Human tissue biobanks as instruments for drug discovery and development: impact on personalized medicine

The journey to establishing an IT-infrastructure within the German Biobank Alliance

Background

Biobanks ensure the long-term storage and accessibility of biospecimens and corresponding data sets. Thus, they form the foundation for many research projects which may contribute to improving medical care. With the establishment of the German Biobank Node and Alliance, expertise in biobanking is bundled and strengthened. An important component within this research infrastructure is the set-up of an information technology (IT) network for allowing feasibility requests across individual biobanks.

Objective

We aim to describe relevant aspects that have shaped the journey to interconnect biobanks, to enhance their visibility within the research-community, to harmonize data, and to enable feasibility searches to support access to available data and biosamples.

Methods

To achieve this task, we resorted to a wide variety of methods: we ran a requirement analysis, decided on the mode of operation for the federated team of IT-developers and on the development approach itself, took related national and international initiatives into account, and concluded with evaluations of the developed software artefacts and the operation of the entire chain of applications.

Results

We drew an IT framework including all heterogeneous data aspects derived from our requirement analysis and developed a comprehensive IT infrastructure. The successful implementation benefited from a smooth interaction of a federated IT team distributed across all participating sites that was even able to manage a major technology change mid-project. Authentication and project management services from associated partners could be integrated and the graphic user interface for an intuitive search tool for biospecimens was designed iteratively. The developed code is open source to ensure sustainability and the local implementation is concluded and functioning. The evaluation of the components was positive.

Conclusions

The entire project had given ample opportunity for challenges, predictable and unpredictable—from the mode of operation to changing some of the initial ideas. We learned our lessons concerning personnel, budget planning and technical as well as manual monitoring as well as some requirements arising only during the process of the project. Nevertheless, we can here report a success story of a network infrastructure, highly agile and much easier in local installation than initially anticipated.

Data quality for federated medical data lakes

Purpose

Medical research requires biological material and data collected through biobanks in reliable processes with quality assurance. Medical studies based on data with unknown or questionable quality are useless or even dangerous, as evidenced by recent examples of withdrawn studies. Medical data sets consist of highly sensitive personal data, which has to be protected carefully and is available for research only after the approval of ethics committees. The purpose of this research is to propose an architecture to support researchers to efficiently and effectively identify relevant collections of material and data with documented quality for their research projects while observing strict privacy rules.

Design/methodology/approach

Following a design science approach, this paper develops a conceptual model for capturing and relating metadata of medical data in biobanks to support medical research.

Findings

This study describes the landscape of biobanks as federated medical data lakes such as the collections of samples and their annotations in the European federation of biobanks (Biobanking and Biomolecular Resources Research Infrastructure – European Research Infrastructure Consortium, BBMRI-ERIC) and develops a conceptual model capturing schema information with quality annotation. This paper discusses the quality dimensions for data sets for medical research in-depth and proposes representations of both the metadata and data quality documentation with the aim to support researchers to effectively and efficiently identify suitable data sets for medical studies.

Originality/value

This novel conceptual model for metadata for medical data lakes has a unique focus on the high privacy requirements of the data sets contained in medical data lakes and also stands out in the detailed representation of data quality and metadata quality of medical data sets.

Study of laboratory staff' knowledge of biobanking in Côte d'Ivoire

Background

A biobank is a structure which collects and manages biological samples and their associated data. The collected samples will then be made available for various uses. The sharing of those samples raised ethical questions which have been answered through specific rules. Thus, a Biobank functioning under tight ethical rules would be immensely valuable from a scientific and an economic view point. In 2009, Côte d’Ivoire established a biobank, which has been chosen to house the regional biobank of Economic Community of West African States (ECOWAS) countries in 2018. To ensure optimal and efficient use of this biobank, the scientific community must be aware of its existence and its role. It was therefore necessary to evaluate the knowledge of laboratories staff on the role and activities of a biobank.

