-
Reviews on Recent Clinical Trials 2015Inclusion of biospecimens in population-based studies is an integral part of understanding disease etiology, identifying biomarkers and developing prevention and... (Review)
Review
Inclusion of biospecimens in population-based studies is an integral part of understanding disease etiology, identifying biomarkers and developing prevention and treatment strategies. The Prostate, Lung, Colorectal, and Ovarian (PLCO) cancer screening trial collected, processed and stored biospecimens from participants to create a biorepository of specimens which serves as a useful resource for a broad research community. PLCO collected blood samples from consented screening arm participants at six screening rounds and a buccal sample from consented control arm participants. In addition, formalin-fixed paraffin embedded tumor tissue specimens were collected for participants in both arms for selected cancer sites. Collection of biospecimens at multiple timepoints (i.e. serial samples) and prior to cancer diagnosis, paired with rich epidemiologic and screening data, makes the PLCO collection of biospecimens a uniquely valuable resource. As such, access to the PLCO biorepository is granted to investigators by a rigorous scientific review process and guided by a steering committee which is responsible for developing and implementing the biospecimen use policies. Here, we describe the procedures for biospecimen collection, processing, storage, requisition, and distribution, as well as data management employed in PLCO. We also provide examples of how the biospecimens have been used to advance cancer research and describe relevant lessons learned to help inform cohorts wishing to add or modify biospecimen collection.
Topics: Biomarkers, Tumor; Biomedical Research; Biopsy, Needle; Colorectal Neoplasms; Early Detection of Cancer; Female; Humans; Lung Neoplasms; Male; Multicenter Studies as Topic; National Cancer Institute (U.S.); Neoplasms; Ovarian Neoplasms; Prostatic Neoplasms; Randomized Controlled Trials as Topic; Tissue Banks; Tissue Embedding; United States
PubMed: 26238117
DOI: 10.2174/1574887110666150730121429 -
Alzheimer's & Dementia (New York, N. Y.) Nov 2017Informed consent forms that restrict the distribution of data and samples have been an impediment to advancing Alzheimer's disease (AD) understandings and treatments.... (Review)
Review
INTRODUCTION
Informed consent forms that restrict the distribution of data and samples have been an impediment to advancing Alzheimer's disease (AD) understandings and treatments. The Coalition Against Major Disease public-private partnership developed concise addenda to responsibly broaden data access of informed consent forms.
METHODS
Coalition Against Major Disease members identified key elements for ensuring data and biospecimen access, and patient privacy protection according to applicable US law. Collaboration with the Alzheimer's Association established the understandability and relevance of the addenda with AD patients and Care Partners.
RESULTS
Two key findings are (1) patients with dementia and Care Partners were shocked that their data and samples are not broadly shared and (2) with diverse feedback, two concise addenda were created to enable data and sample sharing both within and outside future sponsored studies (see Boxes).
DISCUSSION
Increasing the access of valuable anonymized patient-level clinical trial data has the potential to inform the foundational and regulatory science required to deliver innovative treatments for AD.
PubMed: 29124112
DOI: 10.1016/j.trci.2017.08.003 -
Diagnostics (Basel, Switzerland) Apr 2021This study assessed three commercially available cell-free DNA (cfDNA) extraction kits and the impact of a PEG-based DNA cleanup procedure (DNApure) on cfDNA quality and...
This study assessed three commercially available cell-free DNA (cfDNA) extraction kits and the impact of a PEG-based DNA cleanup procedure (DNApure) on cfDNA quality and yield. Six normal donor urine and plasma samples and specimens from four pregnant (PG) women carrying male fetuses underwent extractions with the JBS cfDNA extraction kit (kit J), MagMAX Cell-Free DNA Extraction kit (kit M), and QIAamp Circulating Nucleic Acid Kit (kit Q). Recovery of a PCR product spike-in, endogenous TP53, and Y-chromosome DNA was used to assess kit performance. Nucleosomal-sized DNA profiles varied among the kits, with prominent multi-nucleosomal-sized peaks present in urine and plasma DNA isolated by kits J and M only. Kit J recovered significantly more spike-in DNA than did kits M or Q ( < 0.001) from urine, and similar amounts from plasma ( = 0.12). Applying DNApure to kit M- and Q-isolated DNA significantly improved the amplification efficiency of spike-in DNA from urine ( < 0.001) and plasma ( ≤ 0.013). Furthermore, kit J isolated significantly more Y-chromosome DNA from PG urine compared to kit Q ( = 0.05). We demonstrate that DNApure can provide an efficient means of improving the yield and purity of cfDNA and minimize the effects of pre-analytical biospecimen variability on liquid biopsy assay performance.
