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PubMed2006

The biobank of the Norwegian Mother and Child Cohort Study: a resource for the next 100 years.

INTRODUCTION: Long-term storage of biological materials is a critical component of any epidemiological study. In designing specimen repositories, efforts need to balance future needs for samples with logistical constraints necessary to process and store samples in a timely fashion. OBJECTIVES: In the Norwegian Mother and Child Cohort Study (MoBa), the Biobank was charged with long-term storage of more than 380,000 biological samples from pregnant women, their partners and their children for up to 100 years. METHODS: Biological specimens include whole blood, plasma, DNA and urine; samples are collected at 50 hospitals in Norway. All samples are sent via ordinary mail to the Biobank in Oslo where the samples are registered, aliquoted and DNA extracted. DNA is stored at -20 degrees C while whole blood, urine and plasma are stored at -80 degrees C. RESULTS: As of July 2006, over 227,000 sample sets have been collected, processed and stored at the Biobank. Currently 250-300 sets are received daily. An important part of the Biobank is the quality control program. CONCLUSION: With the unique combination of biological specimens and questionnaire data, the MoBa Study will constitute a resource for many future investigations of the separate and combined effects of genetic, environmental factors on pregnancy outcome and on human morbidity, mortality and health in general.

Adult↗
PubMed2006

Should donors be allowed to give broad consent to future biobank research?

Large international biobank studies can make substantial contributions to scientific research by validation of the biological importance of previous research and by identification of previously unknown causes of disease. However, regulations for patient consent that are too strict and discrepancies in national policies on informed consent might hinder progress. Therefore, establishment of common ground for ethical review of biobank research is essential. In this essay, broad consent is defined on a scale between strictly specified (eg, for a specific study) and blanket consent (ie, with no restrictions regarding the purpose of the research). Future research includes that which might not be planned or even conceptualised when consent is obtained. In conclusion, broad consent and consent for future research are valid ethically and should be recommended for biobank research provided that: personal information related to research is handled safely; donors of biological samples are granted the right to withdraw consent; and new research studies or changes to the legal or ethical authority of a biobank are approved by an ethics-review board.

Confidentiality↗
PubMed2005

Potential harms, anonymization, and the right to withdraw consent to biobank research.

This paper discusses the potential harms involved in biobank research and how ethical review, informed consent, withdrawals, and anonymization of samples should be handled in the light of these harms. There is less risk involved in biobank research than in human subject research; it should therefore be treated differently. In our view, anonymization should not be an automatically permissible response to requests for withdrawal. Nor should a request for withdrawal necessarily stop research on identifiable samples. Apart from not being particularly appropriate for protecting the interests of individuals, anonymization of samples has a negative impact on research. We suggest that the current view on withdrawal from research, supported by the Declaration of Helsinki and subsequent ethical guidelines, be abandoned in the context of biobank research and be replaced by an approach inspired by the Nuremberg Code. This approach requires those wishing to withdraw their samples from research to present sufficient reason for doing so. Our interpretation of 'sufficient reason' includes all those involving genuine, deeply felt concerns that are not based on misconceptions. Still, this underlines the fact that we all share a responsibility for health research and that no one should take withdrawal from biobank research lightly.

Biological Specimen Banks↗
PubMed2004

Study of the involvement of research ethics committees in the constitution and use of biobanks in France.

Concerns are emerging about the protection of individuals who take part in genetic research involving biobanks. We used several items of a questionnaire sent to 48 French research ethics committees (RECs) to investigate the means by which they evaluate the constitution and use of biobanks, and the elements on which conclusions were based. Most RECs felt they should evaluate the constitution of biobanks in protocols, but not all did so in practice. Harmonization of the competence of RECs for evaluating biobanks is required, particularly concerning information, consent, the duration of sample conservation and the communication of research results. Our results, together with those of others, demonstrate the need to develop rules and guidelines based on common ethical approaches, particularly in the European environment.

Bioethical Issues↗
PubMed2001

Biosamples, genomics, and human rights: context and content of Iceland's Biobanks Act.

