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Biospecimen reporting for improved study quality (BRISQ)
Abstract and Figures
Human biospecimens are subject to a number of different collection, processing, and storage factors that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research utilizing human tissues, it is critical that information regarding the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The Biospecimen Reporting for Improved Study Quality guidelines are proposed as an important and timely resource tool to strengthen communication and publications around biospecimen-related research and help reassure patient contributors and the advocacy community that the contributions are valued and respected.
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... Учитывая наличие проблемы недостаточной воспроизводимости результатов научных исследований, ряд организаций и консорциумов опубликовали различные стандарты и рекомендации, посвященные аннотированию биообразцов и правилам изложения при публикации результатов исследований. В 2011г были опубликованы рекомендации BRISQ (Biospecimen Reporting for Improved Study Quality, Правила описания биообразцов для улучшения качества научных исследований) [28,29]. В этих рекомендациях, помимо описания основных харак-3 UK Biobank. ...
... К рекомендуемым характеристикам исследователи относят демографическую информацию, а также время между постановкой диагноза и взятием биообразца. Дополнительными параметрами клинической аннотации, согласно рекомендациям BRISQ, являются стадия заболевания (например, острая или хроническая), время относительно приема лекарственной терапии, различные виды терапии, которые могут повлиять на биообразцы (например, химиоили лучевая терапия, внутривенные инфузии), статус курения, репродуктивный статус [28]. ...
One technology that helps overcome the problem of low research reproducibility is biobanking, which involves maintaining strict quality standards at all stages. In addition to data on the biosample (detailed documentation on sampling, transportation, preparation and subsequent storage), one of the key points is the availability of information about the donor (patient). The aim of this article was to analyze creating clinical abstract of biospecimens, combining data from various biobanks and assessing the possibilities of electronic medical records and other modern technologies for this. The search for publications was carried out in the PUBMED, eLIBRARY.RU, RSCI databases. One approach to creating a clinical description is the targeted collection of information by a specially trained employee. Primary information is most often taken from the individual records of the study participant, which are developed and approved when planning work. An alternative method is the use of electronic medical records and other documents that collect information during the assessment and treatment of patients. There are also mixed types of clinical data collection, a prime example of which is the UK Biobank. Completeness, structure, and standardization are essential characteristics of clinical description associated with biospecimens. Various standards are currently being developed to unify clinical description, making biobanks and collections more available to external researchers and organizations, which is necessary for collaboration and more efficient use of stored biospecimens. Harmonization of clinical description methodology between different biobanks open up broad boundaries for large- scale research within personalized and translational medicine.
... Biospecimen and data provenance can be communicated in several ways ( Table 1). The BRISQ (Biospecimen Reporting for Improved Study Quality) reporting standard includes details of the issuing biobank as an optional data element [7], where an online tool is freely available to generate BRISQ reports that can be published as supplementary files [8]. Descriptions of biospecimens and their provenance can also be added to frameworks such as the MDAR (Materials Design Analysis Reporting) [9] to harmonize biospecimen reporting across different standards and checklists [7]. ...
... The BRISQ (Biospecimen Reporting for Improved Study Quality) reporting standard includes details of the issuing biobank as an optional data element [7], where an online tool is freely available to generate BRISQ reports that can be published as supplementary files [8]. Descriptions of biospecimens and their provenance can also be added to frameworks such as the MDAR (Materials Design Analysis Reporting) [9] to harmonize biospecimen reporting across different standards and checklists [7]. More structured and detailed Materials and methods sections with unlimited word limits [10] further enable researchers to clearly describe the provenance and features of biospecimens and data. ...
Although biobanks can support research across geographic and governance boundaries, biomedical researchers consistently describe preferences for either collaborating with local biobanks or establishing their own biobanks. This article summarizes the potential research impacts of local biobank use and suggests how descriptions of biospecimen provenance can be improved in research publications.
... The study was performed according to the REMARK criteria [26] , and the samples were analysed following BRISQ guidelines [27]. ...
... Thus far, one EV-based biomarker test-the ExoDx Prostate Intelliscore test by ExoDx™ (74) has gained FDA Breakthrough Device Designation, though many others are currently being studied in clinical trials (online Supplemental Table 2). The low rate of clinical translation of biomarkers has resulted in several guidelines to improve study design (75), providing standards for sample collection (76), biomarker reporting (77,78), analytical assay development, and guidelines specific to EV-based studies (22,79,80). Investigators interested in EV-based biomarkers should familiarize themselves with these guidelines to improve outcomes and clinical translation of the biomarker discovery pipeline (Fig. 6). ...
