Challenges on the Development of Biodiversity Biobanks: The Living Archives of Biodiversity

Biodiversity biobanks or ex situ biodiversity biorepositories tend to receive less attention compared with their biomedical counterparts. In this review, we highlight the necessity for these biorepositories by presenting their significant role in health, biodiversity, linking of big data, other translational research, and biodiversity conservation efforts. Moreover, the significant challenges in developing and maintaining biodiversity biobanks based on successful biobanks in some megadiverse developing countries are examined to provide insights into what needs to be done and what can be improved by up-and-coming biodiversity biobanks. These challenges include lack of financial support and political will; availability of experts; development of standard policies; and information management system. In addition, issues regarding access and benefit sharing and Digital Sequence Information must be addressed by biodiversity biobanks.

Removal of platelets from blood plasma to improve the quality of extracellular vesicle research

BACKGROUND

Blood plasma is commonly used for biomarker research of extracellular vesicles (EVs). Removing all cells prior to analysis of EVs is essential.

OBJECTIVES

We therefore studied the efficacy of the most commonly used centrifugation protocol to prepare cell-free plasma.

METHODS

Plasma was prepared according to the double centrifugation protocol of the International Society on Thrombosis and Haemostasis (ISTH) in three independent studies. The concentrations of platelets, platelet-derived EVs, and erythrocyte-derived EVs were measured by calibrated flow cytometry.

RESULTS

The mean platelet concentration ranged from 5.1 × 105 /ml to 2.8 × 107 /ml and differed 55-fold between studies. Thus, the ISTH centrifugation protocol does not remove all platelets and results in variation between studies. As the concentration of platelet-derived EVs and platelets correlates linearly (R2  = .56), and the volume fraction of EVs and platelets in plasma are similar, the presence of platelets affects downstream analysis. To remove platelets a 0.8-μm polycarbonate filter was used to lower the platelet concentration 146-fold (p = .0013), without affecting the concentration of platelet-derived and erythrocyte-derived EVs (p = .982, p = .742).

CONCLUSIONS

To improve the quality of EV research, we recommend (1) measuring and reporting the platelet concentration in plasma used for EV research, or (2) removing platelets by centrifugation followed by filtration.

Evolution of biobanks and ethical governance for the emerging applications in biomedical research

The establishment of a biobank and effective utilization of the biological resources comes with lot of challenges which require operating processes and effective governance structure with public awareness. As biobank is an evolving field of data driven health-care research, guided strategies in line with the national and international statutory body regulations is important. A trustworthy governance is paramount in developing a sustainable way of establishing, maintaining and successful functioning of a biobank. This paper highlights the structure of biobank governance, challenges and processes of effective integration of governance strategies.

Perspectives from a Predominantly African American Community about Biobank Research and a Biobank Consent Form

Minority populations have been underrepresented in clinical trials, as well as in research biobanks that are created to conduct research with participants' biospecimens and related medical and research data. Biobank research raises issues about informed consent and privacy and the confidentiality of participants' personal data. Our study involved three focus groups of 10 adults each that were conducted in a medically underserved, predominantly African American community to elucidate questions and concerns regarding an institutional biobank. Transcripts from the discussion were qualitatively analyzed. Three main themes that arose from the focus groups included the importance of trust, the importance of the community in research, and suggestions to improve trust. The concerns identified in this study provide a starting point for future research to help research institutions become more trustworthy to the communities they serve.

ATLAS: an automated association test using probabilistically linked health records with application to genetic studies

OBJECTIVE

Large amounts of health data are becoming available for biomedical research. Synthesizing information across databases may capture more comprehensive pictures of patient health and enable novel research studies. When no gold standard mappings between patient records are available, researchers may probabilistically link records from separate databases and analyze the linked data. However, previous linked data inference methods are constrained to certain linkage settings and exhibit low power. Here, we present ATLAS, an automated, flexible, and robust association testing algorithm for probabilistically linked data.

MATERIALS AND METHODS

Missing variables are imputed at various thresholds using a weighted average method that propagates uncertainty from probabilistic linkage. Next, estimated effect sizes are obtained using a generalized linear model. ATLAS then conducts the threshold combination test by optimally combining P values obtained from data imputed at varying thresholds using Fisher's method and perturbation resampling.

RESULTS

In simulations, ATLAS controls for type I error and exhibits high power compared to previous methods. In a real-world genetic association study, meta-analysis of ATLAS-enabled analyses on a linked cohort with analyses using an existing cohort yielded additional significant associations between rheumatoid arthritis genetic risk score and laboratory biomarkers.