In recent years, human DNA sampling and collection has accelerated without the development of enforceable rules protecting the human rights of donors. The need for regulation of biobanking is especially acute in Iceland, whose parliament has granted a for-profit corporation, deCODE Genetics, an exclusive license to create a centralized database of health records for studies on human genetic variation. Until recently, how deCODE Genetics would get genetic material for its genotypic-phenotypic database remained unclear. However, in May 2000, the Icelandic Parliament passed the Icelandic Biobanks Act, the world's earliest attempt to construct binding rules for the use of biobanks in scientific research. Unfortunately, Iceland has lost an opportunity for bringing clear and ethically sound standards to the use of human biological samples in deCODE's database and in other projects: the Biobanks Act has extended a notion of "presumed consent" from the use of medical records to the use of patients' biological samples; worse, the act has made it possible--perhaps likely--that a donor's wish to withdraw his/her sample will be ignored. Inadequacies in the Act's legislative process help account for these deficiencies in the protection of donor autonomy.

Blood Specimen Collection↗
PubMed1998

[DNA biobanks. Establishment and maintenance].

The need for extraction, purification and storage of DNA in biobanks is increasing. DNA may be obtained from mouth brush water, guthrie cards, tissue biopsies or venous blood. Sampling conditions depend on the method used for procurement of DNA, e.g. DNA extraction or Ebstein Barr Virus transformation. Exact knowledge about the validity and stability of DNA stored in buffer is still insufficient. Biobanks at hospitals and at research departments are regulated by the Danish Private Registers, etc. Act. Research projects based on DNA biobanks should be notified to the Danish Data Protection Agency and approved by the local ethical committee. Discount, economic, and business class set-ups are different practical and financial models for the structure of DNA biobanking.

Computer Security↗
PubMed2025

Streamlining large-scale genomic data management: Insights from the UK Biobank whole-genome sequencing data.

Biobank-scale whole-genome sequencing (WGS) studies are increasingly pivotal in unraveling the genetic bases of diverse health outcomes. However, managing and analyzing these datasets' sheer volume and complexity presents significant challenges. We highlight the annotated genomic data structure (aGDS) format, substantially reducing the WGS data file size while enabling seamless integration of genomic and functional information for comprehensive WGS analyses. The aGDS format yielded 23 chromosome-specific files for the UK Biobank 500k WGS dataset, occupying only 1.10 tebibytes of storage. We develop the vcf2agds toolkit that streamlines the conversion of WGS data from VCF to aGDS format. Additionally, the STAARpipeline equipped with the aGDS files enabled scalable, comprehensive, and functionally informed WGS analysis, facilitating the detection of common and rare coding and noncoding phenotype-genotype associations. Overall, the vcf2agds toolkit and STAARpipeline provide a streamlined solution that facilitates efficient data management and analysis of biobank-scale WGS data across hundreds of thousands of samples.

Humans↗
PubMed2024

Biobank-wide association scan identifies risk factors for late-onset Alzheimer's disease and endophenotypes.

Rich data from large biobanks, coupled with increasingly accessible association statistics from genome-wide association studies (GWAS), provide great opportunities to dissect the complex relationships among human traits and diseases. We introduce BADGERS, a powerful method to perform polygenic score-based biobank-wide association scans. Compared to traditional approaches, BADGERS uses GWAS summary statistics as input and does not require multiple traits to be measured in the same cohort. We applied BADGERS to two independent datasets for late-onset Alzheimer's disease (AD; n=61,212). Among 1738 traits in the UK biobank, we identified 48 significant associations for AD. Family history, high cholesterol, and numerous traits related to intelligence and education showed strong and independent associations with AD. Furthermore, we identified 41 significant associations for a variety of AD endophenotypes. While family history and high cholesterol were strongly associated with AD subgroups and pathologies, only intelligence and education-related traits predicted pre-clinical cognitive phenotypes. These results provide novel insights into the distinct biological processes underlying various risk factors for AD.

Alzheimer Disease↗
PubMed2005

The ethics of research using biobanks: reason to question the importance attributed to informed consent.