Abstract
Background
Cancer is a dynamic process and thus requires highly informative and reliable biomarkers to help guide patient care. Liquid-based biopsies have emerged as a clinical tool for tracking cancer dynamics. Extracellular vesicles (EVs), lipid bilayer delimited particles secreted by cells, are a new class of liquid-based biomarkers. EVs are rich in selectively sorted biomolecule cargos, which provide a spatiotemporal fingerprint of the cell of origin, including cancer cells.
Content
This review summarizes the performance characteristics of EV-based biomarkers at different stages of cancer progression, from early malignancy to recurrence, while emphasizing their potential as diagnostic, prognostic, and screening biomarkers. We discuss the characteristics of effective biomarkers, consider challenges associated with the EV biomarker field, and report guidelines based on the biomarker discovery pipeline.
Summary
Basic science and clinical trial studies have shown the potential of EVs as precision-based biomarkers for tracking cancer status, with promising applications for diagnosing disease, predicting response to therapy, and tracking disease burden. The multi-analyte cargos of EVs enhance the performance characteristics of biomarkers. Recent technological advances in ultrasensitive detection of EVs have shown promise with high specificity and sensitivity to differentiate early-cancer cases vs healthy individuals, potentially outperforming current gold-standard imaging-based cancer diagnosis. Ultimately, clinical translation will be dictated by how these new EV biomarker-based platforms perform in larger sample cohorts. Applying ultrasensitive, scalable, and reproducible EV detection platforms with better design considerations based upon the biomarker discovery pipeline should guide the field towards clinically useful liquid biopsy biomarkers.
... The preclinical knowledge for ncRNA is not sufficiently informed, however, to follow such a template yet. Instead, the Biospecimen Reporting for Improved Study Quality (BRISQ) guidelines may be the most useful guide (Moore et al., 2011), with a few updated recommendations specific to ncRNA. These concluding recommendations are provided to encourage improved reporting of ncRNA testing conditions currently under emphasized. ...
A frequent topic of biomedical research is the potential clinical use of non-coding (nc) RNAs as quantitative biomarkers for a broad spectrum of health and disease. However, ncRNA analyses have not been pressed into widespread diagnostic use. Strong preclinical evidence suggests obstacles in the translation and reproducibility of this type of biomarker which may result from preanalytical and analytical variation in the non-standardized processes used to collect, process, and store samples, as well as the substantive differences between small and long ncRNA. We performed a narrative review of selected literature, through the lens of key laboratory-developed test (LDT) regulations under the Clinical Laboratory Improvement Amendments (CLIA) in the United States, to study critical gaps in ncRNA validation studies. This review describes the leading candidate ncRNA subclasses, their biogenesis and cellular function, and identifies specific pre-analytical variables with disproportionate impact on testing performance. We summarize these findings with strategic recommendations to clinicians and biomedical scientists involved in the design, conduct, and translation of ncRNA biomarker development.
Extracellular RNA (cell‐free RNA; exRNA) from blood‐derived liquid biopsies is an appealing, minimally invasive source of disease biomarkers. As pre‐analytical variables strongly influence exRNA measurements, their reporting is essential for meaningful interpretation and replication of results. The aim of this review was to chart to what extent pre‐analytical variables are documented, to pinpoint shortcomings and to improve future reporting. In total, 200 blood plasma exRNA studies published in 2018 or 2023 were reviewed for annotation of 22 variables associated with blood collection, plasma preparation, and RNA purification. Our results show that pre‐analytical variables are poorly documented, with only three out of 22 variables described in over half of the publications. The percentage of variables reported ranged from 4.6% to 54.6% (mean 24.84%) in 2023 and from 4.6% to 57.1% (mean 28.60%) in 2018. Recommendations and guidelines (i.e., BRISQ, ASCO‐CAP, BloodPAC, PPMPT, and CEN standards) have currently not resulted in improved reporting. In conclusion, our results highlight the lack of reporting pre‐analytical variables in exRNA studies and advocate for a consistent use of available standards, endorsed by funders and journals.
