Collection, Storage, Retrieval and Distribution of Biological Materials for Research

Adapting Fabric Phase Sorptive Extraction as an Innovative Multitool for Sample Transfer and Extraction in Pharmacokinetic Analysis Followed by LC-MS Determination of Levofloxacin in Plasma Samples

Fabric phase sorptive extraction (FPSE) is a simple microextraction technique that allows analytes to be rescued from matrix components while using a small volume of samples to analyze complex biological systems. This study used FPSE as a microextraction tool and a sample storage and transfer device. Levofloxacin as a model molecule was applied intravenously (IV) to New Zealand male rabbits. The samples were simultaneously extracted by using FPSE and protein precipitation methods. The final solutions were analyzed using LC-MS equipped with an ACE C18 LC Column (150 mm × 4.6 mm, 5 μm) at 25 °C employed in isocratic elution mode using solution A (0.1% formic acid in water)/solution B (0.1% formic acid in acetonitrile) (80:20, v/v). The total analysis time was less than 15 min. The developed method was validated using the ICH M10 bioanalytical method validation and study sample analysis guidelines. The results obtained using FPSE were statistically identical to those obtained using protein precipitation. The plasma samples applied onto FPSE (10 μL onto 1.0 cm × 1.0 cm Biofluid Sampler) were stored in three different temperatures [refrigerator (2-8 °C), at ambient temperature (20 ± 5 °C), and in the stability cabinet (40 °C, 75% humidity)] and three different storage conditions (Eppendorf tubes, plastic containers, and straw paper envelopes). Levofloxacin in plasma samples adsorbed by FPSE biofluid sampler remained stable at 2-8 °C in Eppendorf tubes for at least 1 week. This study showed that FPSE could be used as a sample storage and transfer device for pharmacokinetic applications that need to work with small sample volumes and discard aggressive cold chains to store and transfer the plasma samples.

Updating International Society for Biological and Environmental Repositories Best Practices, Fifth Edition: A New Process for Relevance in an Evolving Landscape

The recently published fifth edition of the International Society for Biological and Environmental Repositories (ISBER) Best Practices signifies a pivotal milestone in navigating the complexities of repository management. Repositories operate within a constantly evolving landscape influenced by the changing fields of biospecimen science, technology, legal requirements, and ethical considerations. This dynamic is further amplified by unprecedented local and global challenges, such as pandemics, conflicts, and supply chain disruptions. Creating this new edition required a comprehensive approach capable of delivering a focused and coherent resource reflecting the broad horizon of its diverse users. The innovative approach used the existing phased development process and integrated the canvassing of opinions, formal evaluation, and real-time collaboration platforms. Merging these techniques enabled efficient collection and effective distillation of the latest in biobanking practices, enhancing the value of the fifth edition for repositories of specimens and associated data. The expanded document is a testament to the collective efforts of many dedicated individuals who have built upon the foundations of prior editions.

Longitudinal studies of child mental disorders in the general population: A systematic review of study characteristics

Introduction

Longitudinal studies of child mental disorders in the general population (herein study) investigate trends in prevalence, incidence, risk/protective factors, and sequelae for disorders. They are time and resource intensive but offer life-course perspectives and examination of causal mechanisms. Comprehensive syntheses of the methods of existing studies will provide an understanding of studies conducted to date, inventory studies, and inform the planning of new longitudinal studies.

Methods

A systematic review of the research literature in MEDLINE, EMBASE, and PsycINFO was conducted in December 2022 for longitudinal studies of child mental disorders in the general population. Records were grouped by study and assessed for eligibility. Data were extracted from one of four sources: a record reporting study methodology, a record documenting child mental disorder prevalence, study websites, or user guides. Narrative and tabular syntheses of the scope and design features of studies were generated.

Results

There were 18,133 unique records for 487 studies-159 of these were eligible for inclusion. Studies occurred from 1934 to 2019 worldwide, with data collection across 1 to 68 time points, with 70% of studies ongoing. Baseline sample sizes ranged from n = 151 to 64,136. Studies were most frequently conducted in the United States and at the city/town level. Internalizing disorders and disruptive, impulse control, and conduct disorders were the most frequently assessed mental disorders. Of studies reporting methods of disorder assessment, almost all used measurement scales. Individual, familial and environmental risk and protective factors and sequelae were examined.

Conclusions

These results summarize characteristics of existing longitudinal studies of child mental disorders in the general population, provide an understanding of studies conducted to date, encourage comprehensive and consistent reporting of study methodology to facilitate meta-analytic syntheses of longitudinal evidence, and offer recommendations and suggestions for the design of future studies. Registration DOI: 10.17605/OSF.IO/73HSW.

Trichomonas vaginalis serostatus and prostate cancer risk in Egypt: a case-control study

Trichomonas vaginalis is one of the most common non-viral sexually transmitted infections (STIs) that has been associated with prostate cancer in some countries. This study aims to investigate if T. vaginalis infection can be a risk factor for prostate cancer in Egypt and its possible relationship with cancer prognostic factors and overall survival. Serum samples were collected from a total of 445 age-matched males; 126 with prostate cancer, 108 with bladder cancer, 91 with different types of cancers, and 120 healthy controls, and then analyzed by ELISA for detection of anti-Trichomonas IgG and prostate-specific antigen (PSA). The results revealed that only 8.3% of controls were seropositive for trichomoniasis, compared with 19% of prostate cancer patients (P = 0.015). There were positive associations between the levels of PSA and tumor stage with T. vaginalis IgG optical density scores among the seropositive cases (P < 0.001 and < 0.05, respectively). However, no significant correlations were detected between seropositivity of T. vaginalis and other prognostic factors or overall survival in those patients. In conclusion, chronic T. vaginalis infection may be associated with prostate cancer, but it does not seem that this STI aggravates the cancer status.