BACKGROUND: During the past decade, the use of stored tissue has become an object of increased ethical query. A Swedish biobank and a biotech company have been praised for solving the ethical problems with explicit informed consent procedures, and we decided to investigate donors' perceptions of the system. METHODS: A questionnaire was sent to a randomized sample of 1200 donors who had donated blood and signed informed consent forms. RESULTS: The response rate was 80.9%. Of the respondents, 64.5% were aware that they had consented to donate a blood sample, 55.4% thought that they had consented to donate phenotypic information, and 31.6% believed that they could withdraw their consent. Among respondents, 3.9% considered informing donors about the research objective as the most important ethical issue in relation to biobanks, and 5.6% were unsatisfied with the information they had been given. There was 85.9% acceptance of surrogate decision making by regional research ethics committees. CONCLUSIONS: Considering that the donors in this study were not always aware of their donation but generally were not unsatisfied with the information they had received, and that they did not rate being informed about the research objective as an important issue, informed consent seems to be an inadequate measure of public acceptance of biobank-based research.

Biotechnology↗
PubMed2006

Human tissue samples and ethics--attitudes of the general public in Sweden to biobank research.

PURPOSE: To survey the attitudes of the general public in Sweden to biobank research and to discuss the findings in the light of some well-known ethical principles. METHODS: A questionnaire was used to survey the opinions of the general public in Sweden, and an ethical analysis (using the principles of autonomy, non-maleficence, beneficence and justice) was performed to discuss the possible conditions of such research. FINDINGS: Between 3 and 9% answered that they did not want their samples to be collected and stored in a biobank. Many respondents required information about the purpose of the research and wanted to be able to consent or refuse. About one third of the respondents said they would have answered differently if financial gain was involved and those who commented indicated a more negative attitude. The principle of autonomy maintains that the right to self-determination should be respected, and the principles of non-maleficence and beneficence that the probable harms and benefits resulting from a particular project by using samples from a biobank should be balanced. The general public disagree about how these principles are to be balanced. INTERPRETATION: In the light of the findings different interpretations of the situation as well as possible alternatives are discussed in this paper.

Adult↗
PubMed2006

Combining efficiency and concerns about integrity when using human biobanks.

In the debate about human bio-sampling the interests of patients and other sample donors are believed to stand against the interests of scientists and of their freedom of research. Scientists want efficient access to and use of human biological samples. Patients and other donors of blood or tissue materials want protection of their integrity. This dichotomy is reflected in the Swedish law on biobanks, which came into effect 1 January 2003. In this article I argue that if the basic interest of scientists using human biological samples is in increasing knowledge and developing better treatments, and if the concept 'integrity' is properly understood, then sample donors should also be interested in promotion of efficiency as well as in the protection of their integrity. The basic premise of this argument is that donors of samples have interests related to the donation and use of samples as well as to the use of the results of the research, that is, new medical products and treatments. They have a role both as donors or participants in research and as end users of the research. I conclude that if (i) access to information acquired through biobank research is strictly limited to researchers, (ii) the information is protected by secrecy safeguards through coding and (iii) the procedures governing the research are open to public and democratic control, then most research using human biobanks may be carried out on the basis of making general information available when collecting biological samples, without further contact with participants.

Access to Information↗
PubMed2004

Governing UK Biobank: the importance of ensuring public trust.

In the autumn of 2003, UK Biobank published the first draft of its Ethics and Governance Framework. Subsequently, this document has been available for interested parties to comment on and the UK Biobank Board of Directors is expected to adopt the final version in 2004. Here, we aim to contribute to this process and highlight to a wider audience some of the inconsistencies in the issues of consent, governance and right of withdrawal that emerge from the draft of the Framework. These issues will have implications for securing the public trust and long-term support that the success of the project depends on. Therefore, they must be considered carefully because the UK Biobank will be the first ever genetic database of a general population of this size to become operational, and will be used as a model for other projects of this kind.

