Did you mean: biospecimens
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Virchows Archiv : An International... Aug 2021The term "biobanking" is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues... (Review)
Review
The term "biobanking" is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.
Topics: Accreditation; Biological Specimen Banks; Biomedical Research; Guidelines as Topic; Humans; Policy Making; Precision Medicine; Specimen Handling; Stakeholder Participation; Terminology as Topic
PubMed: 34255145
DOI: 10.1007/s00428-021-03151-0 -
BioRxiv : the Preprint Server For... Aug 2023Metastasis is the principal cause of cancer death, yet we lack an understanding of metastatic cell states, their relationship to primary tumor states, and the mechanisms...
Metastasis is the principal cause of cancer death, yet we lack an understanding of metastatic cell states, their relationship to primary tumor states, and the mechanisms by which they transition. In a cohort of biospecimen trios from same-patient normal colon, primary and metastatic colorectal cancer, we show that while primary tumors largely adopt LGR5 intestinal stem-like states, metastases display progressive plasticity. Loss of intestinal cell states is accompanied by reprogramming into a highly conserved fetal progenitor state, followed by non-canonical differentiation into divergent squamous and neuroendocrine-like states, which is exacerbated by chemotherapy and associated with poor patient survival. Using matched patient-derived organoids, we demonstrate that metastatic cancer cells exhibit greater cell-autonomous multilineage differentiation potential in response to microenvironment cues than their intestinal lineage-restricted primary tumor counterparts. We identify PROX1 as a stabilizer of intestinal lineage in the fetal progenitor state, whose downregulation licenses non-canonical reprogramming.
PubMed: 37662289
DOI: 10.1101/2023.08.18.553925 -
Journal of Hepatology Jan 2023Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, in part because of inadequate early detection strategies. Current recommendations... (Review)
Review
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, in part because of inadequate early detection strategies. Current recommendations for screening consist of semi-annual abdominal ultrasound with or without serum alpha-fetoprotein in patients with cirrhosis and in demographic subgroups with chronic hepatitis B infection. However, this screening strategy has several deficiencies, including suboptimal early-stage sensitivity, false positives with subsequent harms, inter-operator variability in ultrasound performance, and poor adherence. A blood-based biomarker with sufficient performance characteristics for early-stage disease could overcome several of these barriers to improving early-stage detection. However, prior to use of a biomarker for screening in clinical practice, a multistep validation is required in order to understand test performance characteristics. These steps include case-control validation, followed by validation in prospective cohorts of at-risk patients. Until recently, we lacked adequate longitudinal validation cohorts for early HCC detection; however, several validation cohorts are maturing, including the Hepatocellular Carcinoma Early Detection Study and the Texas Hepatocellular Carcinoma Consortium, which will allow for rigorous validation of candidate biomarkers. While there are several promising biomarkers awaiting validation, in order to supplant abdominal ultrasound, a candidate biomarker must show adequate test performance and overcome practical hurdles to ensure adoption in clinical practice. The promise of blood-based biomarkers is significant, especially given the limitations of ultrasound-based screening; however, they require adequate validation and several logistical obstacles must be overcome prior to clinical implementation.
Topics: Humans; Carcinoma, Hepatocellular; Liver Neoplasms; alpha-Fetoproteins; Prospective Studies; Liver Cirrhosis; Biomarkers; Biomarkers, Tumor
PubMed: 36089157
DOI: 10.1016/j.jhep.2022.08.036 -
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 -
Ochsner Journal 2020The 2018 revisions to the Common Rule that were effective in January 2019 introduced a new category of informed consent: broad consent. Investigators and institutional... (Review)
Review
The 2018 revisions to the Common Rule that were effective in January 2019 introduced a new category of informed consent: broad consent. Investigators and institutional review board (IRB) members need to understand (1) what broad consent is, (2) the role of broad consent under the revised Common Rule, (3) how and when broad consent can be used, (4) exempt research categories that relate to broad consent, and (5) the scope of limited IRB review as it relates to broad consent. Under the prior regulations, researchers had two consent options: obtain study-specific informed consent or request the IRB to waive the requirement to obtain informed consent. The revision to the Common Rule introduced the third option of broad consent, but its applicability is limited. Broad consent can only be used to obtain an individual's consent for the storage, maintenance, and secondary research use of identifiable private information or identifiable biospecimens. The regulatory authority for broad consent is at 45 CFR §46.116(d). None of the required elements of broad consent can be omitted or altered because each element is considered essential. Broad consent shares many of the requirements for study-specific informed consent, but several elements are unique: a description of the types of secondary research that may be conducted; statements describing the private information or biospecimens that might be used in research, whether sharing of the information or biospecimens might occur, and the types of institutions or researchers that might conduct research with the information or biospecimens; information on how long the information or biospecimens may be stored, maintained, and used; a statement that subjects will or will not be informed of the details of any subsequent research; a statement that research results will or will not be disclosed to subjects; and contact information for obtaining answers to questions about the subjects' rights regarding storage and use of information or biospecimens and whom to contact regarding research-related harm. Broad consent provides flexibility that did not exist prior to the revision, giving researchers the option to obtain broad consent for the storage, maintenance, and secondary research use of identifiable private information or identifiable biospecimens. With an understanding of the regulations, an investigator can plan how best to organize his or her research plan and decide whether to obtain study-specific informed consent, to apply for a waiver of consent, or to obtain broad consent.