Methods

This descriptive study was done by questioning staff from laboratories working on human’s health, animals or plants. The laboratories were located in southern Côte d’Ivoire.

Results

A total of 205 people completed the questionnaire. Of these 205 people, 34.63% were biologists, 7.32% engineers, 48.78% technicians and 9.27% PhD students. The average length of work experience was 10.11 ± 7.83 years. In this study, 43.41% of the participants had never heard of biobanking. Only 48.78% of participants had a good understanding of the role of a biobank. Technicians and PhD students were less educated on the notion of biobank (p < 0.000001). Although biologists were more educated on this issue, 21.13% of them had a misconception of biobank. Good knowledge of the role of a biobank was not significantly related to the work experience’s length (p > 0.88).

Conclusion

The level of knowledge of laboratory staff about biobanking needs to be improved. Training on the role, activities and interests of the biobank is important.

Improving Academic Biobank Value and Sustainability Through an Outputs Focus

Although it is generally accepted that human tissue biobanks are important to facilitate progress in health and medical research, many academic biobanks face sustainability challenges. We propose that biobank sustainability is challenged by a lack of available data describing the outputs and benefits that are produced by biobanks, as reflected by a dearth of publications that enumerate biobank outputs. We further propose that boosting the available information on biobank outputs and using a broader range of output metrics will permit economic analyses such as cost-consequence analyses of biobank activity. Output metrics and cost-consequence analyses can allow biobanks to achieve efficiencies, and improve the quality and/or quantity of their outputs. In turn, biobank output measures provide all stakeholders with explicit and accountable data on biobank value, which could contribute to the evolution of biobank operations to best match research needs, and mitigate some threats to biobank sustainability.

Cryo-Gel embedding compound for renal biopsy biobanking

Optimal preservation and biobanking of renal tissue is vital for good diagnostics and subsequent research. Optimal cutting temperature (OCT) compound is a commonly used embedding medium for freezing tissue samples. However, due to interfering polymers in OCT, analysis as mass spectrometry (MS) is difficult. We investigated if the replacement of OCT with Cryo-Gel as embedding compound for renal biopsies would enable proteomics and not disturb other common techniques used in tissue diagnostics and research. For the present study, fresh renal samples were snap-frozen using Cryo-Gel, OCT and without embedding compound and evaluated using different techniques. In addition, tissue samples from normal spleen, skin, liver and colon were analyzed. Cryo-Gel embedded tissues showed good morphological preservation and no interference in immunohistochemical or immunofluorescent investigations. The quality of extracted RNA and DNA was good. The number of proteins identified using MS was similar between Cryo-Gel embedded samples, samples without embedding compound and OCT embedded samples. However, polymers in the OCT disturbed the signal in the MS, while this was not observed in the Cryo-Gel embedded samples. We conclude that embedding of renal biopsies in Cryo-Gel is an excellent and preferable alternative for OCT compound for both diagnostic and research purposes, especially in those cases where proteomic analysis might be necessary.

[Tumor banks and complex data management: Current and future challenges]

Tumor banks are asked to clinical and translationnal research project development in oncology. They strongly participate to the assessment, then to the validation of diagnostic, prognostic and predictive biomarkers. The progressive change of these structures leads to induce a professionalization of their functioning and to identify them as key actors in oncology by the stakeholders of the public and private worlds. The progresses made in biotechnologies and therapeutics are rapidly modifying the impact and the proper functioning of the biobanks. These latter are now facing different challenges, in particular for their sustainability. Among the major issues, the integration of the clinical and biological data becoming increasingly complex leads to urgently consider an optimization of the role of different biobanks in France. Their goal is to be an attractive counterpart face to the international competition. The purpose of this review is to briefly describe the current evolution of the biobanks, then their present and future challenges, and finally the role made by the pathologists in these new issues in oncology field.

Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing

Biobanks operating at ambient temperatures would dramatically reduce the costs associated with standard cryogenic storage. In the present study, we used lyophilization to stabilize unfractionated human cells in a dried state at room temperature and tested the yield and integrity of the isolated RNA by microfluidic electrophoresis, RT-qPCR and RNA sequencing. RNA yields and integrity measures were not reduced for lyophilized cells (unstored, stored for two weeks or stored for two months) compared to their paired controls. The abundance of the selected mRNAs with various expression levels, as well as enhancer-associated RNAs and cancer biomarker long non-coding RNAs (MALAT1, GAS5 and TUG1), were not significantly different between the two groups as assessed by RT-qPCR. RNA sequencing data of three lyophilized samples stored for two weeks at room temperature revealed a high degree of similarity with their paired controls in terms of the RNA biotype distribution, cumulative gene diversity, gene body read coverage and per base mismatch rate. Among the 28 differentially expressed genes transcriptional regulators, as well as certain transcript properties suggestive of a residual active decay mechanism were enriched. Our study suggests that freeze-drying of human cells is a suitable alternative for the long-term stabilization of total RNA in whole human cells for routine diagnostics and high-throughput biomedical research.

Establishing a Dedicated Lung Cancer Biobank at the University Center Hospital of Nice (France). Why and How?

Lung cancer is the major cause of death from cancer in the world and its incidence is increasing in women. Despite the progress made in developing immunotherapies and therapies targeting genomic alterations, improvement in the survival rate of advanced stages or metastatic patients remains low. Thus, urgent development of effective therapeutic molecules is needed. The discovery of novel therapeutic targets and their validation requires high quality biological material and associated clinical data. With this aim, we established a biobank dedicated to lung cancers. We describe here our strategy and the indicators used and, through an overall assessment, present the strengths, weaknesses, opportunities and associated risks of this biobank.

[Biobanking and the further development of precision medicine]

BACKGROUND

Over the last 15 years, an estimated 3000 large centralized biobanks have been established worldwide, making important contributions to the further development of precision medicine. In many cases, these biobanks are affiliated with pathological institutes or work closely with them.

OBJECTIVE

In which translational research projects, and during which phases in the development of new drugs are human bioprobes being used and can their use be easily traced in the literature?

METHODS

PubMed, Internet research, and information from the German Biobank Alliance and the European initiative BBMRI-ERIC.

RESULTS

High-quality biosamples from centralized biobanks are increasingly used in clinical research and development projects. Success stories, where bioprobes have contributed to the further development of precision medicine, are shown in this paper using among others the example of RET gene fusion discovery in lung cancer. Interestingly enough, many key publications in the field of precision medicine do not contain exact references to the biobanks involved.

CONCLUSIONS

The importance of centralized biobanks in translational research and clinical development is constantly increasing. However, in order to ensure the acceptance and visibility of biobanks, their participation in success stories of biomedical progress must be systematically documented and published.

The Need for Research Infrastructures: A Narrative Review of Large-Scale Research Infrastructures in Biobanking

BACKGROUND

Distributed Research Infrastructures are gaining political traction in Europe to facilitate scientific research. This development has gained particular momentum in the area of biobanking where cross-national attempts have been made toward harmonizing the biobanking standards across the European Union through the establishment of the organization BBMRI (BioBanking and Biomolecular Resources Research Infrastructure). BBMRI exists as separate national nodes across several European countries, although Sweden took on a pioneering role in its early stages. Thus, the Swedish node, BBMRI.se, was set up in 2009.

PURPOSE

To document publications addressing the current debate on large-scale distributed medical and/or biobank Research Infrastructures and identify the most pressing issues discussed by these articles through a narrative review.

METHODS

The Web of Science (WOS) and PubMed databases were searched to find prior studies of large-scale medical Research Infrastructures, with no limits set with regard to study design and/or time period. All identified articles published up until March 2016 were included in the initial review.