Disturbances in gut microbiota are prevalent in inflammatory bowel disease (IBD), which includes ulcerative colitis (UC). However, whether these disturbances contribute to development of the disease or are a result of the disease is unclear. In pairs of human twins discordant for IBD, the healthy twin has a higher risk of developing IBD and a gut microbiota that is more similar to that of IBD patients as compared with healthy individuals. Furthermore, appropriate medical treatment may mitigate these disturbances. To study the correlation between microbiota and IBD, we transferred stool samples from a discordant human twin pair: one twin being healthy and the other receiving treatment for UC. The stool samples were transferred from the disease-discordant twins to germ-free pregnant dams. Colitis was induced in the offspring using dextran sodium sulfate. As compared with offspring born to mice dams inoculated with stool from the healthy cotwin, offspring born to dams inoculated with stool from the UC-afflicted twin had a lower disease activity index, less gut inflammation, and a microbiota characterized by higher α diversity and a more antiinflammatory profile that included the presence and higher abundance of antiinflammatory species such as Akkermansia spp., Bacteroides spp., and Parabacteroides spp. These findings suggest that the microbiota from the healthy twin may have had greater inflammatory properties than did that of the twin undergoing UC treatment.
Big data and artificial intelligence are key elements in the medical field as they are expected to improve accuracy and efficiency in diagnosis and treatment, particularly in identifying biomedically relevant patterns, facilitating progress towards individually tailored preventative and therapeutic interventions. These applications belong to current research practice that is data-intensive. While the combination of imaging, pathological, genomic, and clinical data is needed to train algorithms to realize the full potential of these technologies, biobanks often serve as crucial infrastructures for data-sharing and data flows. In this paper, we argue that the ‘data turn’ in the life sciences has increasingly re-structured major infrastructures, which often were created for biological samples and associated data, as predominantly data infrastructures. These have evolved and diversified over time in terms of tackling relevant issues such as harmonization and standardization, but also consent practices and risk assessment. In line with the datafication, an increased use of AI-based technologies marks the current developments at the forefront of the big data research in life science and medicine that engender new issues and concerns along with opportunities. At a time when secure health data environments, such as European Health Data Space, are in the making, we argue that such meta-infrastructures can benefit both from the experience and evolution of biobanking, but also the current state of affairs in AI in medicine, regarding good governance, the social aspects and practices, as well as critical thinking about data practices, which can contribute to trustworthiness of such meta-infrastructures.
“We need less research, better research, and research done for the right reasons!” fue el célebre título de el editorial de Douglas G. Altman, “El escándalo de la pobre investigación médica” (1), el más citado en los últimos 25 años en la revista British Medical Journal. Con casi medio millón de citaciones encontradas en Google Académico como coautor de investigaciones en el campo y en estándares de estadística y publicación biomédica, desde su cargo como profesor de la Universidad de Oxford, director del Centro de Estadística en Medicina y de la investigación en Cáncer del Reino Unido, de la Colaboración Cochrane y de la red EQUATOR (2), Altman transformó la manera tradicional como se presentaban los resultados de las investigaciones, promocionando y divulgando los staments para el sometimiento de manuscritos ante las revistas. Esto significa, se infiere, que debe existir una especie de método de publicación para cada tipo de investigación que tiene que ver con LA PREGUNTA DE INVESTIGACIÓN Y LOS MÉTODOS UTILIZADOS. En esta Editorial de la Revista Colombiana de Cancerología, Este número de la revista del INC se analizan bajo los criterios de Altman, tres investigaciones de calidad que llenan con creces sus preceptos: menos investigación, pero mejor investigación hecha por las razones correctas. Como siempre, la aplicabilidad de sus resultados dependerá de las circunstancias y el contexto idiosincrático de práctica clínica de sus lectores.