Single-particle measurements of filamentous influenza virions reveal damage induced by freezing

Clinical isolates of influenza virus produce pleiomorphic virions, ranging from small spheres to elongated filaments. The filaments are seemingly adaptive in natural infections, but their basic functional properties are poorly understood and functional studies of filaments often report contradictory results. This may be due to artefactual damage from routine laboratory handling, an issue which has been noted several times without being explored in detail. To determine whether standard laboratory techniques could damage filaments, we used immunofluorescence microscopy to rapidly and reproducibly quantify and characterize the dimensions of filaments. Most of the techniques we tested had minimal impact on filaments, but freezing to -70 °C, a standard storage step before carrying out functional studies on influenza viruses, severely reduced their concentration, median length and the infectivity of the whole virion population. We noted that damage from freezing is likely to have affected most of the functional studies of filaments performed to date, and to address this we show that it can be mitigated by snap-freezing or incorporating the cryoprotectant DMSO. We recommend that functional studies of filaments characterize virion populations prior to analysis to ensure reproducibility, and that they use unfrozen samples if possible and cryoprotectants if not. These basic measures will support the robust functional characterizations of filaments that are required to understand their roles in natural influenza virus infections.

A Pregnancy Cohort to Study Multidimensional Correlates of Preterm Birth in India: Study Design, Implementation, and Baseline Characteristics of the Participants

Globally, preterm birth is a major public health problem. In India, 3.6 million of the 27 million infants born annually are preterm. Risk stratification of women based on multidimensional risk factors assessed during pregnancy is critical for prevention of preterm birth. A cohort study of pregnant women was initiated in May 2015 at the civil hospital in Gurugram, Haryana, India. Women are enrolled within 20 weeks of gestation and are followed until delivery and once postpartum. The objectives are to identify clinical, epidemiologic, genomic, epigenomic, proteomic, and microbial correlates; discover molecular-risk markers by using an integrative -omics approach; and generate a risk-prediction algorithm for preterm birth. We describe here the longitudinal study design, methodology of data collection, and the repositories of data, biospecimens, and ultrasound images being created. A total of 4,326 pregnant women, with documented evidence of recruitment before 20 weeks of gestation, have been enrolled through March 2018. We report baseline characteristics and outcomes of the first 2,000 enrolled participants. A high frequency of preterm births (14.9% among 1,662 live births) is noteworthy. The cohort database and the repositories will become global resources to answer critical questions on preterm birth and other birth outcomes.

Ethical Legal and Social Issues of Biobanking: Past, Present, and Future

The past 15 years has seen considerable changes in the research environment. These changes include the development of new sophisticated genetic and genomic technologies, a proliferation of databases containing large amount of genotypic and phenotypic data, and wide-spread data sharing among many institutions, nationally and internationally. These changes have raised new questions regarding how best to protect the participants of biobanking research. In response to these questions, best practices for addressing the legal, ethical, and social issues of biobanking have been developed. In addition, new ethical guidelines related to biobanking have been established, as well as new regulations regarding privacy and human subject protections. Finally, changes in the science and the research environment have raised complex ethical issues related to biobanking, such as questions about the most appropriate consent models to use for biobanking research, commercial use and ownership issues, and whether and how to return individual research results to biobank participants. This article reviews some of the developments over the past 15 years related to the ELSI of biobanking with a look toward the future.

Glycogen synthase kinase-3β regulates fractalkine production by altering its trafficking from Golgi to plasma membrane: implications for Alzheimer's disease

Glycogen synthase kinase-3β (GSK-3β) is a serine-threonine kinase implicated in multiple processes and signaling pathways. Its dysregulation is associated with different pathological conditions including Alzheimer’s disease (AD). Here we demonstrate how changes in GSK-3β activity and/or levels regulate the production and subsequent secretion of fractalkine, a chemokine involved in the immune response that has been linked to AD and to other different neurological disorders. Treatment of primary cultured neurons with GSK-3β inhibitors such as lithium and AR-A014418 decreased full-length fractalkine in total cell extracts. Opposite effects were observed after neuron transduction with a lentiviral vector overexpressing the kinase. Biotinylation assays showed that those changes mainly affect the plasma membrane-associated form of the protein, an observation that positively correlates with changes in the levels of its soluble form. These effects were confirmed in lithium-treated wild type (wt) mice and in GSK-3β transgenic animals, as well as in brain samples from AD patients, evident as age-dependent (animals) or Braak stage dependent changes (humans) in both the membrane-bound and the soluble forms of the protein. Further immunohistochemical analyses demonstrated how GSK-3β exerts these effects by affecting the trafficking of the chemokine from the Golgi to the plasma membrane, in different and opposite ways when the levels/activity of the kinase are increased or decreased. This work provides for the first time a mechanism linking GSK-3β and fractalkine both in vitro and in vivo, with important implications for neurological disorders and especially for AD, in which levels of this chemokine might be useful as a diagnostic tool.

Mouse Sperm Cryopreservation and Recovery of Genetically Modified Mice

Highly definable genetically, the humble mouse is the "reagent" mammal of choice with which to probe and begin to understand the human condition in all its complexities. With the recent advance in direct genome editing via targeted nucleases, e.g., TALEN and CRISPR/Cas9, the possibilities in using these sophisticated tools have increased substantially leading to a massive increase in the variety of strain numbers of genetically modified lines. With this increase comes a greater need to economically and creatively manage their numbers. Further, once characterized, lines may be of limited use but still need to be archived in a format allowing their rapid resurrection. Further, maintaining colonies on "the shelf" is financially draining and carries potential risks including natural disaster loss, disease, and strain contamination. Here we outline a simple and economic protocol to cryopreserve mouse sperm from many different genetic backgrounds, and outline its recovery via in vitro fertilization (IVF). The combined use of sperm cryopreservation and IVF now allows a freedom and versatility in mouse management facilitating rapid line close down with the option to later recover and rapidly expand as needed.