PubMed: 33916811
DOI: 10.3390/diagnostics11040650 -
BMC Pediatrics Mar 2022Patient-level predictors of enrollment in pediatric biorepositories are poorly described. Especially in pandemic settings, understanding who is likely to enroll in a...
BACKGROUND
Patient-level predictors of enrollment in pediatric biorepositories are poorly described. Especially in pandemic settings, understanding who is likely to enroll in a biorepository is critical to interpreting analyses conducted on biospecimens. We describe predictors of pediatric COVID-19 biorepository enrollment and biospecimen donation to identify gaps in COVID-19 research on pediatric biospecimens.
METHODS
We compared data from enrollees and non-enrollees aged 0-25 years with suspected or confirmed COVID-19 infection who were approached for enrollment in the Massachusetts General Hospital pediatric COVID-19 biorepository between April 12, 2020, and May 28, 2020, from community or academic outpatient or inpatient settings. Demographic and clinical data at presentation to care were from automatic and manual chart extractions. Predictors of enrollment and biospecimen donation were assessed with Poisson regression models.
RESULTS
Among 457 individuals approached, 214 (47%) enrolled in the biorepository. A COVID-19 epidemiologic risk factor was recorded for 53%, and 15% lived in a US Centers for Disease Control and Prevention-defined COVID-19 hotspot. Individuals living in a COVID-19 hotspot (relative risk (RR) 2.4 [95% confidence interval (CI): 1.8-3.2]), with symptoms at presentation (RR 1.8 [95% CI: 1.2-2.7]), or admitted to hospital (RR 1.8 [95% CI: 1.2-2.8]) were more likely to enroll. Seventy-nine percent of enrollees donated any biospecimen, including 97 nasopharyngeal swabs, 119 oropharyngeal swabs, and 105 blood, 16 urine, and 16 stool specimens, respectively. Age, sex, race, ethnicity, and neighborhood-level socioeconomic status based on zip code did not predict enrollment or biospecimen donation.
CONCLUSIONS
While fewer than half of individuals approached consented to participate in the pediatric biorepository, enrollment appeared to be representative of children affected by the pandemic. Living in a COVID-19 hotspot, symptoms at presentation to care and hospital admission predicted biorepository enrollment. Once enrolled, most individuals donated a biospecimen.
Topics: Adolescent; Adult; COVID-19; Child; Child, Preschool; Ethnicity; Humans; Infant; Infant, Newborn; Massachusetts; Pandemics; Young Adult
PubMed: 35279115
DOI: 10.1186/s12887-022-03185-6 -
Clinica Chimica Acta; International... Oct 2012Biobanks and biospecimens are critical components for many areas of clinical and basic research. The quality of biospecimens and associated data must be consistent and... (Review)
Review
Biobanks and biospecimens are critical components for many areas of clinical and basic research. The quality of biospecimens and associated data must be consistent and collected according to standardized methods in order to prevent spurious analytical results that can lead to artifacts being interpreted as valid findings. A number of international institutions have taken the initiative to develop and publish best practices, which include technical recommendations for handling biospecimens as well as recommendations for ethical and regulatory practices in biobanking. These sources of guidance have been useful in raising the overall consistency and quality of research involving biospecimens. However, the lack of international harmonization, uneven adoption, and insufficient oversight of best practices are preventing further improvements in biospecimen quality and coordination among collaborators and biobanking networks. In contrast to the more straightforward technical and management issues, ethical and regulatory practices often involve issues that are more controversial and difficult to standardize.
Topics: Biological Specimen Banks; Humans; Informed Consent; International Cooperation; Practice Guidelines as Topic; Quality Control; Specimen Handling
PubMed: 22579478
DOI: 10.1016/j.cca.2012.04.030 -
Genome Medicine Nov 2023Biorepositories archive and distribute well-characterized biospecimens for research to support the development of medical diagnostics and therapeutics. Knowledge of...
BACKGROUND
Biorepositories archive and distribute well-characterized biospecimens for research to support the development of medical diagnostics and therapeutics. Knowledge of biobanking and associated practices is incomplete in low- and middle-income countries where disease burden is disproportionately high. In 2011, the African Society of Human Genetics (AfSHG), the National Institutes of Health (NIH), and the Wellcome Trust founded the Human Heredity and Health in Africa (H3Africa) consortium to promote genomic research in Africa and established a network of three biorepositories regionally located in East, West, and Southern Africa to support biomedical research. This manuscript describes the processes established by H3Africa biorepositories to prepare research sites to collect high-quality biospecimens for deposit at H3Africa biorepositories.
