What went right during the COVID crisis: The capabilities of local actors and lasting innovations in oncology care and research.

This article will elaborate how oncology care and research was adapted during the COVID pandemic in the Metropole of Lyon (France), including the lasting innovations that came out of the crisis. The research method involved 22 semi-structured qualitative interviews of healthcare professionals, managers, and researchers in the Lyon, France region coming from both public and private academic hospitals. The interviews took place from February 2021-December 2022 in order to assess the long-term adaptations and innovations in cancer care organization in the post-COVID era. The main results show adaptations and innovations in 1) new processes and resources to facilitate disciplinary and interdisciplinary work; 2) harmonization and streamlining of patient journeys. In the discussion section, we will mobilize the capabilities approach, an interdisciplinary social sciences approach that focuses on the capabilities of persons to be and to do, to elaborate the conditions by which local actors were able to be agile, to adapt and to innovate in spite of the healthcare emergency and in coherence with their professional and personal values.

Paediatric biobanking for health: The ethical, legal, and societal landscape.

Biobanks play a central role in pediatric translational research, which deals primarily with genetic data from sample-based research. However, participation of children in biobanking has received only limited attention in the literature, even though research in general and in clinical trials in particular have a long history in involving minors. So, we resolved to explore specific challenging ethical, legal, and societal issues (ELSI) in the current pediatric biobanking landscape to propose a way forward for biobanking with children as partners in research. Methodologically, we first established the accessibility and utilization of pediatric biobanks, mainly in Europe. This was supported by a literature review related to children's participation, taking into account not only academic papers but also relevant guidelines and best-practices. Our findings are discussed under five themes: general vulnerability; ethical issues-balancing risks and benefits, right to an open future, return of results including secondary findings; legal issues-capacity and legal majority; societal issues-public awareness and empowerment; and responsible research with children. Ultimately, we observed an on-going shift from the parents'/guardians' consent being a sine-qua-non condition to the positive minor's agreement: confirming that the minor is the participant, not the parent(s)/guardian(s). This ethical rethinking is paving the way toward age-appropriate, dynamic and participatory models of involving minors in decision-making. However, we identified a requirement for dynamic tools to assess maturity, a lack of co-produced engagement tools and paucity of shared best practices. We highlight the need to provide empowerment and capability settings to support researchers and biobankers, and back this with practical examples. In conclusion, equipping children and adults with appropriate tools, and ensuring children's participation is at the forefront of responsible pediatric biobanking, is an ethical obligation, and a cornerstone for research integrity.

A Review of Regulatory Frameworks Governing Biobanking in the Low and Middle Income Member Countries of BCNet.

Biomedical research based on the sharing and use of ever larger volumes of samples and data is increasingly becoming an essential component of scientific discovery. The success of biobanking and genomic research is dependent on the broad sharing of resources for use by investigators. However, important ethical challenges need to be addressed for the sample and data sharing to be successful. Despite low- and middle-income countries (LMICs) carrying a higher burden of disease, biomedical research conducted to date has mainly focused on high-income countries. In order for LMICs to benefit from the advances in such research, normative documents (such as laws and guidelines) play a significant role in allowing LMIC projects to partake and be represented in global biomedical research. The administration and management of the ethical aspects of biobanking, including informed consent, are key components in ensuring that samples and data can legally and ethically be used and shared. As part of its support to the LMIC biobanks, the International Agency for Research on Cancer (IARC) established a biobank and population cohort building network (BCNet) in 2013 with the aims of providing support (including education and training) and facilitating the development and improvement of biobanking infrastructure in LMICs. A comparative analysis of the laws and guidelines in BCNet countries was completed to highlight some of the ethical and legal issues related to biobanking in LMICs and to identify examples of effective systems of governance already in operation.

Extending the Minimum Information About BIobank Data Sharing Terminology to Describe Samples, Sample Donors, and Events.

Introduction: The Minimum Information About BIobank data Sharing (MIABIS) was initiated in 2012. MIABIS aims to create a common biobank terminology to facilitate data sharing in biobanks and sample collections. The MIABIS Core terminology consists of three components describing biobanks, sample collections, and studies, in which information on samples and sample donors is provided at aggregated form. However, there is also a need to describe samples and sample donors at an individual level to allow more elaborate queries on available biobank samples and data. Therefore the MIABIS terminology has now been extended with components describing samples and sample donors at an individual level. Materials and Methods: The components were defined according to specific scope and use cases by a large group of experts, and through several cycles of reviews, according to the new MIABIS governance model of BBMRI-ERIC (Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium). The guiding principles applied in developing these components included the following terms: model should consider only samples of human origin, model should be applicable to all types of samples and all sample donors, and model should describe the current status of samples stored in a given biobank. Results: A minimal set of standard attributes for defining samples and sample donors is presented here. We added an "event" component to describe attributes that are not directly describing samples or sample donors but are tightly related to them. To better utilize the generic data model, we suggest a procedure by which interoperability can be promoted, using specific MIABIS profiles. Discussion: The MIABIS sample and donor component extensions and the new generic data model complement the existing MIABIS Core 2.0 components, and substantially increase the potential usability of this terminology for better describing biobank samples and sample donors. They also support the use of individual level data about samples and sample donors to obtain accurate and detailed biobank availability queries.