Zusammenfassung Ein Großteil der biomedizinischen Forschung ist beobachtend, und die Qualität der veröffentlichten Berichte über diese Forschung
ist oft unzureichend. Dies behindert die Beurteilung der Stärken und Schwächen einer Studie und ihrer Übertragbarkeit. Die
Strengthening the Reporting of Observational Studies in Epidemiology (STROBE-) Initiative hat Empfehlungen entwickelt, was in einem akkuraten und vollständigen Bericht einer Beobachtungsstudie enthalten
sein sollte. Die Empfehlungen wurden von uns so definiert, dass sie 3 Hauptstudientypen abdecken: Kohorten-, Fallkontroll-
und Querschnittsstudien. Im September 2004 veranstalteten wir einen zweitägigen Workshop mit Methodikern, Forschern und Herausgebern
wissenschaftlicher Zeitschriften, um eine Checkliste zu entwerfen. Anschließend wurde der Entwurf bei mehreren Treffen der
Koordinierungsgruppe und nach E-Mail-Diskussionen mit der erweiterten STROBE-Gruppe revidiert und dabei empirische Evidenz
und methodologische Aspekte berücksichtigt. Das Ergebnis des Workshops und des anschließenden iterativen Prozesses aus Beratung
und Revision war eine Checkliste von 22 Punkten (STROBE-Statement), die sich auf die Bereiche Titel, Abstract, Einleitung, Methoden, Ergebnisse und Diskussion eines Artikels beziehen. 18
der Punkte sind relevant für alle 3 Studiendesigns, während 4 der Punkte spezifisch für Kohorten-, Fallkontroll- und Querschnittsstudien
sind. Ein ausführlicher Begleitartikel („Explanation and Elaboration“) wurde separat veröffentlicht und ist auf den Webseiten
von „PLoS Medicine“, „Annals of Internal Medicine“ und „Epidemiology“ frei zugänglich. Wir hoffen, dass das STROBE-Statement
dazu beitragen kann, dass Beobachtungsstudien besser berichtet werden.
Management and traceability of biospecimen preanalytical variations are necessary to provide effective and efficient interconnectivity and interoperability between Biobanks.
Therefore, the International Society for Biological and Environmental Repositories Biospecimen Science Working Group developed a "Standard PREanalytical Code" (SPREC) that identifies the main preanalytical factors of clinical fluid and solid biospecimens and their simple derivatives.
The SPREC is easy to implement and can be integrated into Biobank quality management systems and databases. It can also be extended to nonhuman biorepository areas. Its flexibility allows integration of new novel technological developments in future versions. SPREC version 01 is presented in this article.
Implementation of the SPREC is expected to facilitate and consolidate international multicenter biomarker identification research and biospecimen research in the clinical Biobank environment.
Much biomedical research is observational. The reporting of such research is often inadequate, which hampers the assessment of its strengths and weaknesses and of a study's generalizability. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Initiative developed recommendations on what should be included in an accurate and complete report of an observational study. We defined the scope of the recommendations to cover 3 main study designs: cohort, case-control, and cross-sectional studies. We convened a 2-day workshop in September 2004, with methodologists, researchers, and journal editors, to draft a checklist of items. This list was subsequently revised during several meetings of the coordinating group and in e-mail discussions with the larger group of STROBE contributors, taking into account empirical evidence and methodological considerations. The workshop and the subsequent iterative process of consultation and revision resulted in a checklist of 22 items (the STROBE Statement) that relate to the title, abstract, introduction, methods, results, and discussion sections of articles. Eighteen items are common to all 3 study designs and 4 are specific for cohort, case-control, or cross-sectional studies. A detailed Explanation and Elaboration document is published separately and is freely available at www.annals.org and on the Web sites of PLoS Medicine and Epidemiology. We hope that the STROBE Statement will contribute to improving the quality of reporting of observational studies.
There are major concerns that specific agonal conditions, including coma and hypoxia, might affect ribonucleic acid (RNA) integrity in postmortem brain studies. We report that agonal factors significantly affect RNA integrity and have a major impact on gene expression profiles in microarrays. In contrast to agonal factors, gender, age, and postmortem factors have less effect on gene expression profiles. The Average Correlation Index is proposed as a method for evaluating RNA integrity on the basis of similarity of microarray profiles. Reducing the variance due to agonal factors is critical in investigating small but validated gene expression differences in messenger RNA levels between psychiatric patients and control subjects.