Biological Specimen Banks↗
PubMed2006

Biobanking of fresh frozen tissue: RNA is stable in nonfixed surgical specimens.

Molecular tools for tissue profiling, such as expression microarrays and real-time PCR, generally require collection of fresh frozen tissues as sources of high-quality RNA. The fragile nature of RNA prompted us to examine the effects of storage time and transport conditions with regard to RNA integrity and gene expression in nonfixed surgical human specimens. At surgery, fresh normal tonsil and colon tissue was cut into pieces and snap frozen. Additional fresh tissue pieces were (i) left at room temperature, (ii) kept on ice, (iii) in normal saline or (iv) in a commercial RNA-stabilizing buffer (RNAlater) and snap frozen after 0.5, 1, 3, 6 and 16 h. Structural RNA integrity was analysed by microchip electrophoresis. Surprisingly, RNA remained stable in both tissue types under all conditions tested for up to 6-16 h. Gene expression by real-time PCR of cfos, HIF1alpha, Bcl2, PCNA, TGFbeta1 and SMAD7 was analysed at different storage time points in tonsil tissue. Expression levels were essentially stable when samples were kept on ice, while marked regulation of single genes was observed during storage at room temperature, in normal saline and in RNAlater. Furthermore, we analysed selected tissue types from the local biobank representing 47 normal and malignant tissues transported on ice for up to 2-3 h before biobanking. RNA prepared from 45 of the 47 samples exhibited distinct ribosomal peaks indicating intact RNA. This study shows that RNA degradation is a minor problem during handling of fresh human tissue before biobanking. Our data indicate that nonfixed tissue specimens may be transported on ice for hours without any major influence on RNA quality and expression of the selected genes. However, further studies are warranted to clarify the impact of transport logistics on global gene expression.

Base Sequence↗
PubMed2004

The social and ethical issues of post-genomic human biobanks.

Biobanking - the organized collection of biological samples and associated data - ranges in scope from small collections of samples in academic or hospital settings to large-scale national repositories. Biobanks raise many ethical concerns, to which authorities are responding by introducing specific regulations. Genomics research, which thrives on the sharing of samples and information, is affected by two prominent ethical questions: do ethical principles prevent or promote the sharing of stored biological resources? How does the advent of large-scale biobanking alter the way in which ethical issues are addressed?

Bioethics↗
PubMed2026

Recall-by-genotype of neurodevelopmental disorder copy number variants in a multi-ancestry, healthcare-system biobank.

Clinical biobanks linking electronic health records (EHRs) with genotype data enable the study of genomic risk factors in real-world populations. However, recall-by-genotype (RbG) of psychiatric risk variants in diverse healthcare-system biobanks remains scarce. Leveraging BioMe, a multi-ancestry biobank within the Mount Sinai Health System, we recalled carriers of rare copy number variants (CNVs) that confer increased risk for neurodevelopmental disorders (NDDs) to establish empirical benchmarks for RbG implementation. We recontacted 892 participants: 335 NDD CNV carriers, 217 individuals with schizophrenia without NDD CNVs, and 340 neurotypical controls without NDD CNVs. Participants completed clinical and cognitive assessments. Overall, 18% of recontacted participants responded to recruitment, and 8% completed the study: 30 NDD CNV carriers, 20 individuals with schizophrenia, and 23 controls. The mean age was 48.8 years, 66% were female, and self-reported ancestry was 37% African, 34% Hispanic, and 26% European. Seventy percent of NDD CNV carriers had at least one neuropsychiatric or developmental condition, including mood or anxiety disorders (40%). Among 22 NDD CNV carriers at loci implicated in impaired cognition, performance was lower than controls on Digit Span Backward (β = -1.76, FDR = 0.04) and Digit Span Sequencing (β = -2.01, FDR = 0.04). NDD CNV carriers also outperformed the schizophrenia group on verbal learning (β = 4.5, FDR = 0.05). Recall of individuals-including those with psychiatric illness-yielded phenotypes not captured in EHRs and provides empirical benchmarks relevant to RbG implementation and precision psychiatry in diverse healthcare systems.