RESULTS

A total of 145 articles were retrieved from WOS and PubMed, though merely 17 ultimately made it past the final exclusion criteria. About two-thirds of the articles listed a first author affiliated to a European country. The articles most commonly discussed the need for developing and expanding the use of "infrastructures."

PRACTICAL IMPLICATIONS

The future of scientific research will call for a deeper and more widespread multidisciplinary collaboration. This will emphasize the need of research seeking to optimize the preconditions of securing sustainable scientific collaboration. Future investigators will thus need to understand the components and mechanisms of Research Infrastructures in addition to acquiring knowledge of how to build, manage, brand, and promote them as well.

Biobanks in the era of personalized medicine: objectives, challenges, and innovation: Overview

Biobanks are an important compound of personalized medicine and strongly support the scientific progress in stratification of population and biomarker discovery and validation due to progress in personalized medicine. Biobanks are an essential tool for new drug discoveries and drug development. Biobanks play an important role in the whole process of patient prevention and prediction, follow-up, and therapy monitoring and optimalization. Biobanks have the specificity in that they cover multidisciplinary approach to the human health combining biological and medical approaches, as well as informative bioinformatics technologies, computationing, and modeling. The importance of biobanks has during the last decade increased in variety and capacity from small collections of samples to large-scale national or international repositories. Collected samples are population-based, disease-specific or rare diseases originating from a diverse profile of individuals. There are various purposes of biobanks, such as diagnostics, pharmacology, or research. Biobanks involve, store, and operate with specific personal information, and as a consequence, such a diversity of biobanking is associated with a broad spectrum of ethical and legal issues. Biobanks are an international phenomenon because any single country, state, or society at the moment is not able to cover all issues involving the whole biobank problematic. Biobanks have an enormous innovative potential in the whole process of biomedical research in the twenty-first century.

Metabolomics profiling of pre-and post-anesthesia plasma samples of colorectal patients obtained via Ficoll separation

1H NMR spectroscopy was used to investigate the metabolic consequences of general anesthesia in the plasma of two groups of patients with diagnosis for non-metastatic colorectal cancer and metastatic colorectal cancer with liver-metastasis, respectively. Patients were treated with etomidate or propofol, two frequently used sedation agents. Plasma samples were obtained via Ficoll separation. Here, we demonstrated that this procedure introduces a number of limitations for NMR-based metabolomics studies, due to the appearance of spurious signals. Nevertheless, the comparison of the 1H NMR metabolomic profiles of patients treated with etomidate or propofol at equipotent dose ranges was still feasible and proved that both agents significantly decrease the plasma levels of several NMR-detectable metabolites. Consequently, samples collected during anesthesia are not suitable for metabolic profiling studies aimed at patient stratification, because interpersonal variability are reduced by the overall depression of metabolites levels. On the other hand, this study showed that plasma metabolomics could represent a valuable tool to monitor the effect of different sedation agents and/or the individual metabolic response to anesthesia, providing hints for an appropriate tuning of personalized sedation procedures. In our reference groups, the metabolomic signatures were slightly different in patients anesthetized with etomidate versus propofol. The importance of standardized collection procedures and availability of exhaustive metadata of the experimental design for the accurate evaluation of the significance of the observed changes in metabolites levels are critically discussed.

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.

Spanning the genomics era: the vital role of a single institution biorepository for childhood cancer research over a decade

