hemoglobins; Iron Deficiencies; Iron; Hematology; United Kingdom
PubMed: 36056688
DOI: 10.1111/ijlh.13957