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Part 2
BACKGROUND
The majority of patients with lymphoma undergo a single biopsy for diagnosis, and there are few opportunities to acquire posttreatment material. Fine-needle aspiration (FNA) biopsy is a minimally invasive procedure, and acquiring routine posttreatment material would require minimal effort and provide needed material for gene expression profiling.METHODS
Ex vivo FNA biopsies were performed using a standard clinical technique with 21-gauge, 22-gauge, 23-gauge, and 25-gauge needles for 8 lymph node specimens and were collected in either RNA stabilization reagent (RNAlater) or Trizol. Eight patients with known or suspected Non-Hodgkin lymphoma (NHL) underwent interoperative (in vivo) FNA biopsies based on the best technique derived from the ex vivo aspirates. RNA derived from the in vivo FNA biopsies and the matched, snap-frozen surgical lymph node biopsy remnant was used for gene expression analysis with proprietary U133A chips.RESULTSThe results confirmed the authors' experience, that RNA isolated from FNA biopsies of lymph nodes collected in Trizol is superior both quantitatively and qualitatively to RNA collected in RNAlater. Gene expression profiles of NHL derived from in vivo FNA biopsies and matched, frozen surgical specimens showed good overall correlation.CONCLUSIONS
High-throughput gene expression analysis in patients with NHL derived from material acquired by FNA biopsy is a feasible approach to developing a platform for real-time analysis of treatment responses in this group of patients. Cancer (Cancer Cytopathol) 2006; © 2006 American Cancer Society.
The analysis of RNA from postmortem human brain tissue by reverse transcription-polymerase chain reaction (RT-PCR) provides a practical method to measure both normal and abnormal brain gene expression. A major limitation in using human material is that yields can vary dramatically from individual to individual, making comparisons between samples difficult. In this report, we study the association of pH and several pre- and postmortem factors on the RNA yields from 89 postmortem human occipital cortices. Glyceraldehyde phosphate dehydrogenase (GAPdH) mRNA levels were measured by RT-PCR. A major variant in this method is the priming used in the reverse transcription reaction. Three different methods of reverse transcription were performed and the resultant levels of products compared against the pre- and postmortem factors and pH. The levels of GAPdH correlated significantly to pH and pH itself to the rapidity of death (RoD) (agonal state) indicating that premortem factors may play the greatest role in determining postmortem RNA levels. The three methods of priming showed different sensitivities, most notably that oligo dT priming alone is vulnerable to long freezer intervals (FI). We conclude that premortem factors are the major affectors of RNA levels variations and that the polyA tail region of the molecule appears to be adversely affected by extended freezer storage.
The method of polymerase chain reaction was used to investigate the pre- and postmortem factors which affect the stability of specific mRNAs in the C1 region of human autopsy brain. Eight premortem and 4 postmortem factors were correlated to levels of phenylethanolamine N-methyltransferase (PNMT), three splice forms of amyloid precursor protein (APP) and actin mRNAs in 10 control brains using Pearson's correlation coefficient. Significant negative correlations were found between hypoxia and PNMT mRNA, and between postmortem and storage intervals and APP751 and β-actin mRNAs. A positive correlation was found between death-refrigeration interval and total APP and APP695 mRNAs. There was also a positive correlation between seizure activity and APP770 mRNA. The results indicate that a variety of pre- and postmortem factors can affect mRNA levels. The possible effect of pre- and postmortem factors on specific mRNA levels should be investigated prior to comparing mRNA levels in different disease states.
Instability of tissue protein biomarkers is a critical issue for molecular profiling. Pre-analytical variables during tissue procurement, such as time delays during which the tissue remains stored at room temperature, can cause significant variability and bias in downstream molecular analysis. Living tissue, ex vivo, goes through a defined stage of reactive changes that begin with oxidative, hypoxic and metabolic stress, and culminate in apoptosis. Depending on the delay time ex vivo, and reactive stage, protein biomarkers, such as signal pathway phosphoproteins will be elevated or suppressed in a manner which does not represent the biomarker levels at the time of excision. Proteomic data documenting reactive tissue protein changes post collection indicate the need to recognize and address tissue stability, preservation of post-translational modifications, and preservation of morphologic features for molecular analysis. Based on the analysis of phosphoproteins, one of the most labile tissue protein biomarkers, we set forth tissue procurement guidelines for clinical research. We propose technical solutions for (i) assessing the state of protein analyte preservation and specimen quality via identification of a panel of natural proteins (surrogate stability markers), and (ii) using multi-purpose fixative solution designed to stabilize, preserve and maintain proteins, nucleic acids, and tissue architecture.