The 'genomics era' is considered to have begun with the commencement of the Human Genome Project. As translational genomic studies can only be established when human tissue samples are available for analysis, biospecimens are now proven to be an essential element for their success. During the genomics era the necessity for more extensive biobanking infrastructure has been highlighted. With the increased number of genomic studies into cancer, it is considered that the availability of biospecimens will become the rate limiting step. Despite the efforts in international biobanking, translational genomics is hampered when there low numbers of biospecimens for a particular rare diseases and is most apparent for paediatric cancer. As there is a call for biobanking practice to be responsive to the current experimental needs of the time and for more expansive systems of tissue procurement to be established we have asked the question what role does a single institution biorepository play in the current highly networked world of translational genomics. Here we describe such a case. The Tumour Bank at The Children's Hospital at Westmead (TB-CHW) in the western suburbs of Sydney was formally established in 1998 as a key resource for translational paediatric cancer research. During the genomics era, we show that the TB-CHW has developed into a key biospecimen repository for the cancer research community, during which time it has increasingly found itself having a vital role in the establishment of translational genomics for paediatric cancer. Here we detail metrics that demonstrate how as a single institution biorepository, the TB-CHW has been a strong participant in the advancement of translational genomics throughout the genomics era. This paper describes the significant contribution of a single institutional hospital embedded tumour biobank to the genomic research community. Despite the increased stringencies placed on biobanking practice, the TB-CHW has shown that a single institution biorespository can have a consistent and effective contribution to translational research into rare paediatric malignancy demonstrating its long term benefit throughout the genomics era.

Practical electronic information system and printed recording promote management accuracy in an early-stage small-scale non-automatic biobank

It is particularly necessary for biomedical researchers to obtain applicable biosamples accurately and efficiently, especially from a biobank with multiple-disease catalogs. To optimize the retrieval procedure, especially in the early stages of a non-automatic biobank, we developed a procedure that combined the electronic information system with a graphically designed printed recording system, which assisted in retrieving the samples quickly in a visualized way. In this procedure, we designed tables depending on the structure of equipment and registered the corresponding information in the tables layer by layer. Different samples from different types of diseases were first registered in the electronic system with the specific pre-allocation and barcodes. Then they were stored in the allocated position using their respective barcodes. In this way, the sample number and the location information in the electronic database were completely matched with the printed record. When the samples are needed, it is convenient to check the electronic information with the printed record. This procedure provides a convenient way to record the sample information during its lifecycle, and helps the administrator to double check information about the sample. The current solution offers an easy way for the transformation of a non-automatic biobank from the small-scale early-stage to the large-scale highly-automated level.

Biobanking for Personalized Medicine

A biobank is an entity that collects, processes, stores, and distributes biospecimens and relevant data for use in basic, translational, and clinical research. Biobanking of high-quality human biospecimens such as tissue, blood and other bodily fluids along with associated patient clinical information provides a fundamental scientific infrastructure for personalized medicine. Identification of biomarkers that are specifically associated with particular medical conditions such as cancer, cardiovascular disease and neurological disorders are useful for early detection, prevention, and treatment of the diseases. The ability to determine individual tumor biomarkers and to use those biomarkers for disease diagnosis, prognosis and prediction of response to therapy is having a very significant impact on personalized medicine and is rapidly changing the way clinical care is conducted. As a critical requirement for personalized medicine is the availability of a large collection of patient samples with well annotated patient clinical and pathological data, biobanks thus play an important role in personalized medicine advancement. The goal of this chapter is to explore the role of biobanks in personalized medicine and discuss specific needs regarding biobank development for translational and clinical research, especially for personalized medicine advancement.

Surgical procedures and postsurgical tissue processing significantly affect expression of genes and EGFR-pathway proteins in colorectal cancer tissue

An understanding of tissue data variability in relation to processing techniques during and postsurgery would be desirable when testing surgical specimens for clinical diagnostics, drug development, or identification of predictive biomarkers. Specimens of normal and colorectal cancer (CRC) tissues removed during colon and liver resection surgery were obtained at the beginning of surgery and postsurgically, tissue was fixed at 10, 20, and 45 minutes. Specimens were analyzed from 50 patients with primary CRC and 43 with intrahepatic metastasis of CRC using a whole genome gene expression array. Additionally, we focused on the epidermal growth factor receptor pathway and quantified proteins and their phosphorylation status in relation to tissue processing timepoints. Gene and protein expression data obtained from colorectal and liver specimens were influenced by tissue handling during surgery and by postsurgical processing time. To obtain reliable expression data, tissue processing for research and diagnostic purposes needs to be highly standardized.

