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1.
EJIFCC ; 35(1): 10-22, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38706733

RESUMO

BACKGROUND: BD Barricor™ tubes have been proposed to decrease laboratory turnaround time (TAT). We analytically validated and then clinically verified these tubes for use with Abbott Alinity™ and Siemens Atellica® highly sensitive cardiac troponin I (hs-cTnI) assays. METHODS: hs-cTnI measurements were undertaken in paired Barricor™ and in-use PSTII™ tubes on both systems. 359 matched samples with hs-cTnI levels between 3 and 15,000 ng/L (Atellica® values) were used to assess the hemolysis rate and make method comparisons. 599 paired patient samples were collected on emergency department (ED) admission to compare the performance of the rapid acute myocardial infarction (AMI) rule-out strategy based on hs-cTnI concentrations lower than recommended thresholds (<4 ng/L Alinity™; <5 ng/L Atellica®) when different tubes and systems were employed. RESULTS: No between-tube differences in hemolysis rate were seen when free hemoglobin concentrations in plasma samples were ≥0.25 g/L, even if PSTII™ showed a significant increase of hemolysis rate vs. Barricor™ (31% vs. 22%, p=0.007) when a lower cut-off for hemolysis (≥0.11 g/L) was employed on the Atellica® detection system. The alternate use of these tubes did not influence the hs-cTnI results obtained from either of the two assays, which remained markedly biased (~40%) irrespective of the tube used. The expected optimal ability of very low hs-cTnI values on ED admission for ruling out AMI was confirmed by using both systems regardless of the tube type. CONCLUSIONS: Barricor™ and PSTII™ tubes can provide analytically equivalent hs-cTnI results when used on either Alinity™ or Atellica® hs-cTnI assays.

2.
Cureus ; 16(3): e57243, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38559530

RESUMO

The accuracy of diagnostic results in clinical laboratory testing is paramount for informed healthcare decisions and effective patient care. While the focus has traditionally been on the analytical phase, attention has shifted towards optimizing the preanalytical phase due to its significant contribution to total laboratory errors. This review highlights preanalytical errors, their sources, and control measures to improve the quality of laboratory testing. Blood sample quality is a critical concern, with factors such as hemolysis, lipemia, and icterus leading to erroneous results. Sources of preanalytical errors encompass inappropriate test requests, patient preparation lapses, and errors during sample collection, handling, and transportation. Mitigating these errors includes harmonization efforts, education and training programs, automated methods for sample quality assessment, and quality monitoring. Collaboration between laboratory personnel and healthcare professionals is crucial for implementing and sustaining these measures to enhance the accuracy and reliability of diagnostic results, ultimately improving patient care.

3.
Biopreserv Biobank ; 22(2): 110-114, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-37074140

RESUMO

The characterization of DNA methylation patterns to identify epigenetic markers for complex human diseases is an important and rapidly evolving part in biomedical research. DNA samples collected and stored in clinical biobanks over the past years are an important source for future epigenetic studies. Isolated gDNA is considered stable when stored at low temperatures for several years. However, the effect of multiple use and the associated repeated thawing of long-term stored DNA samples on DNA methylation patterns has not yet been investigated. In this study, we examined the influence of up to 10 freeze and thaw cycles on global DNA methylation by comparing genome-wide methylation profiles. DNA samples from 19 healthy volunteers were either frozen at -80°C or subjected to up to 10 freeze and thaw cycles. Genome-wide DNA methylation was analyzed after 0, 1, 3, 5, or 10 thaw cycles using the Illumina Infinium MethylationEPIC BeadChip. Evaluation of the global DNA methylation profile by beta-value density plots and multidimensional scaling plots revealed an expected clear participant-dependent variability, but a very low variability depending on the freeze and thaw cycles. In accordance, no significant difference in any of the methylated cytosine/guanine sites studied could be detected in the performed statistical analyses. Our results suggest that long-term frozen DNA samples are still suitable for epigenetic studies after multiple thaw cycles.