PubMed: 32284687
DOI: 10.31486/toj.19.0088 -
Biomolecules Apr 2022Various disease-associated forms or strains of α-synuclein (αSyn) can spread and accumulate in a prion-like fashion during synucleinopathies such as Parkinson's... (Review)
Review
Various disease-associated forms or strains of α-synuclein (αSyn) can spread and accumulate in a prion-like fashion during synucleinopathies such as Parkinson's disease (PD), Lewy body dementia (DLB), and multiple system atrophy (MSA). This capacity for self-propagation has enabled the development of seed amplification assays (SAAs) that can detect αSyn in clinical samples. Notably, α-synuclein real-time quaking-induced conversion (RT-QuIC) and protein misfolding cyclic amplification (PMCA) assays have evolved as ultrasensitive, specific, and relatively practical methods for detecting αSyn in a variety of biospecimens including brain tissue, CSF, skin, and olfactory mucosa from synucleinopathy patients. However, αSyn SAAs still lack concordance in detecting MSA and familial forms of PD/DLB, and the assay parameters show poor correlations with various clinical measures. End-point dilution analysis in αSyn RT-QuIC assays allows for the quantitation of relative amounts of αSyn seeding activity that may correlate moderately with clinical measures and levels of other biomarkers. Herein, we review recent advancements in α-synuclein SAAs for detecting αSyn and describe in detail the modified Spearman-Karber quantification algorithm used with end-point dilutions.
Topics: Humans; Lewy Body Disease; Multiple System Atrophy; Parkinson Disease; Prions; Synucleinopathies; alpha-Synuclein
PubMed: 35454165
DOI: 10.3390/biom12040576 -
Clinical Cancer Research : An Official... Jul 2020Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization... (Review)
Review
Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, processing delays and temperatures, tube agitation, centrifugation protocols and speeds, plasma storage duration and temperature, the number of freeze-thaw events, and cfDNA extraction and quantification methods, all of which can also ultimately impact subsequent downstream analysis. Thus, there is a pressing need for widely applicable standards tailored for cfDNA analysis that include all preanalytic steps from blood draw to analysis. The NCI's Biorepositories and Biospecimen Research Branch has developed cfDNA-specific guidelines that are based upon published evidence and have been vetted by a panel of internationally recognized experts in the field. The guidelines include optimal procedures as well as acceptable alternatives to facilitate the generation of evidence-based protocols by individual laboratories and institutions. The aim of the document, which is entitled "Biospecimen Evidence-based Best Practices for Cell-free DNA: Biospecimen Collection and Processing," is to improve the accuracy of cfDNA analysis in both basic research and the clinic by improving and harmonizing practices across institutions.
Topics: Animals; Biomarkers, Tumor; Cell-Free Nucleic Acids; Evidence-Based Practice; Guidelines as Topic; Humans; Liquid Biopsy; Neoplasms; Research; Specimen Handling
PubMed: 32122922
DOI: 10.1158/1078-0432.CCR-19-3015 -
Cell Proliferation Aug 2022Human biospecimens provide the basis for research, leading to a better understanding of human disease biology and discovery of new treatments that are tailored to... (Review)
Review
Human biospecimens provide the basis for research, leading to a better understanding of human disease biology and discovery of new treatments that are tailored to individual patients with cancer or other common complex diseases. The collection, processing, preservation, storage and providing access to these resources are key activities of biobanks. Biobanks must ensure proper quality of samples and data, ethical and legal compliance as well as transparent and efficient access procedures. The standards for biobanking outlined herein are intended to be implemented in biobanks and to supply researchers with high-quality samples fitted for an intended use.
Topics: Biological Specimen Banks; Biomedical Research; Humans
PubMed: 35709534
DOI: 10.1111/cpr.13282 -
Theranostics 2022Nanostructured devices and nanoparticles have fundamentally reshaped the development of precision healthcare in recent decades. Meanwhile, mass spectrometry (MS)-based... (Review)
Review
Nanostructured devices and nanoparticles have fundamentally reshaped the development of precision healthcare in recent decades. Meanwhile, mass spectrometry (MS)-based proteomics has evolved from simple protein sequencing to a powerful approach that identifies disease patterns and signatures, reveals molecular mechanisms of pathological processes, and develops therapeutic or preventive drugs. Significantly, the two distinct disciplines have synergized and expanded our knowledge about human health and disease, as evidenced by a variety of nanotechnology-assisted sample processing strategies, facilitating in-depth proteome profiling and post-translational modifications (PTMs) characterization. This review summarizes recent advances in nanoparticle design for better enrichment of marker proteins and their PTMs from various bio-specimens and emerging nanotechnologies that are applied to MS-based proteomics for precision medicine discovery.
Topics: Humans; Mass Spectrometry; Nanostructures; Precision Medicine; Protein Processing, Post-Translational; Proteome; Proteomics
PubMed: 35401834
DOI: 10.7150/thno.64325 -
Biomarker Insights 2022Preserved biospecimens held in biobank inventories and clinical archives are important resources for biomarker research. Recent advances in technologies have led to an... (Review)
Review
Preserved biospecimens held in biobank inventories and clinical archives are important resources for biomarker research. Recent advances in technologies have led to an increase in use of clinical archives in particular, in order to study retrospective cohorts and to generate data relevant to tissue biomarkers. This raises the question of whether the current sizes of biobank inventories are appropriate to meet the demands of biomarker research. This commentary discusses this question by considering data concerning overall biobank and biospecimen numbers to estimate current biospecimen supply and use. The data suggests that biospecimen supply exceeds current demand. Therefore, it may be important for individual biobanks to reassess the targets for their inventories, consider culling unused portions of these inventories, and shift resources towards providing prospective custom biobanking services.
PubMed: 35464611
DOI: 10.1177/11772719221091750