Analysis of reproducibility and variability from a frozen sample aliquotter by metabolomics analysis

PURPOSE

A novel frozen sample aliquotter, which consists of a drilling system in which a coring probe extracts multiple frozen cores from one frozen sample, was developed to avoid thawing and refreezing of samples. The aliquotter was tested to determine if it is suitable for metabolomics analyses in reproducibility and variability studies.

METHOD

Twenty volunteers (10 males and 10 females) were enrolled in this study. Each of the volunteers' serum was aliquotted to one 1.8 mL tube and one 150 μL tube (control). Then the serum was frozen at -80°C for 2 weeks. Four frozen cores were taken from the perimeter of each of the 1.8 mL parent tubes by the aliquotter. The cores, the frozen serum remaining in the parent samples after extracting four frozen cores (Remainder), and control were analyzed using a gas chromatography time-of-flight mass spectrometry platform to test the reproducibility and variability of the samples in metabolomics analyses.

RESULT

There were no significant differences between the Core, Remainder, and Control groups based on multivariate analysis of metabolomics analyses. In the reproducibility study, the average CV for the cores was 10.07%. In the variability study, the average changes ranged from 81.07% to 119.82% and 81.06% to 119.74% for Core and Remainder samples compared to Control, respectively.

CONCLUSION

The frozen sample aliquotter technology can extract multiple consistently homogenous aliquots without thawing the parent sample, and the coring process with serum produces good samples for metabolomics analyses.

DogMATIC--A Remote Biospecimen Collection Kit for Biobanking

Canine tumors are valuable comparative oncology models. This research was designed to create a sustainable biobank of canine mammary tumors for breast cancer research. The aim was to provide a well-characterized sample cohort for specimen sharing, data mining, and long-term research aims. Canine mammary tumors are most frequently managed at a local veterinary clinic or hospital. We adopted a biobank framework based on a large number of participating veterinary hospitals and clinics acting as collection centers that were serviced by a centralized storage facility. Recruitment was targeted at rural veterinary clinics. A tailored, stable collection kit (DogMATIC) was designed that was used by veterinarians in remote or rural locations to collect both fresh and fixed tissue for submission to the biobank. To validate this methodology the kit design, collection rate, and sample quality were analyzed. The Australian Veterinary Cancer Biobank was established as a network of 47 veterinary clinics and three veterinary pathology laboratories spanning over 200,000 km(2). In the first 12 months, 30 canine mammary tumor cases were submitted via the DogMATIC kit. Pure intact RNA was isolated in over 80% of samples with an average yield of 14.49 μg. A large network biobank, utilizing off-site collection with the DogMATIC kit, was successfully coordinated. The creation of the Australian Veterinary Cancer Biobank has established a long-term, sustainable, comparative oncology research resource in Australia. There are broader implications for biobanking with this very different form of collection and banking.

Certification for biobanks: the program developed by the Canadian Tumour Repository Network (CTRNet)

Two core aspects of the discipline of biobanking are biospecimen quality and good governance. Meeting the demands of both sample quality and governance can be challenging, especially in a resource limited environment. Frequently, differences between biobank processes reduce the ability for cooperative action and specimen sharing with researchers. In the Canadian context, we have made an attempt to identify these gaps and have provided a framework to support excellence, initially for tumor biobanks. The Canadian Tumour Repository Network (CTRNet) was established with funding from the Canadian Institute of Health Sciences (CIHR) Institute of Cancer Research (ICR) to foster translational research through improved access to high quality tumour biospecimens. Consistent with this mandate, CTRNet has focused on the establishment and deployment of common standards to harmonize biospecimen quality and approaches to governance. More recently, CTRNet has implemented a certification program to communicate these standards in conjunction with simultaneous exposure to education focusing on the rationale and foundations underlying these standards. The CTRNet certification program comprises registration and certification steps as two linked phases. In the registration phase, launched in November 2011, biobanks are registered into the system and individuals complete an introductory educational module. In the subsequent certification phase, the type of biobank is classified and assigned relevant educational modules and adoption of relevant standards of practice is confirmed through review of documentation including policies and protocols that address the CTRNet Required Operational Practices (ROPs). An important feature of the program is that it is intended for all types of tumor biobanks, so the scope and extent of assessment is scaled to the type of biobank. This program will provide an easily adoptable and flexible mechanism to communicate common standards through education and address both quality assurance and governance across the broad spectrum of biobanks.