BBMRI-ERIC as a resource for pharmaceutical and life science industries: the development of biobank-based Expert Centres

Biological resources (cells, tissues, bodily fluids or biomolecules) are considered essential raw material for the advancement of health-related biotechnology, for research and development in life sciences, and for ultimately improving human health. Stored in local biobanks, access to the human biological samples and related medical data for transnational research is often limited, in particular for the international life science industry. The recently established pan-European Biobanking and BioMolecular resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to improve accessibility and interoperability between academic and industrial parties to benefit personalized medicine, disease prevention to promote development of new diagnostics, devices and medicines. BBMRI-ERIC is developing the concept of Expert Centre as public-private partnerships in the precompetitive, not-for-profit field to provide a new structure to perform research projects that would face difficulties under currently established models of academic-industry collaboration. By definition, Expert Centres are key intermediaries between public and private sectors performing the analysis of biological samples under internationally standardized conditions. This paper presents the rationale behind the Expert Centres and illustrates the novel concept with model examples.

Developing an institutional cancer biorepository for personalized medicine

High quality human biospecimens, such as tissue, blood, cell derivatives, and associated patient clinical information, are key elements of a scientific infrastructure that supports discovery and identification of molecular biomarkers and diagnostic agents. The goal of most biorepositories is to collect, process, store, and distribute human biospecimen for use in basic, translational and clinical research. A biorepository serving as the central hub provides investigators with an invaluable resource with appropriately examined and characterized biospecimens with associated patient clinical information. Expertise in standardization, quality control, and information technology, and awareness of cutting edge research developments are generally required for biorepository development and management. The availability of low cost whole genome profiles of individual tumors has opened up new possibilities for personalized medicine to deliver the most appropriate treatments to individual patients with minimal toxicity. A biorepository in support of personalized medicine thus requires the highest standards of operation and adequate funding, training and certification. This review provides an overview of the development of an institutional cancer biorepository for clinical research and personalized medicine advancement.

Public-private relationships in biobanking: a still underestimated key component of open innovation

Access to human bioresources is essential to the understanding of human diseases and to the discovery of new biomarkers aimed at improving the diagnosis, prognosis, and the predictive response of patients to treatments. The use of biospecimens is strictly controlled by ethical assessment, which complies with the laws of the country. These laws regulate the partnerships between the biobanks and industrial actors. However, private-public partnerships (PPP) can be limiting for several reasons, which can hamper the discovery of new biological tests and new active molecules targeted to human diseases. The bottlenecks and roadblocks in establishing these partnerships include: poor organization of the biobank in setting up PPP, evaluation of the cost of human samples, the absence of experience on the public side in setting up contracts with industry, and the fact that public and private partners may not share the same objectives. However, it is critical, in particular for academic biobanks, to establish strong PPP to accelerate translational research for the benefits of patients, and to allow the sustainability of the biobank. The purpose of this review is to discuss the main bottlenecks and roadblocks that can hamper the establishment of PPP based on solid and trusting relationships.

Standardization developments for large scale biobanks in smoking related diseases - a model system for blood sample processing and storage

BACKGROUND

Biobank samples stored in biobanks give researchers and respiratory healthcare institutions access to datasets of analytes valuable for both diagnostic and research practices. The usefulness of these samples in clinical decision-making is highly dependent on their quality and integrity. New procedures that better preserve sample integrity and reduce degradation are being developed to meet the needs of both present and future biobanking. Hereby we present an automatic sample workflow scheme that is designed to handle high numbers of blood samples.

METHODS

Blood fractions are aliquoted, heat sealed using novel technology, and stored in 384 tube high-density sample arrays.

