Biobank Material Research Articles

Negative Association Between Allopregnanolone and Cerebral Serotonin Transporter Binding in Healthy Women of Fertile Age.

Allopregnanolone is a metabolite of the sex hormone progesterone, with suggested relevance for female mood disorders. While allopregnanolone and serotonin are known to influence psychological well-being, the molecular and psychological specifics of their relationship are to date poorly understood, especially in women of fertile age who experience regular fluctuations of progesterone across the menstrual cycle. Availability of serotonin in the synaptic cleft is regulated by the serotonin transporter (SERT), which can be imaged in the living human brain by use of positron emission tomography (PET) and the radiotracer [11C]DASB. To evaluate sex-specific allopregnanolone-SERT interactions, the present study investigated the relationship between cerebral SERT availability, serum allopregnanolone levels and psychological well-being in women of fertile age. Brain imaging data, self-reported symptoms of mental distress and emotion regulation, and biobank material from ninety healthy women were available from the Center for Integrated Molecular Brain Imaging (CIMBI) database. Age, BMI, and daylight minutes were included as covariates in the analyses and SERT genotype (5-HTTLPR) was considered a potential confounder. Lower serum allopregnanolone levels were associated with higher SERT binding in the prefrontal cortex. Moreover, allopregnanolone levels were negatively associated with measures of alertness, although this finding was not mediated by prefrontal cortex SERT binding. These findings suggest a link between the typical psychological well-being experienced in the follicular phase when allopregnanolone levels are low and higher SERT in the prefrontal cortex, a region for higher cognitive functions and top-down regulation of emotions.

Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing.

Probing an individual cell's gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a powerful tool for studying transcriptional profiles of cells, particularly in heterogeneous tissues such as the central nervous system. However, dissociation methods required for single cell sequencing can lead to experimental changes in the gene expression and cell death. Furthermore, these methods are generally restricted to fresh tissue, thus limiting studies on archival and bio-bank material. Single nucleus RNA sequencing (snRNA-Seq) is an appealing alternative for transcriptional studies, given that it accurately identifies cell types, permits the study of tissue that is frozen or difficult to dissociate, and reduces dissociation-induced transcription. Here, we present a high-throughput protocol for rapid isolation of nuclei for downstream snRNA-Seq. This method enables isolation of nuclei from fresh or frozen spinal cord samples and can be combined with two massively parallel droplet encapsulation platforms.

Ethics of dead participants: policy recommendations for biobank research

Respecting people’s consent choices for use of their material and data is a cornerstone of biobank ethics. Participation in biobanks is characteristically based on broad consent that presupposes an ongoing...

Validation of genetic predictors of late radiation-induced morbidity in prostate cancer patients

Introduction: Normal tissue morbidity sets the dose limit for radiotherapy (RT) in cancer treatment and has importance for quality of life for cancer survivors. A previous study of prostate cancer patients treated with RT generated clinical data for radiation-induced morbidity measured by anorectal physiological methods and validated questionnaires. Other studies have identified genetic predictors associated with late radiation-induced morbidity outcome. We have expanded biobank material aiming to validate single nucleotide polymorphisms (SNPs) and a gene expression classifier with endpoints on patient-reported outcomes and biomechanical properties of the anorectum from our cohort matching originally published endpoints.Materials and methods: The present cohort of prostate cancer patients was treated with RT curative intent in 1999–2007. Nine SNPs associated with late radiation-induced morbidity were tested in 96 patients (rs2788612, rs1800629, rs264663, rs2682585, rs2268363, rs1801516, rs13035033, rs7120482 and rs17779457). A validated gene expression profile predictive of resistance to radiation-induced skin fibrosis was tested in 42 patients. An RT-induced anorectal dysfunction score (RT-ARD) served as a fibrosis-surrogate and a measure of overall radiation-induced morbidity.Results: The lowest p-value found in the genotype analyses was for SNP rs2682585 minor allele (A) in the FSHR gene and the RT-ARD score with odds ratios (OR) = 1.76; 95% CI (0.98–3.17) p = .06, which was out of concordance with original data showing a protective effect of the minor allele. The gene expression profile in patients classified as fibrosis-resistant was associated with high RT-ARD scores OR 4.18; 95% CI (1.1–16.6), p = .04 conflicting with the hypothesis that fibrosis-resistant patients would experience lower RT-ARD scores.Conclusions: We aimed to validate nine SNPs and a gene expression classifier in a cohort of prostate cancer patients with unique scoring of radiation-induced morbidity. One significant association was found, pointing to the opposite direction of originally published data. We conclude that the material was not able to validate previously published genetic predictors of radiation-induced morbidity.