Assuntos
Metilação de DNA , DNA , Humanos , Congelamento , DNA/genética , Voluntários Saudáveis , Genômica
4.
Biopreserv Biobank ; 22(2): 115-122, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-37889987

RESUMO

Biological samples are important resources for scientific research. These samples are stored in biobanks over years until needed, and some of them can never be retrieved if they are improperly stored, causing them to be wasted. Thus, they are priceless, and they should be used correctly and effectively. Sample quality substantially affects biomedical research results. However, sample misidentification or mix-up is common. It is necessary to establish quality standards for sample identification. In this study, we used the Advanta Sample ID genotyping panel to detect homology identification and cross-contamination. We compared the single-nucleotide polymorphism (SNP) typing results of two different samples and calculated the similarity score of homologous sample pairs and nonhomologous sample pairs. Through analysis, we obtained a similarity score cutoff point of 0.8620, which was an effective way to distinguish homology and nonhomology. Cross-contamination was detected in two sets of mixtures (STD8:STD6 and jj3:1-P) mixed at a series of special ratios. Sensitivity was dependent on the sample characteristics and mixing ratios. Finally, we assessed the effect of sample degradation degree on SNP genotyping and found that degraded samples with a minimal DNA integrity number of 1.9 had complete genotyping results. On the whole, this study shows that the Sample ID panel is reliable for homology identification and cross-contamination analysis. Moreover, this technology has promising further applications in biological sample quality control.


Assuntos
Bancos de Espécimes Biológicos , Polimorfismo de Nucleotídeo Único , Genótipo
5.
Pathol Res Pract ; 252: 154943, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37977036

RESUMO

The nucleic acid integrity of head and neck squamous cell carcinoma (HNSCC) samples is poor, and the material available for genetic analysis is limited. Therefore, to expand the effectiveness of personalized medicine in patients with HNSCC, a new sampling method is needed. In total, 128 samples from 44 patients with HNSCC were studied: 32 genetic analysis samples (GASs) collected as 5 × 5 × 5 mm tissue fragments from resected large tumors and immediately embedded in a small formalin bottle within 10 min (i.e., the ischemic time), 43 primary tumor components (primary), 14 decalcified tumor (DC) samples, 32 metastatic tumors in lymph nodes (LNs), and 7 parakeratinized components (PKCs). The nucleic acid quality in the GAS, primary, DC, LN, and PKC groups was compared and next-generation sequencing (NGS) was performed. DNA integrity number and percentage of RNA fragments with > 200 nucleotides were significantly higher in the GAS group than those in the other groups. RNA integrity number decreased first in LN, followed by GAS, primary, and DC. No significant differences were observed in DIN, RIN and DV200 among the PKC, primary and LN. Following methyl green-pyronin staining, preserved DNA and RNA were not visualized in DC samples. Most NGS metrics did not differ significantly among primary, LN, and PKC samples. In conclusion, GASs should be collected during routine hospital activities. When the volume of viable materials is limited, PKCs should be considered for genetic analysis.


Assuntos
Neoplasias de Cabeça e Pescoço , Ácidos Nucleicos , Humanos , Carcinoma de Células Escamosas de Cabeça e Pescoço/genética , Estudos Retrospectivos , Neoplasias de Cabeça e Pescoço/genética , Neoplasias de Cabeça e Pescoço/cirurgia , DNA , Manejo de Espécimes , RNA
6.
Clin Chem Lab Med ; 2023 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-38008748

RESUMO

OBJECTIVES: This paper evaluates 16 year results of the Allergy EQA program shared by EQA organisers in Belgium, Finland, Portugal, and The Netherlands. METHODS: The performance of Thermo Fisher and Siemens user groups (in terms of concordance between both groups, between laboratory CV, prevalence of clinically significant errors) and suitability of samples (stability and validity of dilution of patient samples) are evaluated using data of 192 samples in the EQA programs from 2007 to 2022. Measurands covered are total IgE, screens and mixes, specific IgE extracts and allergen components. RESULTS: There is perfect (53 %), acceptable (40 %) and poor (6 %) concordance between both method groups. In case of poor concordance the best fit with clinical data is seen for Thermo Fisher (56 %) and Siemens (26 %) respectively. The between laboratory CV evolves from 7.8 to 6.6 % (Thermo Fisher) and 7.3 to 7.7 % (Siemens). The prevalence of blunders by individual laboratories is stable for Siemens (0.4 %) and drops from 0.4 to 0.2 % for Thermo Fisher users. For IgE, the between year CV of the mean of both user groups is 1 %, and a fifteen-fold dilution of a patient sample has an impact of 2 and 4 % on the recovery of Thermo Fisher and Siemens user groups. CONCLUSIONS: The analytical performance of Thermo Fisher is slightly better than that of Siemens users but the clinical impact of this difference is limited. Stability of the sample and the low impact of dilution on the recovery of measurands demonstrates the suitability for purpose of the EQA program.