The establishment of an ISO compliant cancer biobank for Jordan and its neighboring countries through knowledge transfer and training

Research studies aimed at advancing cancer prevention, diagnosis, and treatment depend on a number of key resources, including a ready supply of high-quality annotated biospecimens from diverse ethnic populations that can be used to test new drugs, assess the validity of prognostic biomarkers, and develop tailor-made therapies. In November 2011, KHCCBIO was established at the King Hussein Cancer Center (KHCC) with the support of Seventh Framework Programme (FP7) funding from the European Union (khccbio.khcc.jo). KHCCBIO was developed for the purpose of achieving an ISO accredited cancer biobank through the collection, processing, and preservation of high-quality, clinically annotated biospecimens from consenting cancer patients, making it the first cancer biobank of its kind in Jordan. The establishment of a state-of-the-art, standardized biospecimen repository of matched normal and lung tumor tissue, in addition to blood components such as serum, plasma, and white blood cells, was achieved through the support and experience of its European partners, Trinity College Dublin, Biostór Ireland, and accelopment AG. To date, KHCCBIO along with its partners, have worked closely in establishing an ISO Quality Management System (QMS) under which the biobank will operate. A Quality Policy Manual, Validation, and Training plan have been developed in addition to the development of standard operating procedures (SOPs) for consenting policies on ethical issues, data privacy, confidentiality, and biobanking bylaws. SOPs have also been drafted according to best international practices and implemented for the donation, procurement, processing, testing, preservation, storage, and distribution of tissues and blood samples from lung cancer patients, which will form the basis for the procurement of other cancer types. KHCCBIO will be the first ISO accredited cancer biobank from a diverse ethnic Middle Eastern and North African population. It will provide a unique and valuable resource of high-quality human biospecimens and anonymized clinicopathological data to the cancer research communities world-wide.

Biorepository development research: a detailed topic follow-up to the blueprint for the development of a community-based hospital biorepository

Background research may be time consuming but is an essential component in producing a compliant, efficient, and quality biorepository. This article addresses 5 fundamental considerations associated with biorepository development. The process begins with community and stakeholder buy-in. Once this phase is complete and stakeholder approval is achieved, several crucial elements remain. When proceeding, it is important to consider researcher needs, initial facility setup requirements, start-up funding sources, biorepository site visits, regulations, and best practices. Multiple sources should be utilized when exploring these topics and should include guidance documents, regulations, existing literature, and "borrowed knowledge" from others who have been through the process. Thorough research during this initial phase and the subsequent tailoring of this information to fit the specific institution's needs will contribute significantly to the success of the biorepository.

Toward a common language for biobanking

To encourage the process of harmonization, the biobank community should support and use a common terminology. Relevant terms may be found in general thesauri for medicine, legal instruments or specific glossaries for biobanking. A comparison of the use of these sources has so far not been conducted and would be a useful instrument to further promote harmonization and data sharing. Thus, the purpose of the present study was to investigate the preference of definitions important for sharing biological samples and data. Definitions for 10 terms -[human] biobank, sample/specimen, sample collection, study, aliquot, coded, identifying information, anonymised, personal data and informed consent-were collected from several sources. A web-based questionnaire was sent to 560 European individuals working with biobanks asking to select their preferred definition for the terms. A total of 123 people participated in the survey, giving a response rate of 23%. The result was evaluated from four aspects: scope of definitions, potential regional differences, differences in semantics and definitions in the context of ontologies, guided by comments from responders. Indicative from the survey is the risk of focusing only on the research aspect of biobanking in definitions. Hence, it is recommended that important terms should be formulated in such a way that all areas of biobanking are covered to improve the bridges between research and clinical application. Since several of the terms investigated here within can also be found in a legal context, which may differ between countries, establishing what is a proper definition on how it adheres to law is also crucial.

Biobanking in a constantly developing medical world

Biobank is a very sophisticated system that consists of a programmed storage of biological material and corresponding data. Biobanks are created to be used in medical research, in clinical and translational medicine, and in healthcare. In the past 20 years, a large number of biobanks have been set up around the world, to support the modern research directions in medicine such as omix and personalized medicine. More recently, embryonic and adult stem cell banks have been developed. Stem cell banking was reported to be required for medical research as well as clinical transplant applications. The quality of the samples stored in a biobank is very important. The standardization is also important; the biological material stored in a biobank must be processed in a manner that allows compatibility with other biobanks that preserve samples in the same field. In this paper, we review some issues related to biobanks purposes, quality, harmonization, and their financial and ethical aspects.

GSK-3β overexpression causes reversible alterations on postsynaptic densities and dendritic morphology of hippocampal granule neurons in vivo

Adult hippocampal neurogenesis (AHN) is crucial for the maintenance of hippocampal function. Several neurodegenerative diseases such as Alzheimer's disease (AD) are accompanied by memory deficits that could be related to alterations in AHN. Here, we took advantage of a conditional mouse model to study the involvement of glycogen synthase kinase-3β (GSK-3β) overexpression (OE) in AHN. By injecting GFP- and PSD95-GFP-expressing retroviruses, we have determined that hippocampal GSK-3β-OE causes dramatic alterations in both dendritic tree morphology and post-synaptic densities in newborn neurons. Alterations in previously damaged neurons were reverted by switching off the transgenic system and also by using a physiological approach (environmental enrichment) to increase hippocampal plasticity. Furthermore, comparative morphometric analysis of granule neurons from patients with AD and from GSK-3β overexpressing mice revealed shared morphological alterations. Taken together, these data indicate that GSK-3β is crucial for hippocampal function, thereby supporting this kinase as a relevant target for the treatment of AD.