The WMA Declaration of Taipei: Human databases and biobanks for the common good

On 22 October 2016, the World Medical Association (WMA) announced that it had approved new ethical guidelines for physicians involved in the collection and use of identifiable health data and biological material in health databases and biobanks, and that these guidelines would help people control the use of their health data. The WMA believed this would be achieved by respecting the rights to autonomy, privacy and confidentiality which individuals should be entitled to and as set out in the guidelines. In this way they would be able to exercise control over the secondary use of their personal data and biological material, both in and beyond research.[1] The guidelines, named The Declaration of Taipei,[2] were approved by delegates at the WMA’s annual assembly in Taiwan.

Neonatal vitamin D status is not associated with later risk of type 1 diabetes: results from two large Danish population-based studies.

The aim of this work was to assess whether neonatal levels of 25-hydroxyvitamin D (25(OH)D) are associated with risk of developing type 1 diabetes before the age of 18years. Two large-scale studies with different designs-a case-cohort and a case-control-were conducted using Danish national register data and biobank material. Weighted Cox regression and conditional logistic regression were used to calculate HRs and ORs, respectively. The concentration of 25(OH)D was assessed from neonatal dried blood spots using highly sensitive liquid chromatography-tandem mass spectrometry. Quintiles of 25(OH)D3 were used in the main analyses. The case-cohort study included 912 type 1 diabetes cases and 2866 individuals without type 1 diabetes born in Denmark between 1981 and 2002 and followed up until the end of 2012. The case-control study included 527 matched case-control pairs born between 1981 and 1999 and followed up until May 2004. Both studies found no association between 25(OH)D3 levels and later risk of developing type 1 diabetes. The neonatal total 25(OH)D levels in the studies were low: 46% (case-cohort study) and 51% (case-control study) of individuals had 25(OH)D levels <25nmol/l. Our two large-scale national studies showed that 25(OH)D3 levels around the time of birth were not associated with later type 1 diabetes risk. Whether higher levels of 25(OH)D3 during pregnancy, acquired by higher doses of supplementation than are recommended today in most countries, could protect the offspring against type 1 diabetes cannot be ruled out by the present studies.

Biobanken – zwischen Forschungs- und Spenderinteressen

The establishment and operation of research biobanks are still not regulated by special laws. As a consequence, the acquisition, storage and use of biobank materials and data are only covered by quite general legal regulations. The way in which these rules are to be interpreted in relation to the specific problems of biobanks is rather controversial. The central question revolves around the tense relationship between the right to privacy of the donor and the academic freedom of the researchers. This article gives an overview of the current discussion and suggestions for practice.

Biobank Report: United Kingdom.

The United Kingdom is a leader in genomics research, and the presence of numerous types of biobanks and the linking of health data and research within the UK evidences the importance of biobank-based research in the UK. There is no biobank-specific law in the UK and research on biobank materials is governed by a confusing set of statutory law, common law, regulations, and guidance documents. Several layers of applicable law, from European to local, further complicate an understanding of privacy protections. Finally, biobanks frequently contain data in addition to the samples; the legal framework in the UK generally differentiates between data and samples and the form of the data affects the applicability of legal provisions. Biobanks must be licensed by the Human Tissue Authority; certain projects must be reviewed by Research Ethics Committees, and all projects are encouraged to be reviewed by them. Data Access Committees in biobanks are also common in the UK. While this confusing array of legal provisions leaves privacy protections in biobanking somewhat unclear, changes at the EU level may contribute to harmonization of approaches to privacy.