7.
Biopreserv Biobank ; 2023 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-37878356

RESUMO

Development of novel biomarkers for diagnosis of disease and assessment of treatment efficacy utilizes a wide range of biospecimens for discovery research. The fitness of biospecimens for the purpose of biomarker development depends on the clinical characteristics of the donor and on a number of critical and potentially uncontrolled pre-analytical variables. Pre-analytical factors influence the reliability of the biomarkers to be analyzed and can seriously impact analytic outcomes. Sample quality stratification assays and tools can be utilized by biorepositories to minimize bias resulting from samples' inconsistent quality. In this study, we evaluated the quality of biobanked specimens by comparing analytical outcomes at 1, 5, and 10 years after collection. Our results demonstrate that currently available assays and tools can be used by biobank laboratories to support objective biospecimen qualification. We have established a workflow to monitor the quality of different types of biospecimens and, in this study, present the results of a qualification exercise applied to fluid samples and their derivatives in the context of urological diseases.

8.
Cells ; 12(18)2023 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-37759487

RESUMO

Over the past decade, adeno-associated viruses (AAVs) have attained significant prominence in gene therapy and genome editing applications, necessitating the development of robust and precise methodologies to ensure the quality and purity of AAV products. Existing AAV characterization techniques have proven effective for the analysis of pure and homogeneous AAV samples. However, there is still a demand for a rapid and low-sample-consumption method suitable for the characterization of lower purity or heterogeneous AAV samples commonly encountered in AAV products. Addressing this challenge, we propose the SEC-MP method, which combines size exclusion chromatography (SEC) with mass photometry (MP). In this novel approach, SEC effectively separates monomeric AAV particles from impurities, while the UV detector determines the virus particle concentration. MP complements this process by estimating the fraction of fully packaged AAVs in the total population of AAV particles. This combined methodology enables accurate determination of the titer of effective, fully packaged AAVs in samples containing aggregates, incorrectly packaged AAVs with incomplete genomes, protein or DNA fragments, and other impurities. Our experimental results demonstrate that SEC-MP provides valuable guidance for sample quality control and subsequent applications in the field of AAV research.

9.
Front Surg ; 10: 1171382, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37576920

RESUMO

Aim: To evaluate the efficacy and safety of simple TaTNE in the treatment of low rectal cancer compared with laparoscopic transabdominal TME. Methods: We collected patients with low rectal cancer admitted to our hospital between January 2019 and November 2021 who received simple TaTME or laparoscopic transabdominal TME. The main outcome was the integrity of the TME specimen. Secondary outcomes were the number of lymph nodes dissected, intraoperative blood loss, operative time, surgical conversion rate, Specimen resection length, circumferential margin (CRM), and distal resection margin (DRM), complication rate. In addition, the Wexner score and LARS score of fecal incontinence were performed in postoperative follow-up. Results: Pathological tissues were successfully resected in all patients. all circumferential margins of the specimen were negative. Specimen resection length was not statistically significant (9.94 ± 2.85 vs. 8.90 ± 2.49, P > 0.05). The incidence of postoperative complications in group A (n = 0) was significantly lower than that in group B (n = 3) (P > 0.05). There was no significant difference in operation time between group A and group B (296 ± 60.36 vs. 305 ± 58.28, P > 0.05). Among the patients with follow-up time less than 1 year, there was no significant difference in Wexner score and LARS score between group A and group B (P > 0.05). However, in patients who were followed up for more than 1 year, the Wexner score in group A (9.25 ± 2.73) was significantly lower than that in group B (17.36 ± 10.95) and was statistically significant (P < 0.05). Conclusion: For radical resection of low rectal cancer, Simple TaTME resection may be as safe and effective as laparoscopic transabdominal TME, and the long-term prognosis may be better.