METHODS
The biorepositories harmonized practices between the biorepositories and the research sites. The biorepositories developed guidelines to establish best practices and define biospecimen requirements; standard operating procedures (SOPs) for common processes such as biospecimen collection, processing, storage, transportation, and documentation as references; requirements for minimal associated datasets and formats; and a template material transfer agreements (MTA) to govern biospecimen exchange. The biorepositories also trained and mentored collection sites in relevant biobanking processes and procedures and verified biospecimen deposit processes. Throughout these procedures, the biorepositories followed ethical and legal requirements.
RESULTS
The 20 research projects deposited 107,982 biospecimens (76% DNA, 81,067), in accordance with the ethical and legal requirements and established best practices. The biorepositories developed and customized resources and human capacity building to support the projects. [The biorepositories developed 34 guidelines, SOPs, and documents; trained 176 clinicians and scientists in over 30 topics; sensitized ethical bodies; established MTAs and reviewed consent forms for all projects; attained import permits; and evaluated pilot exercises and provided feedback.
CONCLUSIONS
Biobanking in low- and middle-income countries by local skilled staff is critical to advance biobanking and genomic research and requires human capacity and resources for global partnerships. Biorepositories can help build human capacity and resources to support biobanking by partnering with researchers. Partnerships can be structured and customized to incorporate document development, ethics, training, mentorship, and pilots to prepare sites to collect, process, store, and transport biospecimens of high quality for future research.
Topics: Humans; Biological Specimen Banks; Africa; Biomedical Research; Genomics; Genome
PubMed: 37932809
DOI: 10.1186/s13073-023-01235-x -
Methods in Molecular Biology (Clifton,... 2019Blood is a widely used biospecimen in the field of biobanking, secondary to the ease with which it is collected along with the wide variety of analytes obtained from it... (Review)
Review
Blood is a widely used biospecimen in the field of biobanking, secondary to the ease with which it is collected along with the wide variety of analytes obtained from it for analysis. It carries the potential to further the search for biomarkers in countless diseases; therefore, the standardization and optimization of blood collection procedures is of importance in assuring reproducibility of results. Here, we briefly review procedures for the procurement, storage, and use of blood and its fractions for biobanking purposes. Select commonly used methods for collecting blood with various vacutainer blood collection tubes are described, along with optimal storage conditions of various samples in short- and long-term situations.
Topics: Biological Specimen Banks; Biomarkers; Blood Specimen Collection; Humans; Specimen Handling
PubMed: 30539437
DOI: 10.1007/978-1-4939-8935-5_9 -
Biopreservation and Biobanking Oct 2021Amyotrophic lateral sclerosis (ALS) is a rare neurological condition affecting upper and lower motor neurons. The National ALS Biorepository (referred to as the...
Amyotrophic lateral sclerosis (ALS) is a rare neurological condition affecting upper and lower motor neurons. The National ALS Biorepository (referred to as the Biorepository) was initiated in 2015, with biospecimen collection beginning in 2017, as a repository for biospecimens for future ALS research. To help ensure the usefulness of the Biorepository, a biospecimen demand analysis is conducted on an annual basis, as well as an analysis of the utilization of the Biorepository. To determine the types of biospecimens to be collected for the Biorepository, an in-depth initial examination occurred followed by ongoing biospecimen demand and utilization analyses. The initial examination included input from an expert panel, discussions with ALS research experts, review of other ALS biorepositories, assessment of biospecimen demand, and analysis of the biospecimen types historically used in ALS research. Of all biospecimen types reported in the literature, the most frequently used were DNA, postmortem spinal cord, blood, and cerebrospinal fluid; while the frequently reported types of biospecimens used in ALS-related grants were induced pluripotent stem cells, brain, blood, and spinal cord. Continuous analysis of potential sample demand and tissues collected, based on an analysis of the literature and funded grants, and actual sample requests can assist the Biorepository in ensuring that the appropriate samples are available for researchers when they are needed.
Topics: Amyotrophic Lateral Sclerosis; Brain; Humans
PubMed: 34264761
DOI: 10.1089/bio.2021.0039 -
JAMA Network Open Jan 2024Tick-borne diseases (TBDs) other than Lyme disease, such as spotted fever group rickettsiosis, ehrlichiosis, and galactose-α-1,3-galactose (α-gal) syndrome, are an...
IMPORTANCE
Tick-borne diseases (TBDs) other than Lyme disease, such as spotted fever group rickettsiosis, ehrlichiosis, and galactose-α-1,3-galactose (α-gal) syndrome, are an emerging public health issue. Long-term sequelae secondary to Ehrlichia or Rickettsia infection are uncommon; however, musculoskeletal symptoms are often attributed to prior tick exposure.