Tensions Between Policy and Practice in Finnish Biobank Legislation.

In 2012 a new biobanking law came into effect in Finland which, according to some, is one of the most comprehensive and broad national biobanking legislations in the world to date. The law covers both clinical and research collections and provides institutions with great flexibility in terms of transferring existing collections into a biobank. The law also includes provisions for individuals whose samples are stored in the biobank to request information regarding the studies in which the sample has been used. However, this provision also compels biobanks to provide an account of the significance of the research findings to their individual health. This legal provision has created tension between policy and practice in that most biobanks will struggle to interpret and apply this provision in practice. The relationship between the rights and needs to conduct research using biobank material and individual rights of access is sometimes unclear and fraught with interpretational challenges. The derivation of national interpretations of European Directives and Conventions gives rise to what I call interpretive regulatory dissonance. This is expected to be a challenge for harmonizing European and global biobanking activities in the future.

Abstract 556: Targeted Screening Reveals microRNAs of Therapeutic Interest in Radiotherapy-Induced Vascular Disease

Radiotherapy is an established therapeutic method in many different cancer types. The success of modern cancer treatment raises a new problem, namely radiotherapy-induced vascular disease (vRTx) or vasculopathy, which typically emerges in irradiated areas of the heart, neck and brain and manifests itself as coronary disease, heart failure or carotid stenosis. A chronic inflammatory response likely underlies vRTx. Like in atherosclerosis, complex biological processes such as vascular cell proliferation, remodeling, oxidative stress, and tumor growth factor β (TGF-β)-regulated nuclear factor kappa B (NF-κB) activation are involved. These processes are tightly regulated by a multitude of factors, which separately are difficult to influence. A set of miRNAs known to orchestrate these processes in other disease contexts likely also play a role in vRTx, and might be modifiable in order to treat or prevent RTx-induced vascular disease. We selected miR-29b, miR-125a, miR-126, miR-143, miR-145, miR-146a, miR-155, miR-221, miR-222, and miR-503 and determined their potential contribution to vRTx. Utilizing unique biobank material from microvascular free tissue transfer reconstructions, where irradiated (R) vascular tissue (branches from external carotid arteries and internal jugular veins) can be compared with non-irradiated control tissue (NR) within the same patient (n=10), we could precisely determine which miRNAs become deregulated after irradiation. Currently we are using a mouse model of local irradiation for further analysis and assessment of miRNA modulation effects. Apoe -/- mice are irradiated in the mediastinal area; control littermates were sham irradiated. We checked the expression of the 10 pre-selected miRNAs in R vs. NR vascular tissue (ascending and thoracic aorta). Of the 10 miRNAs, three (miR-29b up-; miR-143, miR-145 downregulated) were significantly differentially regulated between R and NR human arteries. miR-146a trended upward, but not significantly. Ongoing studies are aimed at histological analysis of mouse R vs. NR tissue, functional modulation of deregulated miRNAs in vivo to assess vRTx outcome, and in vitro assessment of miRNA expression differences in different human vascular cell lines exposed to radiation.

Regulating biobanking with children's tissue: a legal analysis and the experts' view.

Many current paediatric studies concern relationships between genes and environment and discuss aetiology, treatment and prevention of Mendelian and multifactorial diseases. Many of these studies depend on collection and long-term storage of data and biological material from affected children in biobanks. Stored material is a source of personal information of the donor and his family and could be used in an undesirable context, potentially leading to discrimination and interfering with a child's right to an open future. Here, we address the normative framework regarding biobanking with residual tissue of children, protecting the privacy interests of young biobank donors (0-12 years). We analyse relevant legal documents concerning storage and use of children's material for research purposes. We explore the views of 17 Dutch experts involved in paediatric biobank research and focus on informed consent for donation of leftover tissue as well as disclosure of individual research findings resulting from biobank research. The results of this analysis show that experts have no clear consensus about the appropriate rules for storage of and research with children's material in biobanks. Development of a framework that provides a fair balance between fundamental paediatric research and privacy protection is necessary.