10.
Front Public Health ; 11: 1066934, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37033037

RESUMO

A nasopharyngeal swab (NPS) is the most frequently collected sample type when molecular diagnosis of respiratory viruses, including SARS CoV-2, is required. An optimal collection technique would provide sufficient sample quality for the diagnostic process and would minimize the discomfort felt by the patient. This study compares a simplified NPS collection procedure with only one rotation of the swab to a more standard procedure with five rotations. Swabs were collected from 76 healthy volunteers by the same healthcare professional on 2 consecutive days at a similar hour to minimize variability. The number of Ubiquitin C copy number per sample was measured by real-time quantitative PCR and patient discomfort was assessed by questionnaire. No statistically significant difference (p = 0.15) was observed in the Ubiquitin C copy number per sample between a NPS collected with one rotation (5.2 ± 0.6 log UBC number copies/sample) or five rotations (5.3 ± 0.5 log UBC number copies/sample). However, a statistically significant difference was observed in discomfort between these two procedures, the second being much more uncomfortable. Additional analysis of the results showed a weak correlation between discomfort and the number of human cells recovered (Spearman's rho = 0.202) and greater discomfort in younger people. The results of this study show that a NPS collected with one slow rotation has the same quality as a NPS collected with five rotations. However, the collection time is shorter and, most importantly, less unpleasant for patients.


Assuntos
COVID-19 , Humanos , Ubiquitina C , Nasofaringe , SARS-CoV-2 , Manejo de Espécimes/métodos
11.
Cancer Genomics Proteomics ; 20(3): 211-221, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37093689

RESUMO

The growing demand for personalized medicine we are currently witnessing has given rise to more in-depth research in the field of biomarker discovery and, thus, in biological banks that hold the ability to process, collect, store, and distribute "high-quality" biological specimens. However, the notion of "specimen quality" is subject to change with technological advancements. In this perspective, we propose that the notion of sample quality should shift from a broad definition of "high-quality" to a "fit-for-purpose" concept more suitable for precision medicine studies. Digital twins are a digital replica of real entities. These are largely adopted in any digitalized domain and are currently finding applications in biomedicine. The adoption of digital twins for biosamples, proposed in this paper, can provide prompt information about the whole lifecycle of the physical twin (i.e., the biosample) and substantially extend the possible matching criteria between the available samples and the researchers' and physicians' requests. This fine-tuning matching could greatly contribute to improving the "fit-for-purpose" quality, not only for studies based on current needs, but also to improve the identification of the best available samples in future situations, determined by the evolution of technologies and biosciences. Assuming and exploiting a data-science view in our biobank perspective, the more (accurate) data there are available, the more information can be extrapolated from them, the more opportunities there are for matching future, currently unknown, needs. This should be a mandatory principle that the 'time machines' called biobanks should follow.


Assuntos
Pesquisa Biomédica , Humanos , Bancos de Espécimes Biológicos , Medicina de Precisão
12.
Acta Clin Croat ; 62(2): 345-354, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38549592

RESUMO

The aim of this study was to establish the impact of air transport on blood samples packaged with and without cooling elements and effect of outdoor temperature on sample quality. Venous samples from 38 blood donors in winter and 36 in summer were tested for hemolysis and complete blood count. One tube per subject was kept in controlled conditions at +4 °C. Two sets of tubes were sent by plane from Zagreb to Brussels, one with and one without cooling elements, and another two sets were sent to London following the same principle. Packages with cooling elements were stored in controlled warehousing conditions at airports (+2 °C to +8 °C), whereas packages without cooling elements were stored in ambient warehouse conditions. Data loggers were used for temperature monitoring. Our research revealed statistically significant differences in several hematologic parameters when comparing the samples stored in controlled laboratory conditions and those transported by plane. These differences were more pronounced in the samples transported during the summer. Transport conditions without cooling elements had additional negative impact on the sample quality. Transport of samples using cooling elements and controlled warehousing conditions at airports are sometimes not sufficient to maintain laboratory storage conditions.