Development and progress of Ireland's biobank network: Ethical, legal, and social implications (ELSI), standardized documentation, sample and data release, and international perspective

Biobank Ireland Trust (BIT) was established in 2004 to promote and develop an Irish biobank network to benefit patients, researchers, industry, and the economy. The network commenced in 2008 with two hospital biobanks and currently consists of biobanks in the four main cancer hospitals in Ireland. The St. James's Hospital (SJH) Biobank coordinates the network. Procedures, based on ISBER and NCI guidelines, are standardized across the network. Policies and documents-Patient Consent Policy, Patient Information Sheet, Biobank Consent Form, Sample and Data Access Policy (SAP), and Sample Application Form have been agreed upon (after robust discussion) for use in each hospital. An optimum sequence for document preparation and submission for review is outlined. Once consensus is reached among the participating biobanks, the SJH biobank liaises with the Research and Ethics Committees, the Office of the Data Protection Commissioner, The National Cancer Registry (NCR), patient advocate groups, researchers, and other stakeholders. The NCR provides de-identified data from its database for researchers via unique biobank codes. ELSI issues discussed include the introduction of prospective consent across the network and the return of significant research results to patients. Only 4 of 363 patients opted to be re-contacted and re-consented on each occasion that their samples are included in a new project. It was decided, after multidisciplinary discussion, that results will not be returned to patients. The SAP is modeled on those of several international networks. Biobank Ireland is affiliated with international biobanking groups-Marble Arch International Working Group, ISBER, and ESBB. The Irish government continues to deliberate on how to fund and implement biobanking nationally. Meanwhile BIT uses every opportunity to promote awareness of the benefits of biobanking in events and in the media.

The rationale and design of Insight into Nephrotic Syndrome: Investigating Genes, Health and Therapeutics (INSIGHT): a prospective cohort study of childhood nephrotic syndrome

BACKGROUND

Nephrotic syndrome is one of the most commonly diagnosed kidney diseases in childhood and its progressive forms can lead to chronic kidney disease (CKD) and/or end-stage renal disease (ESRD). There have been few longitudinal studies among a multi-ethnic cohort to determine potential risk factors influencing disease susceptibility, treatment response, and progression of nephrotic syndrome. Temporal relationships cannot be studied through cross-sectional study design. Understanding the interaction between various factors is critical to developing new strategies for treating children with kidney disease. We present the rationale and the study design of a longitudinal cohort study of children with nephrotic syndrome, the Insight into Nephrotic Syndrome: Investigating Genes, Health and Therapeutics (INSIGHT) study. The specific aims are to determine: 1) socio-demographic, environmental, and genetic factors that influence disease susceptibility; 2) rates of steroid treatment resistance and steroid treatment dependence, and identify factors that may modify treatment response; 3) clinical and genetic factors that influence disease susceptibility and progression to CKD and ESRD; and 4) the interaction between the course of illness and socio-demographic, environmental, and clinical risk factors.

METHODS/DESIGN

INSIGHT is a disease-based observational longitudinal cohort study of children with nephrotic syndrome. At baseline, participants complete questionnaires and provide biological specimen samples (blood, urine, and toenail clippings). Follow-up questionnaires and repeat biological specimen collections are performed annually for up to five years.

DISCUSSION

The proposed cohort will provide the structure to test various risk factors predicting or influencing disease susceptibility, treatment response, and progression to CKD among children with nephrotic syndrome.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier NCT01605266.

Biobanking, consent, and certificates of confidentiality: does the ANPRM muddy the water?

In its Advanced Notice of Proposed Rule Making (ANPRM), the U.S. Department of Health and Human Services proposed substantial changes to how biospecimen research is treated under the regulations governing human subjects research. Currently, much of this research can be conducted without consent because it may not be considered "human subjects" research, is considered exempt, or consent may be waived. Responding to criticisms that scientific changes have made biospecimen research riskier than contemplated when the Common Rule was last amended, the ANPRM proposes to require written consent for biospecimen research, even if they have been stripped of identifiers or initially collected for a non-research purpose. The ANPRM's recognition of these risks is consistent with relatively recent NIH recommendations that research projects involving genetics, genomics, or biospecimen repositories should consider getting a Certificate of Confidentiality to provide additional protections to participants where breach of confidentiality is typically the primary risk. Ironically, the ANPRM proposals may make it more difficult to provide these protections. Our paper explores the implications of the conflicting requirements of the Certificate and the ANPRM proposals and makes recommendations for achieving the dual goals of appropriate consent and adequate confidentiality protections.

Reporting recommendations for tumor marker prognostic studies (REMARK): explanation and elaboration

BACKGROUND

The Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) checklist consists of 20 items to report for published tumor marker prognostic studies. It was developed to address widespread deficiencies in the reporting of such studies. In this paper we expand on the REMARK checklist to enhance its use and effectiveness through better understanding of the intent of each item and why the information is important to report.

METHODS

REMARK recommends including a transparent and full description of research goals and hypotheses, subject selection, specimen and assay considerations, marker measurement methods, statistical design and analysis, and study results. Each checklist item is explained and accompanied by published examples of good reporting, and relevant empirical evidence of the quality of reporting. We give prominence to discussion of the 'REMARK profile', a suggested tabular format for summarizing key study details.

SUMMARY

The paper provides a comprehensive overview to educate on good reporting and provide a valuable reference for the many issues to consider when designing, conducting, and analyzing tumor marker studies and prognostic studies in medicine in general. To encourage dissemination of the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): Explanation and Elaboration, this article has also been published in PLoS Medicine.

The interference of cold ischemia time in the quality of total RNA from frozen tumor samples

Tumor Banks were created to organize the collection, storage and distribution of biological samples from oncological patients, facilitating its use in cancer research. To ensure the quality of the samples from our bank, we implemented standard operating procedures international. In order to evaluate the influence of cold ischemia time (time between surgical removal of the specimen and the snap freezing of the sample) on the quality of the samples (evaluated by measurement integrity of their RNA), collected during 10 months two tumor samples from each donor, one with up to 30 min of cold ischemia and other with exact 45 min, totaling 100 different donors and 200 samples, 40 from each of the following organs: breast, thyroid, stomach, lung and colorectum. We extracted total RNA from the samples and with the aid of a Bioanalyser, evaluate their quality, comparing it with cold ischemia times in different organs. Among the samples up to 30 min and the samples with exact 45 min, we respectively found 63 (64.3 %) and 36 (36 %) with intact RNA, 11 (11.2 %) and 17 (17 %) partially degraded and 24 (24.5 %) and 47 (47 %) degraded (p < 0.001). Thyroid and colorectal samples were more sensitive to variations in cold ischemia time (p = 0.006 and p = 0.03, respectively). Stomach and lungs were less sensitive (p = 0.919 and p = 0.384, respectively). We concluded that the cold ischemia time up to 30 min was more efficient to maintain the integrity of RNA in most samples, and that RNA degradation varied according to the different topographies.