Causal pathways for asthma (CASPAR) – MoBa “a happy hunting ground”

Large population-based research cohorts, together with national health registries and biobanks are core components in a modern infrastructure for knowledge. Along with the other Nordic countries, Norway has unique opportunities for high quality research based on cohorts, biobanks and registries. Cohorts, biobanks and registries provide a basis for discovering causes and mechanisms of disease as well as for following the development of disease, effects of treatment and consequences of disease. The purpose of this manuscript is to give a brief outline of a project that makes use of these unique opportunities by using data from The Norwegian Mother and Child cohort study (MoBa) to address research questions of common interest, and thus encourage other research groups to use this “happy hunting ground”.The present study, Causal Pathways for Asthma (CASPAR) funded by the Research Council of Norway, is a subproject of MoBa. The project is designed to take advantage of the potential for research on human biological material in biobanks, by coupling analysis results with data from health surveys, health registries and the health services. The present study is based on an ongoing collaboration between the Norwegian Institute of Public Health (NIPH), the National Institute of Environmental Health Sciences (NIEHS) in the US and several other national and international collaborators within The MoBa Asthma Group. The main aim of the study is to examine a number of hypothesis regarding in utero and early life exposures in relation to the development of different phenotypes of asthma and allergies in childhood.For the majority of children who become asthmatic and allergic, the differentiation of their immune system into an atopic phenotype probably begins before birth and is established within the first six years of life. This study will advance knowledge of the mechanisms whereby diet and environmental exposures influences gene expression to alter risk of atopic disease. The prime purpose is to build up new knowledge on asthma pathogenesis. There is a great need to develop a new paradigm of disease pathogenesis that takes advantages of applied molecular approaches to asthma and atopic diseases as it occurs in humans at different stages of development. This project takes advantage not only of the basic MoBa samples and infrastructure including links to other national health registries, but also a new national supplementary study of MoBa that includes measures of prenatal exposures in maternal plasma believed to have epigenetic influences on asthma/atopy development and data on genome wide methylation of cord blood DNA.

The Dutch Parelsnoer Institute - Neurodegenerative diseases; methods, design and baseline results

BackgroundThe Parelsnoer Institute is a collaboration between 8 Dutch University Medical Centers in which clinical data and biomaterials from patients suffering from chronic diseases (so called “Pearls”) are collected according to harmonized protocols. The Pearl Neurodegenerative Diseases focuses on the role of biomarkers in the early diagnosis, differential diagnosis and in monitoring the course of neurodegenerative diseases, in particular Alzheimer’s disease.The objective of this paper is to describe the design and methods of the Pearl Neurodegenerative Diseases, as well as baseline descriptive variables, including their biomarker profile.MethodsThe Pearl Neurodegenerative Diseases is a 3-year follow-up study of patients referred to a memory clinic with cognitive complaints. At baseline, all patients are subjected to a standardized examination, including clinical data and biobank materials, e.g. blood samples, MRI and cerebrospinal fluid. At present, in total more than 1000 patients have been included, of which cerebrospinal fluid and DNA samples are available of 211 and 661 patients, respectively. First descriptives of a subsample of the data (n = 665) shows that patients are diagnosed with dementia (45%), mild cognitive impairment (31%), and subjective memory complaints (24%).DiscussionThe Pearl Neurodegenerative Diseases is an ongoing large network collecting clinical data and biomaterials of more than 1000 patients with cognitive impairments. The project has started with data analyses of the baseline characteristics and biomarkers, which will be the starting point of future specific research questions that can be answered by this unique dataset.

Can Drying Be an Alternative Tissue Preservation Method in Cancer Research Biobanking?