Assuntos
Temperatura Baixa , Humanos , Temperatura
13.
Bioanalysis ; 14(20): 1305-1315, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-36541270

RESUMO

Aim: A sensitive and selective method for the determination of nirmatrelvir in dried human blood collected by Tasso-M20 was developed and validated from 20.0 to 20,000 ng/ml. Materials & methods: Nirmatrelvir and its stable-labeled internal standard were isolated from approximately 20 µl of blood dried on one volumetric absorptive pad inside the Tasso-M20 device by extraction with methanol, followed by dilution of the supernatant. The extracts were analyzed by high-performance liquid chromatography coupled with tandem mass spectrometric detection. Results & conclusion: The method was fully validated. Hematocrit levels do not impact assay accuracy. Stabilities to cover sample drying and storage at a variety of conditions were conducted. The validated method was used in multiple clinical studies with excellent performance.


Assuntos
Teste em Amostras de Sangue Seco , Espectrometria de Massas em Tandem , Humanos , Cromatografia Líquida/métodos , Teste em Amostras de Sangue Seco/métodos , Cromatografia Líquida de Alta Pressão/métodos , Espectrometria de Massas em Tandem/métodos , Lactamas , Reprodutibilidade dos Testes
14.
J Clin Lab Anal ; 36(7): e24531, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35666551

RESUMO

BACKGROUND: The development of next-generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations. METHODS: Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques. RESULTS: Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions. CONCLUSION: Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.


Assuntos
DNA , Leucócitos Mononucleares , DNA/genética , Humanos , Reprodutibilidade dos Testes , Saliva , Manejo de Espécimes/métodos
15.
Syst Biol Reprod Med ; 68(4): 258-271, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35658756

RESUMO

Standardizing RNA quality is key to interpreting RNA-seq data as a compromised sample can mask the underlying biology. The challenge remains when evaluating RNA quality in samples with high RNA fragmentation. For example, programmed fragmentation and cytoplasmic expulsion, integral to sperm maturation, is a prime example of the complexities of interpreting RNA-seq data, given that fragmentation can be random and\or targeted. To meet this challenge, we developed an algorithm that accurately measures RNA quality in samples with high fragmentation, such as spermatozoa. The integrity of 1,000 previously identified abundant sperm transcripts were independently visualized and evaluated using the Transcript Integrity Index (TII) algorithm to identify intact transcripts. Full-length transcripts from visual and the TII algorithm were evaluated for testis preference in humans using the GTEx tissues database. Samples were then filtered by the Interquartile Range (IQR), identifying those in which the greatest number of transcripts failed to pass the visual or TII thresholds. Transcript lists were overlapped, forming the set of intact transcripts used as TII standards. Each sample was re-evaluated as a function of this TII set of intact transcripts, with poor quality samples identified as those failing in the largest number of transcripts. While ontologically enriched in roles related to spermatogenesis and/or fertilization, samples did not segregate based on birth outcome. The TII algorithm proved an effective means to identify samples of similar quality from sperm, a cell type enriched in biologically fragmented RNAs. The algorithm should facilitate other studies using samples compromised by high levels of RNA fragmentation, such as Formalin-Fixed Paraffin-Embedded samples. Requisite to assessing male health, TII provides a solution to the long-sought-after standard that identifies samples of similar quality.