Centralization of the IARC Biobank: Combining Multiple Sample Collections into a Common Platform.

The International Agency for Research on Cancer (IARC) is the World Health Organization's (WHO) cancer research agency. The agency conducts research on cancer with worldwide collaborations, adopting a multidisciplinary approach of epidemiology and laboratory-based studies on cancer causes, as well as preventive interventions. The IARC Biobank stores multiple collections of samples and conducts preanalytical services for studies conducted worldwide in support of the research activities. Traditionally, the multiple collections from these studies were managed by the individual research groups in different project-specific databases. In 2010, a program to centralize sample collections into a single platform was initiated by adopting a common database with the introduction of a minimum dataset for sample collections received at IARC. The process involved checking data files, verifying the storage location of samples, conducting data harmonization, and importing or migrating existing data from project-specific spreadsheets and databases into the common database. In addition to the creation of a common biobank database and an up-to-date inventory of IARC's biological resources, a governance structure was established. The creation of the Biobank Steering Committee and the adoption of an access policy is to facilitate and guide the sharing of IARC's resources in a transparent manner, while taking into account Ethical, Legal, and Social Issues.

Barriers and Opportunities in Consent and Access Procedures in Low- and Middle-Income Country Biobanks: Meeting Notes from the BCNet Training and General Assembly.

As biobanking research in low- and middle-income countries (LMICs) continues to grow, novel legal and policy considerations have arisen. Also, while an expansive literature has developed around these issues, the views and concerns of individual researchers in these contexts have been less actively studied. These meeting notes aim to contribute to the growing literature on biobanking in LMICs by communicating a number of challenges and opportunities identified by biobank researchers themselves. Specifically, we describe concerns that emerge in consent and access policy domains. First, we present a review of the literature on distinct policy and legal concerns faced in LMICs, giving special attention to the general absence of practitioner perspectives. From there, we outline and discuss considerations that were raised by meeting participants at a Biobank and Cohort Building Network (BCNet) Ethical, Legal, and Social Issues training program. We conclude by proposing that the unique perspectives of biobank researchers in LMICs should be given serious attention and further research on these perspectives should be conducted.

Training the Next Generation of Biobankers: A Two-Year Master's Course in the Management of Biobanks.

The growing complexity of biobanking requires dedicated professional staff who are trained in multiple aspects of the biobanking process, including technical, managerial, regulatory, and ethical aspects, and who have a good understanding of the challenges of biospecimen research, but also of the challenges related to the sustainability of future biobanks. Up to the present, biobanking staff have been trained in an ad-hoc manner, usually through specific short duration courses, for example, summer schools. In this article, we describe the development/establishment of a systematic 2-year training program at the Master level intended for students with a background in life sciences and providing them with a professional qualification as a "Biobank Manager." This course was developed in 2010 as a joint initiative of the Catholic University of Lyon and the University of Nice-Sophia-Antipolis (France). The multidisciplinary training offers courses on biobank design and infrastructure, on pre- and postanalytical processing of different types of biospecimens, on protocol development, on ethical and regulatory aspects, as well as an introduction to epidemiology and translational research. In parallel, students also receive generic training in management, budget planning, data analysis, and statistics, as well as 11 months of hands-on training in various biobanks handling human, animal, plant, or microbial biospecimens. Four groups of students have graduated since 2012, for a total of 44 students, who all found jobs in biobanking within 6 months of graduation.

Infrastructure and facilities for human biobanking in low- and middle-income countries: a situation analysis.

OBJECTIVE: To collect information on biobanking facilities in low- and middle-income countries (LMICs) as a first step towards establishing an LMIC biobank and cohort building network (BCNet) to support research, with a focus on cancer control. METHOD: Sixty centres were identified from sources including cancer centres, universities, hospitals, and public health facilities and invited to participate in a survey between December 2012 and March 2013. RESULTS: Of the 27 centres (45%) that responded, most have existed for <10 years. They store between 1,000 and 1,000,000 research samples as well as samples remaining after clinical diagnosis. Sample storage is mostly in freezers, although 45% (9/20) of the centres do not have regular access to electricity. Biobank managers, sample management systems, and mechanisms for follow-up using linkages are uncommon. Many (80%; 21/26) of the centres have regulations to govern research, but regulations for the use of biobank resources (samples and data) are not well developed. CONCLUSIONS: Biobanking facilities are being developed in LMICs. Shortcomings in international visibility, sample sharing regulations, standardization, quality assurance, and sample management systems could be alleviated by international networking. Stakeholders need to work together to increase access to high-quality biological resources for scientific research.

Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.

The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as "warm ischemia". Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC) and 3 lung carcinomas (LC) cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN) revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of -3.5%/hr (95% CI: -7.0%/hr to 0.1%/hr; p = 0.054). In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5) and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1) was identified (FDR <0.05). Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.

Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.

The European Prospective Investigation into Cancer and nutrition (EPIC) is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS) and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88%) performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.

The European Prospective Investigation into Cancer and Nutrition biobank.

The European Prospective Investigation into Cancer and Nutrition (EPIC) is a multi-center prospective cohort study designed to investigate the relationship between nutrition and cancer, with the potential for studying many etiologic or genetic factors as well as other disease end-points. The study includes 521,448 participants (367,993 women and 153,455 men, mostly aged 35-70 years) recruited in 23 centers located in ten European countries, who are followed up for cancer incidence and cause-specific mortality for several decades. At enrolment, which took place between 1992 and 2000 at each of the centers, information was collected through a non-dietary questionnaire on lifestyle variables and through a dietary questionnaire addressing usual diet. Anthropometric measurements were performed and blood samples taken, from which plasma, serum, red cells, and buffy coat fractions were separated and aliquoted. A central biobanking facility, located at the International Agency for Research on Cancer, Lyon, was developed for the long-term storage of the specimens in liquid nitrogen. The biobank operates as a service provider and sample distribution center for scientific consortia engaged in studies involving biomarker analyses. To date, EPIC represents the largest single resource worldwide for prospective investigations on the etiology of cancers that can integrate questionnaire data on lifestyle and diet, and can also provide access to measurements of biomarkers of diet and of endogenous metabolism (e.g., hormones and growth factors) and genetic polymorphisms. This chapter describes the building up of the EPIC central biobank and the mechanisms that have been developed to manage the access to specimens by a large number of different users.

International efforts to develop biospecimen best practices.

Variables introduced during the processes involved in biospecimen collection, processing, storage, and analysis are among the potential sources of bias in biomarker research. International efforts are under way to develop best practices to standardize biospecimen handling protocols. In general, documents on best practices address three major recurring themes: technical best practices on infrastructure and specimen handling, recommendations on informatics and data management, and recommendations on ethical, legal, and social issues. There are many areas of agreement among various international efforts, but no single set of practices has emerged as a unifying document. The ethical, legal, and social issues are particularly difficult to harmonize due to the many country-specific issues that are governed by a variety of local and federal rules and regulations. Given the increasingly international nature of research involving biomarkers and biospecimens, it will be necessary to continue to cooperate in the development of harmonized evidence-based best practices. Several international organizations including the International Cancer Genome Consortium are engaged in such efforts.

The role of the pathologist in tissue banking: European Consensus Expert Group Report.

Human tissue biobanking encompasses a wide range of activities and study designs and is critical for application of a wide range of new technologies (-"omics") to the discovery of molecular patterns of disease and for implementation of novel biomarkers into clinical trials. Pathology is the cornerstone of hospital-based tissue biobanking. Pathologists not only provide essential information identifying the specimen but also make decisions on what should be biobanked, making sure that the timing of all operations is consistent with both the requirements of clinical diagnosis and the optimal preservation of biological products. This document summarizes the conclusions of a Pathology Expert Group Meeting within the European Biological and Biomolecular Research Infrastructure (BBMRI) Program. These recommendations are aimed at providing guidance for pathologists as well as for institutions hosting biobanks on how to better integrate and support pathological activities within the framework of biobanks that fulfill international standards.

Pathology as the cornerstone of human tissue banking: European consensus expert group report.

Aside from ethical considerations, the primary requirement for usage of human tissues in basic or translational research is the thorough characterization of tissues. The second, but equally essential, requirement is that tissues be collected, processed, annotated, and preserved in optimal conditions. These requirements put the pathologist at the center of tissue banking activities and of research aimed at discovering new biomarkers. Pathologists not only provide information identifying the specimen but also make decisions on what materials should be biobanked, on the preservation conditions, and on the timeline of events that precede preservation and storage. This central position calls for increased recognition of the role of the pathologist by the biomolecular community and places new demands on the pathologist's workload and scope of scientific activities. These questions were addressed by an Expert Group Meeting of the European Biological and Biomolecular Research Infrastructure (BBMRI). While detailed recommendations are published elsewhere (Bevilacqua et al., Virchows Archivs, 2010, in press), this article outlines the strategic and technological issues identified by the Expert Group and identifies ways forward for better integration of pathology in the current thrust for development of biomarker-based "personalized medicine."