The currently available methods for conservation of biobank material are mainly based on formalin fixation or the use of different freezing techniques. For molecular biological analysis, it is common to use quick freezing and low-temperature storage of the tissue materiel. This is a very energy-intensive and expensive method that requires advanced infrastructure, including monitoring and control procedures. The purpose of this work has been to study drying as an alternative process to cryogenic storage of undried biobank material, especially for use in cancer research groups. Fast freezing has been shown to be suitable to preserve the integrity of RNAs, while traditional formalin fixation preserves proteins and thus morphology in a good way. Various fresh-harvested murine tissues, such as lung, heart, skeletal muscle, liver, and kidney, were quickly frozen in liquid nitrogen and then subsequently dried at +5°C and −10°C, respectively, in a heat pump dryer. After drying, the RNA integrity was measured. The dried material was then stored for five months at +4°C and −20°C in commercial refrigerators, with subsequent measurement of RNA integrity. Dried materials were also evaluated with light microscopy and by electron microscopy with respect to tissue and cell structure. The same pattern was found for all five murine tissues. We conclude that drying at temperatures below 0°C is most careful to preserve the RNA integrity, with approximately the same RIN score of dried and non-dried samples for all five tissues. What characterized the general pattern of stored samples is that drying leads to a preservation of RNA integrity. Moreover, architecture in tissue resembled normal sections prepared from fresh tissue. In some places in the rim of the tissue sample, the lung tissue revealed alveolar-like morphology. In the electron microscope, few organelles other than the nuclei could be identified. Drying of biological material is a promising and cost-effective method for biobanks that store tissue, compared to cryogenic storage of undried material. Degradation of RNA, measured by the RIN number, is a critical factor in storing biobank tissue. In low-temperature dried material, the RIN factor is at the same level as storage of undried material at cryogenic temperatures, which is the common way of storing biobank material today. In this study, a heat pump dryer was used successfully to establish drying temperatures below and above the freezing point of the material. Further work has to be done in order to study different drying methods, drying conditions, and drying costs.

Analysis of the research sample collections of Uppsala biobank.

Uppsala Biobank is the joint and only biobank organization of the two principals, Uppsala University and Uppsala University Hospital. Biobanks are required to have updated registries on sample collection composition and management in order to fulfill legal regulations. We report here the results from the first comprehensive and overall analysis of the 131 research sample collections organized in the biobank. The results show that the median of the number of samples in the collections was 700 and that the number of samples varied from less than 500 to over one million. Blood samples, such as whole blood, serum, and plasma, were included in the vast majority, 84.0%, of the research sample collections. Also, as much as 95.5% of the newly collected samples within healthcare included blood samples, which further supports the concept that blood samples have fundamental importance for medical research. Tissue samples were also commonly used and occurred in 39.7% of the research sample collections, often combined with other types of samples. In total, 96.9% of the 131 sample collections included samples collected for healthcare, showing the importance of healthcare as a research infrastructure. Of the collections that had accessed existing samples from healthcare, as much as 96.3% included tissue samples from the Department of Pathology, which shows the importance of pathology samples as a resource for medical research. Analysis of different research areas shows that the most common of known public health diseases are covered. Collections that had generated the most publications, up to over 300, contained a large number of samples collected systematically and repeatedly over many years. More knowledge about existing biobank materials, together with public registries on sample collections, will support research collaborations, improve transparency, and bring us closer to the goals of biobanks, which is to save and prolong human lives and improve health and quality of life.

Motivations and barriers to sharing biological samples: a case study.

One of the most significant impediments to the current goals of genomic research is the limited availability of high quality biological samples. Despite efforts to increase both the quality and quantity of samples collected, access to such samples remains limited. This may be due, at least in part, to a general reluctance of biobanking professionals, clinicians, and researchers to share biological specimens with others. Ethnographic methods were used in a biobank setting to explore professionals’ perspectives toward and practices of sharing samples. Several motivations and barriers to sharing that may influence research practice were identified. Contrary to existing literature that suggests that professionals are unlikely to share samples with one another, the participants of this study were open to and supportive of sharing samples for research. However, clear communication and effective infrastructure are needed to support the distribution of biobank materials.