Assuntos
RNA , Espermatozoides , Humanos , Masculino , RNA/genética , RNA/metabolismo , Análise de Sequência de RNA , Espermatogênese , Espermatozoides/metabolismo , Testículo/metabolismo
16.
Stat Med ; 41(18): 3511-3526, 2022 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-35567357

RESUMO

The continuous evolution of metabolomics over the past two decades has stimulated the search for metabolic biomarkers of many diseases. Metabolomic data measured from urinary samples can provide rich information of the biological events triggered by organ rejection in pediatric kidney transplant recipients. With additional validation, metabolic markers can be used to build clinically useful diagnostic tools. However, there are many methodological steps ranging from data processing to modeling that can influence the performance of the resulting metabolomic classifiers. In this study we focus on the comparison of various classification methods that can handle the complex structure of metabolomic data, including regularized classifiers, partial least squares discriminant analysis, and nonlinear classification models. We also examine the effectiveness of a physiological normalization technique widely used in the clinical and biochemical literature but not extensively analyzed and compared in urine metabolomic studies. While the main objective of this work is to interrogate metabolomic data of pediatric kidney transplant recipients to improve the diagnosis of T cell-mediated rejection (TCMR), we also analyze three independent datasets from other disease conditions to investigate the generalizability of our findings.


Assuntos
Transplante de Rim , Biomarcadores/urina , Criança , Análise Discriminante , Humanos , Análise dos Mínimos Quadrados , Metabolômica/métodos
17.
Anal Chim Acta ; 1182: 338968, 2021 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-34602206

RESUMO

Optimal handling is the most important means to ensure adequate sample quality. We aimed to investigate whether pre-centrifugation delay time and temperature could be accurately predicted and to what extent variability induced by pre-centrifugation management can be adjusted for. We used untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics to predict and evaluate the influence of pre-centrifugation temperature and delayed time on plasma samples. Pre-centrifugation temperature (4, 25 and 37 °C; classification rate 87%) and time (5-210 min; Q2 = 0.82) were accurately predicted using Random Forest (RF). Metabolites uniquely reflecting temperature and temperature-time interactions were discovered using a combination of RF and generalized linear models. Time-related metabolite profiles suggested a perturbed stability of the metabolome at all temperatures in the investigated time period (5-210 min), and the variation at 4 °C was observed in particular before 90 min. Fourteen and eight metabolites were selected and validated for accurate prediction of pre-centrifugation temperature (classification rate 94%) and delay time (Q2 = 0.90), respectively. In summary, the metabolite profile was rapidly affected by pre-centrifugation delay at all temperatures and thus the pre-centrifugation delay should be as short as possible for metabolomics analysis. The metabolite panels provided accurate predictions of pre-centrifugation delay time and temperature in healthy individuals in a separate validation sample. Such predictions could potentially be useful for assessing legacy samples where relevant metadata is lacking. However, validation in larger populations and different phenotypes, including disease states, is needed.


Assuntos
Metaboloma , Espectrometria de Massas em Tandem , Centrifugação , Cromatografia Líquida , Humanos , Plasma
18.
Diagn Microbiol Infect Dis ; 100(4): 115388, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34030102

RESUMO

BACKGROUND: The continuous evolution of influenza viruses is monitored by the World Health Organization Global Influenza Surveillance and Response System. Sample quality is essential for surveillance quality. METHODS: To evaluate the RNA degradation of clinical samples, influenza-like illness samples were collected from four sentinel hospitals, and seasonal influenza was tested by real-time reverse transcription polymerase chain reaction and quantified by digital reverse transcription polymerase chain reaction at different time points. RESULTS: RNA degradation was observed in the majority of samples eight days after sample collection. A significant and faster rate of RNA content reduction was observed in low viral load samples (<10 copies/µl) than in high viral load samples (>10 copies/µl), stored at 2 to 8°C for up to eight days. RNase P (RNP) RNA, which is a key indicator to evaluate sample collection quality, was detected. Sample collection quality was uneven in different hospitals. CONCLUSION: Low viral load samples increase the risk of false negatives due to RNA degradation to undetectable levels.