The human side of cancer biobanking

The future success of translational research is critically dependent on the procurement and availability of high-quality tissue specimens linked to accurate histopathologic and clinical information about the individual banked specimen. The international community has awakened to this critical need only recently. Three major roadblocks have hindered the success of previous biobank consortiums: (1) Ethical issues surrounding patient consent and ownership of intellectual property, (2) Failure to properly preserve the molecular content of the tissue, and failure to reliably document clinical data linked to the specimen, and (3) Management issues: inadequate funding, competition for use of the tissue, inadequate personnel and facilities, and absence of dedicated database software. This chapter reviews these critical roadblocks and discusses international efforts to provide strategies to implement high-quality biobanks.

New strategies and designs in pancreatic cancer research: consensus guidelines report from a European expert panel

Although the treatment of pancreatic ductal adenocarcinoma (PDAC) remains a huge challenge, it is entering a new era with the development of new strategies and trial designs. Because there is an increasing number of novel therapeutic agents and potential combinations available to test in patients with PDAC, the identification of robust prognostic and predictive markers and of new targets and relevant pathways is a top priority as well as the design of adequate trials incorporating molecular-driven hypothesis. We presently report a consensus strategy for research in pancreatic cancer that was developed by a multidisciplinary panel of experts from different European institutions and collaborative groups involved in pancreatic cancer. The expert panel embraces the concept of exploratory early proof of concept studies, based on the prediction of response to novel agents and combinations, and randomised phase II studies permitting the selection of the best therapeutic approach to go forward into phase III, where the recommended primary end point remains overall survival. Trials should contain as many translational components as possible, relying on standardised tissue and blood processing and robust biobanking, and including dynamic imaging. Attention should not only be paid to the pancreatic cancer cells but also to microenvironmental factors and stem/stellate cells.

Intersection of biobanking and clinical care: should discrepant diagnoses and pathological findings be returned to research participants?

Diagnostic discrepancies occur when the diagnosis made on a biospecimen during the course of review at a biobank differs from the original clinical diagnosis. These diagnostic discrepancies detected during biobanking present unique challenges that are distinct from other types of research results or incidental findings. The proposed process for reporting diagnostic discrepancies or pathological incidental findings identified through a quality assurance evaluation at the biobank includes verification of the biospecimen identity, verification of the diagnosis within the biobank, and re-review of the case by the pathologist at the biospecimen collection site. If the pathologist at the biobank and the original pathologist do not reach agreement, an impartial and knowledgeable third party is consulted. The decision as to whether and how to notify research participants of any confirmed changes in diagnosis would be determined by institutional procedures. Implementation of this proposed process will require clear delineation of the roles and responsibilities of all involved parties in order to promote excellence in patient care and ensure that researchers have access to biospecimens of requisite quality.Genet Med 2012:14(4):417-423.

Practical implementation issues and challenges for biobanks in the return of individual research results

Whether or not to give research results back to individuals whose specimens are used for biomedical research is a subject of considerable controversy. Much of the debate has been focused around the ethical and legal concerns with some consideration of broader social issues such as whether or not people will be affected by such information for employment or health care. Much less attention has been paid to biobanks that collect the specimens used to generate the research findings and the issues and operational requirements for implementing return of individual research results. In this article, we give the biobanks' perspective and highlight that given the diversity among the types of biobanks, it may be difficult to design and implement a blanket policy in this complex area. We discuss the variability in the types of biobanks and some important issues that should be considered in determining whether or not research results should be provided to individuals whose specimens are used in biomedical research. We also discuss challenges that should be considered in implementing any approaches to the return of research results.

Automated Web-Based Request Mechanism for Workflow Enhancement in an Academic Customer-Focused Biorepository

Informatics systems, particularly those that provide capabilities for data storage, specimen tracking, retrieval, and order fulfillment, are critical to the success of biorepositories and other laboratories engaged in translational medical research. A crucial item-one easily overlooked-is an efficient way to receive and process investigator-initiated requests. A successful electronic ordering system should allow request processing in a maximally efficient manner, while also allowing streamlined tracking and mining of request data such as turnaround times and numerical categorizations (user groups, funding sources, protocols, and so on). Ideally, an electronic ordering system also facilitates the initial contact between the laboratory and customers, while still allowing for downstream communications and other steps toward scientific partnerships. We describe here the recently established Web-based ordering system for the biorepository at Washington University Medical Center, along with its benefits for workflow, tracking, and customer service. Because of the system's numerous value-added impacts, we think our experience can serve as a good model for other customer-focused biorepositories, especially those currently using manual or non-Web-based request systems. Our lessons learned also apply to the informatics developers who serve such biobanks.

Donation intentions for cancer genetics research among African Americans

AIMS

Scientific agencies rely on individuals to donate their DNA to support research on chronic conditions that disproportionately affect African Americans; however, donation is variable in this population. The purpose of this study was to identify sociodemographic characteristics, health care variables, and cultural values having significant independent associations with intentions to donate blood or saliva samples for cancer genetics research among African American adults.