Circulating free DNA in plasma or serum as biomarker of carcinogenesis: practical aspects and biological significance.

The presence of small amounts of tumor DNA in cell free DNA (CFDNA) circulating in the plasma or serum of cancer patients was first demonstrated 30 years ago. Since then, overall plasma DNA concentration in cancer patients and genetic or epigenetic alterations specific to tumor DNA have been investigated in patients diagnosed with different types of cancer. The proportion of patients with altered CFDNA varies with the pathology and the nature of the marker. However, several studies have reported the presence of altered CFDNA in over 50% of cancer patients, suggesting that this marker may be common and amenable for a variety of clinical and epidemiological studies. Because the mechanisms and timing of CFDNA release in the blood stream are poorly understood, only few studies have addressed the use of CFDNA for early cancer detection or as a biomarker for mutagenesis and tumourigenesis in molecular epidemiology. In this review, we discuss the technical issues involved in obtaining, using and analyzing CFDNA in cancer or healthy subjects. We also summarize the literature available on the mechanisms of CDNA release as well as on cross-sectional or prospective studies aimed at assessing the clinical and biological significance of CFDNA. These studies show that, in some circumstances, CFDNA alterations are detectable ahead of cancer diagnosis, raising the possibility of exploiting them as biomarkers for monitoring cancer occurrence. Testing these hypotheses will require well-designed studies, assessing multiple markers with quantitative and sensitive methods, with adequate follow-up of subjects, and we provide recommendations for the development of such studies.

TP53 and KRAS2 mutations in plasma DNA of healthy subjects and subsequent cancer occurrence: a prospective study.

In cancer patients, plasma often contains mutant DNA released by cancer cells. We have assessed the significance of plasma DNA mutations for subsequent cancer development in healthy subjects in a large longitudinal prospective study. The European Prospective Investigation into Cancer and Nutrition study was analyzed with a nested case-control design. Cases were nonsmokers or ex-smokers for >10 years and newly diagnosed with lung, bladder, or upper aerodigestive tract cancers or leukemia accrued after a median follow-up of 6.3 years. Controls were matched 2:1 for follow-up, age, sex, area of recruitment, and smoking status. KRAS2 mutations were detected by mutant-enriched PCR and sequencing (n = 1,098). TP53 mutations were detected by denaturing high-performance liquid chromatography, temporal temperature gradient electrophoresis, and sequencing (n = 550). KRAS2 or TP53 mutations were detected in 13 of 1,098 (1.2%) and 20 of 550 (3.6%) subjects, respectively, 16 of whom developed cancer on average after 18.3 months of follow-up. Among 137 subjects who developed bladder cancer, 5 had KRAS2 mutations [odds ratio (OR), 4.25; 95% confidence interval (95% CI), 1.27-14.15] and 7 had TP53 mutations (OR, 1.81; 95% CI, 0.66-4.97). There was a nonsignificant trend for association between TP53 mutations and bulky adducts in lymphocyte DNA (OR, 2.78; 95% CI, 0.64-12.17). This is the first report of TP53 or KRAS2 mutations in the plasma of healthy subjects in a prospective study, suggesting that KRAS2 mutation is detectable ahead of bladder cancer diagnosis. TP53 mutation may be associated with environmental exposures. These observations have implications for monitoring early steps of carcinogenesis.

Amount of DNA in plasma and cancer risk: a prospective study.

Levels of plasma DNA concentrations in cancer patients have been shown to be higher than the plasma DNA concentrations found in healthy subjects. The value of plasma DNA levels for development of neoplastic or pulmonary disease was evaluated in a large prospective study. Plasma samples (n = 1,184) were analyzed from 776 controls, 359 cases of cancer (lung, bladder, oral cavity, pharynx, larynx, leukemia) and 49 deaths from chronic obstructive pulmonary disease (COPD), including never smokers and ex-smokers, from 9 countries across Europe. The amount of plasma DNA was variable across the European Prospective Investigation into Cancer and Nutrition (EPIC) centers. High DNA concentrations in some centers might be due to the type of population recruited and/or the treatment of the samples. An elevated and statistically significant odds ratio (OR) was found for COPD deaths (OR = 2.53; 95% CI = 1.06-6.02), while nonsignificant increased ORs were present for oral cancers, cancers of the pharynx and larynx and leukemia. When the analyses were stratified by time since recruitment (below or above 36 months), the increased ORs were limited to the more recent period of recruitment, i.e., a time elapsed between blood drawing and disease onset lower than 36 months. This was particularly true for COPD deaths (OR = 12.7; 95% CI = 1.57-103) and leukemia (OR = 2.37; 95% CI = 1.20-4.67).