Journal Article↗
PubMed2025

An Annotated Biobank of Triple-Negative Breast Cancer Patient-Derived Xenografts Features Treatment-Naïve and Longitudinal Samples during Neoadjuvant Chemotherapy.

UNLABELLED: Triple-negative breast cancer (TNBC) that fails to respond to neoadjuvant chemotherapy (NACT) can be lethal. Developing effective strategies to eradicate chemoresistant disease requires experimental models that recapitulate the heterogeneity characteristic of TNBC. To that end, we established a biobank of 92 orthotopic patient-derived xenograft (PDX) models of TNBC from the tumors of 75 patients enrolled in A Robust TNBC Evaluation fraMework to Improve Survival clinical trial (ARTEMIS, NCT02276443), including 12 longitudinal sets generated from serial patient biopsies collected throughout NACT treatment and from metastatic disease. Models were established from both chemosensitive and chemoresistant tumors, and nearly 30% of the PDX models were capable of metastasizing to the lungs. Comprehensive molecular profiling demonstrated conservation of genomes and transcriptomes between patient and corresponding PDX tumors, with representation of all major transcriptional subtypes. Transcriptional changes observed in the longitudinal PDX models highlighted dysregulation in pathways associated with DNA integrity, extracellular matrix interactions, the ubiquitin-proteasome system, epigenetics, and inflammatory signaling. These alterations revealed a complex network of adaptations associated with chemoresistance. Overall, this PDX biobank provides a valuable tool for tackling the most pressing issues facing the clinical management of TNBC. SIGNIFICANCE: The development of a patient-derived xenograft biobank that comprehensively captures the genomic and transcriptional diversity of triple-negative breast cancer promises to be a robust resource to investigate and overcome chemoresistance and metastasis.

Animals↗
PubMed2005

Will investments in large-scale prospective cohorts and biobanks limit our ability to discover weaker, less common genetic and environmental contributors to complex diseases?

Increasing the size of prospective cohorts and biobanks is one approach to discovering previously unknown contributors to complex diseases, but it may come at the price of concealing contributors that are less common across all the participants in those larger studies and of limiting hypothesis generation. Prospective cohorts and biobanks constitute significant, long-term investments in research infrastructure that will have ongoing consequences for opportunities in biomedical research for the foreseeable future. Thus, it is important to think about how these major additions to research infrastructure can be designed to be more productive in generating hypotheses for novel environmental contributors to complex diseases and to help identify genetic and environmental contributors that may not be common across the larger samples but are more frequent within local or ancestral subsets. Incorporating open-ended inquiries and qualitative information about local communal and ecologic contexts and the political, economic, and other social structures that affect health status and outcome will enable qualitative hypothesis generation in those localized contexts, as well as the collection of more detailed genealogic and family health history information that may be useful in designing future studies. Using communities as building blocks for larger cohorts and biobanks presents some practical and ethical challenges but also enhances opportunities for interdisciplinary, multilevel investigations of the multifactorial contributors to complex diseases.

Disease↗
PubMed2026

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses.

Electronic health record (EHR)-linked biobanks generate unprecedented genomic and phenotypic datasets, but their scientific utility is constrained by data fragmentation across institutional silos and incompatible computing infrastructures, forcing researchers to rewrite ad-hoc scripts for each new environment. We present the PMBB Geno-Pheno Toolkit, a suite of modular Nextflow pipelines for biobank-scale association analyses. This note focuses on the toolkit's SAIGE family of pipelines - supporting genome-wide (GWAS), exome-wide (ExWAS), and phenome-wide (PheWAS) association testing - together with the companion GWAMA and ExWAS meta-analysis pipelines that enable cross-biobank replication. All components are containerized (Docker/Apptainer) and orchestrated with Nextflow, allowing the same workflows to run unmodified on local HPC clusters, cloud platforms, and the All of Us Research Workbench. Complementary toolkit pipelines for PLINK-based GWAS, polygenic scoring, LD-based clumping, and phenotype harmonization are also available and briefly noted.

Journal Article↗