METHOD

Cross-sectional survey of donation intentions.

RESULTS

The majority of respondents (73%) were willing to donate a biological sample for cancer genetics research. The results of the multivariate regression model found that respondents who received care at a facility other than a doctor's office (e.g., community center) were about five times more likely to be willing to donate a sample for cancer genetics research (odds ratio [OR]=5.28, 95% confidence interval [CI]=1.16-24.12, p=0.03); whereas, greater levels of religiosity (OR=0.09, 95% CI=0.01-0.75, p=0.02) and present temporal orientation (OR=0.23, 95% CI=0.06-0.79, p=0.02) were associated with a lower likelihood of donating a sample.

CONCLUSION

Efforts to enhance donation of biological samples for cancer genetics research may need to target diverse clinical sites for recruitment. Additionally, recruitment materials may need to address cultural values related to religiosity and present temporal orientation.

Translational research in pediatrics: tissue sampling and biobanking

Translational research is expanding and has become a focus of National Research funding agencies, touted as the primary avenue to improve health care practice. The use of human tissues for research on disease etiology is a pillar of translational research, particularly with innovations in research technologies to investigate the building blocks of disease. In pediatrics, translational research using human tissues has been hindered by the many practical and ethical considerations associated with tissue procurement from children and also by a limited population base for study, by the increasing complexities in conducting clinical research, and by a lack of dedicated child-health research funding. Given these obstacles, pediatric translational research can be enhanced by developing strategic and efficient biobanks that will provide scientists with quality tissue specimens to render accurate and reproducible research results. Indeed, tissue sampling and biobanking within pediatric academic settings has potential to impact child health by promoting bidirectional interaction between clinicians and scientists, helping to maximize research productivity, and providing a competitive edge for attracting and maintaining high-quality personnel. The authors of this review outline key issues and practical solutions to optimize pediatric tissue sampling and biobanking for translational research, activities that will ultimately reduce the burden of childhood disease.

Best practices for fungal germplasm repositories and perspectives on their implementation

In over 50 years, the Fungal Genetics Stock Center has grown to become a world-recognized biological resource center. Along with this growth comes the development and implementation of myriad practices for the management and curation of a diverse collection of filamentous fungi, yeast, and molecular genetic tools for working with the fungi. These practices include techniques for the testing, manipulation, and preservation of individual fungal isolates as well as for processing of thousands of isolates in parallel. In addition to providing accurate record keeping, an electronic managements system allows the observation of trends in strain distribution and in sample characteristics. Because many ex situ fungal germplasm repositories around the world share similar objectives, best-practice guidelines have been developed by a number of organizations such as the Organization for Economic Cooperation and Development or the International Society for Biological and Environmental Repositories. These best-practice guidelines provide a framework for the successful operation of collections and promote the development and interactions of biological resource centers around the world.

Biorepository regulatory considerations: a detailed topic follow-up to the blueprint for the development of a community-based hospital biorepository

Human specimen and associated clinical data are crucial resources for uncovering new biomarkers as well as identifying factors in the pathogenesis of disease. As tissue banking becomes more widespread in response to increased researcher demand, the need for specific guidance documents and standards to be developed and/or updated becomes more urgent. This article discusses 4 aspects of current regulation and guidance considerations. First is the application of the Common Rule and the Privacy Rule to the Institutional Review Board review process. Second is the honest broker concept, which supports the further protection of donor confidentiality and allows for future updates to data. The third consideration discusses the regulatory approval process. Finally, inconsistencies between regulatory bodies are identified and possible ways to reconcile those inconsistencies are suggested.

The Establishment of the First Cancer Tissue Biobank at a Hispanic-Serving Institution: A National Cancer Institute-Funded Initiative between Moffitt Cancer Center in Florida and the Ponce School of Medicine and Health Sciences in Puerto Rico

Population-based studies are important to address emerging issues in health disparities among populations. The Partnership between the Moffitt Cancer Center (MCC) in Florida and the Ponce School of Medicine and Health Sciences (PSMHS) in Puerto Rico (the PSMHS-MCC Partnership) was developed to facilitate high-quality research, training, and community outreach focusing on the Puerto Rican population in the island and in the mainland, with funding from the National Cancer Institute. We report here the establishment of a Tissue Biobank at PSMHS, modeled after the MCC tissue biorepository, to support translational research projects on this minority population. This facility, the Puerto Rico Tissue Biobank, was jointly developed by a team of basic and clinical scientists from both institutions in close collaboration with the administrators and clinical faculty of the tissue accrual sites. The efforts required and challenges that needed to be overcome to establish the first functional, centralized cancer-related biobank in Puerto Rico, and to ensure that it continuously evolves to address new needs of this underserved Hispanic population, are described. As a result of the collaborative efforts between PSMHS and MCC, a tissue procurement algorithm was successfully established to acquire, process, store, and conduct pathological analyses of cancer-related biospecimens and their associated clinical-pathological data from Puerto Rican patients with cancer recruited at a tertiary hospital setting. All protocols in place are in accordance with standard operational procedures that ensure high quality of biological materials and patient confidentiality. The processes described here provide a model that can be applied to achieve the establishment of a functional biobank in similar settings.