CPC-072 Inclusion of Pharmacogenetics Studies, Patient-Reported Outcomes and Cost Measures in Clinical Trials; Variables Added in Recent Years

BackgroundPharmacogenetic studies analyse the variability of drug response; patient-reported outcome (PRO) measures complement traditional measures. Pharmacoeconomic studies tell us the efficiency of different therapeutic alternatives.Purpose To evaluate the use of...

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability

BackgroundThe objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits.MethodsClinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources.ResultsAn IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients.ConclusionsWe provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market.

The Diabetes Pearl: Diabetes biobanking in The Netherlands

BackgroundType 2 diabetes is associated with considerable comorbidity and severe complications, which reduce quality of life of the patients and require high levels of healthcare. The Diabetes Pearl is a large cohort of patients diagnosed with type 2 diabetes, covering different geographical areas in the Netherlands. The aim of the study is to create a research infrastructure that will allow the study of risk factors, including biomarkers and genetic determinants for severe diabetes complications.Methods/designBaseline examinations began November 2009 and will continue through 2012. By the end of 2012, it is expected that 7000 patients with type 2 diabetes will be included in the Diabetes Pearl cohort. To ensure quality of the data collected, standard operation procedures were developed and used in all 8 recruitment centers. From all patients who provide informed consent, the following information is collected: personal information, medication use, physical examination (antropometry, blood pressure, electrocardiography (ECG), retina photographs, ankle-brachial index, peripheral vibration perception), self-report questionnaire (socio-economic status, lifestyle, (family) history of disease, and psychosocial well-being), laboratory measurements (glucose, A1c, lipid profile, kidney function), biobank material (storage of urine and blood samples and isolated DNA). All gathered clinical data and biobank information is uploaded to a database for storage on a national level. Biobanks are maintained locally at all recruitment centers.DiscussionThe Diabetes Pearl is large-scale cohort of type 2 diabetes patients in the Netherlands aiming to study risk factors, including biomarkers and genetic markers, for disease deterioration and the development of severe diabetes complications. As a result of the well-designed research design and the national coverage, the Diabetes Pearl data can be of great value to national and international researchers with an interest in diabetes related research.

Patient consent to the use of genetic material in Poland and worldwide

Currently developed and functioning models of so-called informed consent seem to be insufficient in case of the application, handling, or use of the genetic material, and may lead to over-interpretation or misinterpretation of the formal rules for using the stored genetic material. In medical practice, the aim is to obtain patient’s consent to any interventions not only therapeutic, but also other, having a diagnostic character. These interventions often lacking direct medicinal goal, are often associated with a high risk to the health of the patient, who should be informed about that. The most common form of consent is called informed consent, in which the emphasis is primarily put on the patient’s understanding of what needs to be signed on a specific form. The informed consent is a fundamental element of the subjective permission to submit to any intervention that interferes in bodily-mental realm of man. Currently valid provisions contained in a number of non-synchronized with each other regulatory acts selectively treat the concept of informed consent in the case of working with genetic material (the use, processing) and its terminal (temporary) use. The issue of storing genetic material in biobanks (both worldwide and in Poland) does not have a leading and promoting solution, and the present standards specifying the type and nature of consent are rather formal parts of different formal acts than a single standardized model. There is a need to have a new uniform interpretation of the law, which could be the basis for the concept of consent as a declaration of intent for the use of genetic material. The report presents a formal-legal approach to the issue of the concept and scope of consent as a declaration of intent, in the case of genetic material use. The currently existing in Poland and in the world legal solutions of the interpretations of the concept and scope of consent, as a declaration of intent for the use of genetic material, have been analyzed. The actual and hypothetical disputable and interpretation issues have been discussed. The paper presents original solution clarifying the issues of informed consent, which can be used in practice.