DISCUSSION

Weighted average imputation weathers false matches and increases contribution of true matches to mitigate linkage error-induced bias. The threshold combination test avoids arbitrarily choosing a threshold to rule a match, thus automating linked data-enabled analyses and preserving power.

CONCLUSION

ATLAS promises to enable novel and powerful research studies using linked data to capitalize on all available data sources.

Characteristics of the MACS/WIHS Combined Cohort Study: Opportunities for Research on Aging With HIV in the Longest US Observational Study of HIV

In 2019, the National Institutes of Health combined the Multicenter AIDS Cohort Study (MACS) and the Women's Interagency HIV Study (WIHS) into the MACS/WIHS Combined Cohort Study (MWCCS). In this paper, participants who made a study visit during October 2018-September 2019 (targeted for MWCCS enrollment) are described by human immunodeficiency virus (HIV) serostatus and compared with people living with HIV (PLWH) in the United States. Participants include 2,115 women and 1,901 men with a median age of 56 years (interquartile range, 48-63); 62% are PLWH. Study sites encompass the South (18%), the Mid-Atlantic/Northeast (45%), the West Coast (22%), and the Midwest (15%). Participant race/ethnicity approximates that of PLWH throughout the United States. Longitudinal data and specimens collected for 35 years (men) and 25 years (women) were combined. Differences in data collection and coding were reviewed, and key risk factor and comorbidity data were harmonized. For example, recent use of alcohol (62%) and tobacco (28%) are common, as are dyslipidemia (64%), hypertension (56%), obesity (42%), mildly or severely impaired daily activities (31%), depressive symptoms (28%), and diabetes (22%). The MWCCS repository includes serum, plasma, peripheral blood mononuclear cells, cell pellets, urine, cervicovaginal lavage samples, oral samples, B-cell lines, stool, and semen specimens. Demographic differences between the MACS and WIHS can confound analyses by sex. The merged MWCCS is both an ongoing observational cohort study and a valuable resource for harmonized longitudinal data and specimens for HIV-related research.

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

Strengthening the global network for sharing of marine biological collections: recommendations for a new agreement for biodiversity beyond national jurisdiction

Biological collections are fundamental to marine scientific research and understanding of biodiversity at various scales. Despite their key importance, sample collections and the institutes that house them are often underfunded and receive comparatively little attention in the discussions associated with global biodiversity agreements. Furthermore, access to collections can be limited by inadequate systems, infrastructure, and networks. With negotiations underway for a new implementing agreement on biodiversity beyond national jurisdiction, marine genetic resources (MGR), including questions on the sharing of benefits, remains the most debated and contentious element. Disparities remain between States regarding access to and utilization of marine biological samples (including MGR) from areas beyond national jurisdiction. Addressing capacity gaps related to collections could provide a point of agreement during negotiations and enhance global inclusivity in access to and utilization of MGR. Here, we examine both existing capacity and regional gaps in marine collections. We propose the strengthening of a distributed network of marine biological collections, building on existing initiatives and emphasizing best practices to bridge regional gaps. Our recommendations include: promoting scientific best practice for the curation of collections; alignment with ocean observing, and sampling initiatives; a potential pairing scheme for collections in developing and developed States; raising awareness of collections and benefits to marine science including through a global registry/directory; and promoting sustainable funding mechanisms to support collections and sustain global generation of contributors and users.

A pan-Canadian prospective study of young women with breast cancer: the rationale and protocol design for the RUBY study

Introduction

The understanding of the biology and epidemiology of, and the optimal therapeutic strategies for, breast cancer (bca) in younger women is limited. We present the rationale, design, and initial recruitment of Reducing the Burden of Breast Cancer in Young Women (ruby), a unique national prospective cohort study designed to examine the diagnosis, treatment, quality of life, and outcomes from the time of diagnosis for young women with bca.

Methods

Over a 4-year period at 33 sites across Canada, the ruby study will use a local and virtual recruitment model to enrol 1200 women with bca who are 40 years of age or younger at the time of diagnosis, before initiation of any treatment. At a minimum, comprehensive patient, tumour, and treatment data will be collected to evaluate recurrence and survival. Patients may opt to complete patient-reported questionnaires, to provide blood and tumour samples, and to be contacted for future research, forming the core dataset from which 4 subprojects evaluating genetics, lifestyle factors, fertility, and local management or delivery of care will be performed.