Assuntos
Vírus da Influenza A Subtipo H1N1/genética , Influenza Humana/diagnóstico , Estabilidade de RNA , RNA Viral/metabolismo , Manejo de Espécimes/normas , Carga Viral/estatística & dados numéricos , Hospitais/estatística & dados numéricos , Humanos , Influenza Humana/virologia , RNA Viral/genética , Vigilância de Evento Sentinela
19.
Structure ; 29(2): 186-195.e6, 2021 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-33217329

RESUMO

Recent advances in single-particle cryogenic electron microscopy (cryo-EM) have enabled the structural determination of numerous protein assemblies at high resolution, yielding unprecedented insights into their function. However, despite its extraordinary capabilities, cryo-EM remains time-consuming and resource-intensive. It is therefore beneficial to have a means for rapidly assessing and optimizing the quality of samples prior to lengthy cryo-EM analyses. To do this, we have developed a native mass spectrometry (nMS) platform that provides rapid feedback on sample quality and highly streamlined biochemical screening. Because nMS enables accurate mass analysis of protein complexes, it is well suited to routine evaluation of the composition, integrity, and homogeneity of samples prior to their plunge-freezing on EM grids. We demonstrate the utility of our nMS-based platform for facilitating cryo-EM studies using structural characterizations of exemplar bacterial transcription complexes as well as the replication-transcription assembly from the SARS-CoV-2 virus that is responsible for the COVID-19 pandemic.


Assuntos
Microscopia Crioeletrônica/métodos , Espectrometria de Massas/métodos , Imagem Individual de Molécula/métodos , Escherichia coli , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Metiltransferases/química , Metiltransferases/metabolismo , RNA Helicases/química , RNA Helicases/metabolismo , SARS-CoV-2/enzimologia , SARS-CoV-2/ultraestrutura , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo
20.
Clin Gastroenterol Hepatol ; 19(4): 825-835.e7, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-32652307

RESUMO

BACKGROUND & AIMS: Given the lack of procedure standardization, findings vary from analyses of pancreatic tissues collected by endoscopic ultrasound-guided fine-needle biopsy. It is not clear which needle and technique yield the best specimen for analysis. We compared the specimen quality and accuracy of diagnoses made from samples collected by fine-needle biopsy needles using different collection techniques. METHODS: Patients found to have pancreatic masses during imaging (n = 129) were assigned randomly to groups from whom pancreatic tissue samples were collected by reverse-bevel, Menghini-tip, franseen, or fork-tip needles. A second randomization determined the technical sequence of biopsies in each patient (suction, no suction, and stylet retraction). Two independent pathologists, blinded to the type of needle and sampling technique, analyzed all the samples. Final diagnoses of malignancy were made based on surgical resection, death from cancer progression, or findings from radiology or clinical follow-up evaluations (reference standard). The primary objective was to compare the cellularity of the samples collected, defined as the proportion of core tissue in the biopsy sample. Secondary objectives were to compare the accuracy of diagnoses made from biopsy samples and identify factors associated with high cellularity. RESULTS: One-hundred and nine patients had a final diagnosis of malignancy (84.5%) and 20 patients had benign disease (15.5%). Samples collected by fork-tip or franseen needles had significantly higher cellularity than samples collected by reverse-bevels or Menghini-tip needles (P < .001). Neoplasias were identified with greater than 90% accuracy using samples collected by fork-tip or franseen needles (P < .001 compared with other needles). On multivariable regression analysis, use of franseen needles (odds ratio [OR], 4.42; 95% CI, 2.58-7.58; P < .001) or fork-tip needles (OR, 3.86; 95% CI, 2.24-6.64; P < .001), stylet retraction (OR, 2.13; 95% CI, 1.21-3.72; P = .008), no suction (OR, 2.74; 95% CI, 1.57-4.80; P < .001), and pancreatic mass larger than 3 cm (OR, 1.92; 95% CI, 1.21-3.05; P = .005) were associated with high cellularity of the sample. CONCLUSIONS: In patients with suspected pancreatic cancer, samples with the highest degree of cellularity in a single biopsy, resulting in a diagnostic accuracy of 90% of higher, were collected by fine-needle biopsy using the franseen or fork-tip needle. Clinicaltrials.gov no: NCT04085055.


Assuntos
Agulhas , Neoplasias Pancreáticas , Aspiração por Agulha Fina Guiada por Ultrassom Endoscópico , Humanos , Pâncreas/diagnóstico por imagem , Neoplasias Pancreáticas/diagnóstico , Ultrassonografia
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