OBJECTIVE
To evaluate the potential associations between prior exposure to TBDs and musculoskeletal symptoms, including radiographic osteoarthritis.
DESIGN, SETTING, AND PARTICIPANTS
This cross-sectional study analyzed serum samples from the fourth visit (2017-2018) of the Johnston County Osteoarthritis (JoCo OA) project, an ongoing longitudinal, population-based study in Johnston County, North Carolina. Biospecimen testing and analysis were performed between May 2022 and November 2023. Participants in the JoCo OA project are noninstitutionalized White and Black Johnston County residents 45 years or older.
MAIN OUTCOME AND MEASURES
The primary outcome was seropositivity with Ehrlichia IgG, Rickettsia IgG, and/or α-gal IgE and musculoskeletal symptoms. Secondary outcomes included risk factors associated with elevated α-gal IgE and weighted population point prevalence rates. Participants completed questionnaires, underwent physical assessments, and provided biospecimens for serological testing. Multivariable models were used to estimate associations of interest.
RESULTS
Of the 605 participants who completed the fourth visit of the JoCo OA project, 488 (80.7%) had serum samples available for testing. The 488 participants had a median (IQR) age of 72 (68-78) years and included 336 females (68.9%) and 161 Black (33.0%) and 327 White (67.0%) individuals. The overall weighted point prevalence was 8.6% (95% CI, 5.9%-11.3%) for Ehrlichia IgG, 17.1% (95% CI, 12.6%-21.5%) for Rickettsia IgG, and 19.6% (95% CI, 15.3%-23.8%) for α-gal IgE level greater than 0.1 IU/mL. Only α-gal IgE was associated with knee pain, aching or stiffness (mean ratio, 1.30; 95% CI, 1.09-1.56). Antibodies to Rickettsia, Ehrlichia, and α-gal were not associated with symptomatic radiographic knee osteoarthritis. Male sex (odds ratio [OR], 2.63; 95% CI, 1.55-4.47), current smoker status (OR, 3.55; 95% CI, 1.38-9.18), and an attached tick bite in the past 5 years (OR, 3.99; 95% CI, 2.22-7.15) were all risk factors that were associated with α-gal IgE level greater than 0.1 IU/mL. Despite only 84 individuals (17.2%) recalling a tick bite in the past 5 years, 178 (36.5%) had evidence of prior tick-borne exposure, suggesting frequent human-tick interactions.
CONCLUSIONS AND RELEVANCE
Results of this cross-sectional study indicate no association between Ehrlichia or Rickettsia seropositivity and chronic musculoskeletal symptoms or osteoarthritis. Further investigation is needed into the pathogenesis of α-gal syndrome and interventions to reduce human-tick interactions.
Topics: Female; Male; Humans; Aged; Musculoskeletal Pain; Tick Bites; Cross-Sectional Studies; Galactose; Tick-Borne Diseases; Immunoglobulin G; Osteoarthritis; Immunoglobulin E
PubMed: 38206624
DOI: 10.1001/jamanetworkopen.2023.51418 -
Biopreservation and Biobanking Jun 2014Effective tracking of biospecimens within a biobank requires that each biospecimen has a unique identifier (ID). This ID can be found on the sample container as well as...
Effective tracking of biospecimens within a biobank requires that each biospecimen has a unique identifier (ID). This ID can be found on the sample container as well as in the biospecimen management system. In the latter, the biospecimen ID is the key to annotation data such as location, quality, and sample processing. Guidelines such as the Best Practices from the International Society of Biological and Environmental Repositories only state that a unique identifier should be issued for each sample. However, to our knowledge, all guidelines lack a specific description of how to actually generate such an ID and how this can be supported by an IT system. Here, we provide a guide for biobankers on how to generate a biospecimen ID for your biobank. We also provide an example of how to apply this guide using a longitudinal multi-center research project (and its biobank). Starting with a description of the biobank's purpose and workflows through to collecting requirements from stakeholders and relevant documents (i.e., guidelines or data protection concepts), and existing IT-systems, we describe in detail how a concept to develop an ID system can be developed from this information. The concept contains two parts: one is the generation of the biospecimen ID according to the requirements of stakeholders, existing documentation such as guidelines or data protection concepts, and existing IT-infrastructures, and the second is the implementation of the biospecimen IDs and related functionalities covering the handling of individual biospecimens within an existing biospecimen management system. From describing the concept, the article moves on to how the new concept supports both existing or planned biobank workflows. Finally, the implementation and validation step is outlined to the reader and practical hints are provided for each step.
Topics: Biological Specimen Banks; Computer Security; Data Curation; Humans; Specimen Handling
PubMed: 24955734
DOI: 10.1089/bio.2013.0085