Summary

The ruby study will be the most comprehensive repository of data, biospecimens, and patient-reported outcomes ever collected with respect to young women with bca from the time of diagnosis, enabling research unique to that population now and into the future. This research model could be used for other oncology settings in Canada.

Enhanced Quality Metrics for Assessing RNA Derived From Archival Formalin-Fixed Paraffin-Embedded Tissue Samples

Formalin-fixed paraffin-embedded (FFPE) tissues provide an important resource for toxicogenomic research. However, variability in the integrity or quality of RNA obtained from archival FFPE specimens can lead to unreliable data and wasted resources, and standard protocols for measuring RNA integrity do not adequately assess the suitability of FFPE RNA. The main goal of this study was to identify improved methods for evaluating FFPE RNA quality for whole-genome sequencing. We examined RNA quality metrics conducted prior to RNA-sequencing in paired frozen and FFPE samples with varying levels of quality based on age in block and time in formalin. RNA quality was measured by the RNA integrity number (RIN), a modified RIN called the paraffin-embedded RNA metric, the percentage of RNA fragments >100-300 nucleotides in size (DV100-300), and 2 quantitative PCR-based methods. This information was correlated to sequencing read quality, mapping, and gene detection. Among fragmentation-based methods, DV and PCR-based metrics were more informative than RIN or paraffin-embedded RNA metric in determining sequencing success. Across low- and high-quality FFPE samples, a minimum of 80% of RNA fragments >100 nucleotides (DV100 > 80) provided the best indication of gene diversity and read counts upon sequencing. The PCR-based methods further showed quantitative reductions in amplifiable RNA of target genes related to sample age and time in formalin that inform input quantity of FFPE RNA for sequencing. These results should aid in screening and prioritizing archival FFPE samples for retrospective analyses of gene expression.

Population's perspectives toward biobanks in scientific research: a study from Jordan

Background

Biobanks (biorepositories) were established to compile collected bio-specimens for future research and usage. The collection/storage of bio-specimens triggers several social, legal, and ethical implications where public attitudes can represent the core measurement/parameter in defining the most acceptable practices and ethical approaches when dealing with biobanks.

Aim

The aim of this study was to explore and understand population’s perspectives, expectations, and concerns toward biobanks in Jordan.

Methods

A cross-sectional survey that included closed-ended questions was distributed among Jordanians. A total of 500 participants who are representative of the Jordanian population were included in this study.

Results

There was overwhelming support (>85%) for the establishment of biobanks in Jordan, and most of the participants agreed on the importance of biobanks and samples’ donation for promoting medical research. Enthusiasm in biobanking participation was associated with the sociodemographic characteristics of participants including age, educational level, and previous knowledge of biobanks. Moreover, considering sample donation as a religiously good deed appeared to have the strongest positive correlation with willingness to donate bio-specimens for future research. Also, participants’ trust in medical and research services, especially the protection of their privacy and confidentiality, was the most critical concern when they decided to participate in biobanks.

Conclusion

Population’s attitude toward biobanks in Jordan was positive and promising, and can encourage the future establishment of different biobanks. It is also necessary to take into consideration certain sociodemographic characteristics when discussing specific information with potential biobanks’ donors.

Standard Versus Simplified Consent Materials for Biobank Participation: Differences in Patient Knowledge and Trial Accrual

Replacing standard consent materials with simplified materials is a promising intervention to improve patient comprehension, but there is little evidence on its real-world implementation. We employed a sequential two-arm design to compare the effect of standard versus simplified consent materials on potential donors' understanding of biobank processes and their accrual to an active biobanking program. Participants were female patients of a California breast health clinic. Subjects from the simplified arm answered more items correctly ( p = .064), reported "don't know" for fewer items ( p = .077), and consented to donate to the biobank at higher rates ( p = .025) than those from the standard arm. Replacing an extant consent form with a simplified version is feasible and may benefit patient comprehension and study accrual.

A Federated Network for Translational Cancer Research Using Clinical Data and Biospecimens

Advances in cancer research and personalized medicine will require significant new bridging infrastructures, including more robust biorepositories that link human tissue to clinical phenotypes and outcomes. In order to meet that challenge, four cancer centers formed the Text Information Extraction System (TIES) Cancer Research Network, a federated network that facilitates data and biospecimen sharing among member institutions. Member sites can access pathology data that are de-identified and processed with the TIES natural language processing system, which creates a repository of rich phenotype data linked to clinical biospecimens. TIES incorporates multiple security and privacy best practices that, combined with legal agreements, network policies, and procedures, enable regulatory compliance. The TIES Cancer Research Network now provides integrated access to investigators at all member institutions, where multiple investigator-driven pilot projects are underway. Examples of federated search across the network illustrate the potential impact on translational research, particularly for studies involving rare cancers, rare phenotypes, and specific biologic behaviors. The network satisfies several key desiderata including local control of data and credentialing, inclusion of rich phenotype information, and applicability to diverse research objectives. The TIES Cancer Research Network presents a model for a national data and biospecimen network.

Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for transcriptomic research. However, use of FFPE samples in genomic studies has been limited by technical challenges resulting from nucleic acid degradation. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues preserved in formalin for different amounts of time using 2 DNA microarray protocols and 2 whole-transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other methods by having the highest correlations of differentially expressed genes (DEGs), and best overlap of pathways, between FRO and FFPE groups. The effect of sample time in formalin (18 h or 3 weeks) on gene expression profiles indicated that test article treatment, not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18 h and 3 week FFPE samples compared with FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of time in paraffin on genomic profiles. Ribo-depletion RNA-seq analysis of 8-, 19-, and 26-year-old control blocks resulted in comparable quality metrics, including expected distributions of mapped reads to exonic, untranslated region, intronic, and ribosomal fractions of the transcriptome. Overall, our results indicate that FFPE samples are appropriate for use in genomic studies in which frozen samples are not available, and that ribo-depletion RNA-seq is the preferred method for this type of analysis in archival and long-aged FFPE samples.

EngageUC: Developing an Efficient and Ethical Approach to Biobanking Research at the University of California

Biorepositories, or biobanks, provide researchers with access to biological samples and associated data in support of translational research. Efficient operation and ethical stewardship of biobanks involves coordinated efforts among multiple stakeholders including researchers who manage and use the repository, institutional officials charged with its oversight, and patients and volunteers who contribute samples and data. As advancements in translational research increasingly involve more data derived from larger numbers of diverse samples, the size and governance challenges facing biorepositories have grown. We describe an approach to developing efficient and ethical biobank governance that includes all major stakeholders. This model provides a pathway for addressing the technical and ethical challenges that must be resolved to ensure biorepositories continue to support translational research.

Biospecimens, biobanking and global cancer research collaborations

The disparities in prostate cancer incidence and mortality continue to be a global public health problem. Efforts to address the prostate cancer disparity in black men have been met with a number of challenges, specifically in the accessibility to biospecimens in the context of global prostate cancer collaborations. During the International Educational Workshop at the Science of Global Prostate Cancer Disparities conference held 1–4 November 2012 in Nassau, the Bahamas, an overview of biobanking and biospecimen repositories, and materials transfer in global prostate cancer collaborations were discussed. The challenges faced by low-resource countries were identified, and potential solutions were recommended.

Use of human specimens in research: the evolving United States regulatory, policy, and scientific landscape

The use of human specimens in research has contributed to significant scientific and medical advancements. However, the development of sophisticated whole genome and informatics technologies and the increase in specimen and data sharing have raised new questions about the identifiability of specimens and the protection of participants in human specimen research. In the US, new regulations and policies are being considered to address these changes. This review discusses the current and proposed regulations as they apply to specimen research, as well as relevant policy discussions. It summarizes the ways that researchers and other stakeholders can provide their input to these discussions and policy development efforts. Input from all the stakeholders in specimen research will be essential for the development of policies that facilitate such research while at the same time protecting the rights and welfare of research participants.

Leveraging a clinical research information system to assist biospecimen data and workflow management: a hybrid approach

BACKGROUND

Large multi-center clinical studies often involve the collection and analysis of biological samples. It is necessary to ensure timely, complete and accurate recording of analytical results and associated phenotypic and clinical information. The TRIBE-AKI Consortium http://www.yale.edu/tribeaki supports a network of multiple related studies and sample biorepository, thus allowing researchers to take advantage of a larger specimen collection than they might have at an individual institution.

DESCRIPTION

We describe a biospecimen data management system (BDMS) that supports TRIBE-AKI and is intended for multi-center collaborative clinical studies that involve shipment of biospecimens between sites. This system works in conjunction with a clinical research information system (CRIS) that stores the clinical data associated with the biospecimens, along with other patient-related parameters. Inter-operation between the two systems is mediated by an interactively invoked suite of Web Services, as well as by batch code. We discuss various challenges involved in integration.

CONCLUSIONS

Our experience indicates that an approach that emphasizes inter-operability is reasonably optimal in allowing each system to be utilized for the tasks for which it is best suited.