New concepts of biobanks--strategic chance for uro-oncology

Cancer, as well as other common diseases, is a complex condition that not only causes a major threat to human health, but also represents a huge burden to society in terms of healthcare cost and loss of economic productivity. Treatment improvements remain elusive, since the causes of cancer are due to a huge number of small and possibly additive effects arising from genetic susceptibility, lifestyle, and environmental conditions. Thus, progress in translational cancer research investigating these changes and their complex interaction is highly dependent on large series of cases (affected and unaffected individuals) including high quality samples and their associated data. Therefore, large and well-organized biobanks have been established, are underway, or are planned in many countries and institutions. The integration of these resources with powerful molecular and "omics" approaches, integrated bioinformatic tools hold the promise to further advance our knowledge of disease development, thus leading to better prevention and treatment strategies. However, these valuable and irreplaceable collections typically suffer from underutilization, due to fragmentation of the collections and their accessibility, lack of common management strategies, including consensus on standard operating procedures, unique policies of utilization, and distribution as well as missing input on a broad basis reflecting research needs on an interdisciplinary, multi-institutional fashion beyond project-driven interest. The uro-oncologic community has not yet contributed to these efforts to its full potential, and broad knowledge on the contemporary developments in the field of biobanking and input into these efforts are still missing. This review presents an overview on biobanking and may serve as an update to be integrated into future discussions on managing biobanks involving uro-oncology. It is based on the discussions at the last meeting of the International Bladder Cancer Network in Barcelona (Spain) in fall 2008 and has been also largely influenced by the works and discussions of the Marble Arch International Working Group on Biobanking for Biomedical Research.

The sophisticated mouse: protecting a precious reagent

Definable, genetically and environmentally, the humble mouse has become a reagent with which to probe the human condition. The information thus gained is leading to a greater understanding of inter-individual variation in drug responses and disease processes and is forming the basis for personalized medicine. Inbred mice are the tool of choice as each strain is essentially clonal in nature creating a defined, uniform setting where the effects of genetic background and modifications can be evaluated coherently. However, the creation and characterization of novel mouse strains remain expensive and time consuming. Further, the continual maintenance of these valuable animals as live colonies is financially draining and carries continual potential risks, including disastrous loss due to fire, flood, disease, etc. There are also other more insidious disasters including genetic contamination and genetic drift, either of which can go undiscovered until their effects ruin experiments. With this in mind, we strongly recommend that all mouse strains be cryopreserved as a matter of standard mouse management. Cryopreservation is a powerful colony management tool, assuring strains are available upon demand, for example, for regulatory requirements, re-initiation of projects, collaborations, re-evaluation of data etc. However, it is essential that any cryopreservation approach be cost-effective for both strain closure and strain recovery. In this chapter, we describe the variables which can afflict an inbred mouse's genetic background (and hence phenotype), options to consider for strain archiving, and describe how to economically store and recover strains by sperm cryopreservation.

Informed consent in genomics and genetic research

There are several features of genetic and genomic research that challenge established norms of informed consent. In this paper, we discuss these challenges, explore specific elements of informed consent for genetic and genomic research conducted in the United States, and consider alternative consent models that have been proposed. All of these models attempt to balance the obligation to respect and protect research participants with the larger social interest in advancing beneficial research as quickly as possible.

Evolutionary concepts in biobanking - the BC BioLibrary

BACKGROUND

Medical research to improve health care faces a major problem in the relatively limited availability of adequately annotated and collected biospecimens. This limitation is creating a growing gap between the pace of scientific advances and successful exploitation of this knowledge. Biobanks are an important conduit for transfer of biospecimens (tissues, blood, body fluids) and related health data to research. They have evolved outside of the historical source of tissue biospecimens, clinical pathology archives. Research biobanks have developed advanced standards, protocols, databases, and mechanisms to interface with researchers seeking biospecimens. However, biobanks are often limited in their capacity and ability to ensure quality in the face of increasing demand. Our strategy to enhance both capacity and quality in research biobanking is to create a new framework that repatriates the activity of biospecimen accrual for biobanks to clinical pathology.

METHODS

The British Columbia (BC) BioLibrary is a framework to maximize the accrual of high-quality, annotated biospecimens into biobanks. The BC BioLibrary design primarily encompasses: 1) specialized biospecimen collection units embedded within clinical pathology and linked to a biospecimen distribution system that serves biobanks; 2) a systematic process to connect potential donors with biobanks, and to connect biobanks with consented biospecimens; and 3) interdisciplinary governance and oversight informed by public opinion.

RESULTS

The BC BioLibrary has been embraced by biobanking leaders and translational researchers throughout BC, across multiple health authorities, institutions, and disciplines. An initial pilot network of three Biospecimen Collection Units has been successfully established. In addition, two public deliberation events have been held to obtain input from the public on the BioLibrary and on issues including consent, collection of biospecimens and governance.

CONCLUSION

The BC BioLibrary framework addresses common issues for clinical pathology, biobanking, and translational research across multiple institutions and clinical and research domains. We anticipate that our framework will lead to enhanced biospecimen accrual capacity and quality, reduced competition between biobanks, and a transparent process for donors that enhances public trust in biobanking.

Past, present, and future of environmental specimen banks

Environmental specimen banks are an essential part of the infrastructure of environmental sciences. They have various functions: (1) evaluation of governmental environmental policy-making and regulations; (2) a resource for animal health evaluation; (3) research tools to investigate time trends in ecosystems; (4) detection of newly emerging chemicals in the time trends; (5) validations of computer models for environmental phenomena; (6) source identification of contaminants; (7) a tool for food safety; (8) evaluation of genetic selection pressure due to environmental changes. In this review paper, we present a detailed description of the Kyoto University Human Specimen Bank (history, protocol and questionnaires) and provide brief outlines of other representative environmental specimen banks. We then review two illustrative cases in which environmental specimen banks have unveiled insidious contaminations of polybrominated diphenyl ethers and perfluorooctanoic acids. Finally, we give a perspective of new functions for environmental specimen banks in the next 20 years.