RESULTS

The newly developed 384 biobank rack system is especially suited for preserving identical small aliquots. We provide data on robotic processing of clinical samples at -80°C, following initial processing, analysis and shipping between laboratories throughout Europe. Subsequent to unpacking, re-sorting, and storage at these sites, the samples have been returned for analysis. Biomarker analysis of 13 common tests in the clinical chemistry unit of the hospital provides evidence of qualitative and stable logistics using the 384-sample tube system.

CONCLUSIONS

This technology development allows rapid access to a given sample in the frozen archive while maintaining individual sample integrity with sample tube confinement and quality management.

An omics strategy for discovering pulmonary biomarkers potentially relevant to the evaluation of tobacco products

Smoking is known to cause serious lung diseases including chronic bronchitis, chronic obstructive lung disease, obstruction of small airways, emphysema and cancer. Tobacco smoke is a complex chemical aerosol containing at least 8000 chemical constituents, either tobacco derived or added by tobacco product manufacturers. Identification of all of the toxic agents in tobacco smoke is challenging, and efforts to understand the mechanisms by which tobacco use causes disease will be informed by new biomarkers of exposure and harm. In 2009, President Obama signed into law the Family Smoking Prevention and Tobacco Control Act granting the US FDA the authority to regulate tobacco products to protect public health. This perspective article presents the background, rationale and strategy for using omics technologies to develop new biomarkers, which may be of interest to the FDA when implementing the Family Smoking Prevention and Tobacco Control Act.

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability

BACKGROUND

The 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.

METHODS

Clinical 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.

RESULTS

An 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.

CONCLUSIONS

We 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.

Isothermal vitrification methodology development for non-cryogenic storage of archival human sera

Biorepositories worldwide collect human serum samples and store them for future research. Currently, hundreds of biorepositories across the world store human serum samples in refrigerators, freezers, or liquid nitrogen without following any specific cryopreservation protocol. This method of storage is both expensive and potentially detrimental to the biospecimens. To decrease both cost of storage and the freeze/thaw stresses, we explored the feasibility of storing archival human serum samples at non-cryogenic temperatures using isothermal vitrification. When biospecimens are vitrified, biochemical reactions can be stopped, the specimen ceases to degrade, and macromolecules can be stabilized without requiring cryogenic storage. In this study, 0.2, 0.4, or 0.8M trehalose; 0, 0.005 or 0.01M dextran; and 0 or 10% (v/v) glycerol was added to human serum samples. The samples were either dried diffusively as sessile droplets or desiccated under vacuum after they are adsorbed onto glass microfiber filters. The glass transition temperatures (Tg) of the desiccated samples were measured by temperature-ramp Fourier Transform Infrared (FTIR) spectroscopy. Sera samples vitrified at 4±2°C when 0.8M trehalose and 0.01M dextran were added and the samples were vacuum dried for two hours. Western immunoblotting showed that vitrified serum proteins were minimally degraded when stored for up to one month at 4°C. About 80% of all proteins were recovered after storage at 4°C on glass microfiber filters, and recovery did not decrease with storage time. These results demonstrated the feasibility of long-term storage of vitrified serum at hypothermic (and non-cryogenic) temperatures.

Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies

The current paradigm of human genetics research is to analyze variation of a single data type (i.e., DNA sequence or RNA levels) to detect genes and pathways that underlie complex traits such as disease state or drug response. While these studies have detected thousands of variations that associate with hundreds of complex phenotypes, much of the estimated heritability, or trait variability due to genetic factors, remain unexplained. We may be able to account for a portion of the missing heritability if we incorporate a systems biology approach into these analyses. Rapid technological advances will make it possible for scientists to explore this hypothesis via the generation of high-throughput omics data - transcriptomic, proteomic and methylomic to name a few. Analyzing this 'meta-dimensional' data will require clever statistical techniques that allow for the integration of qualitative and quantitative predictor variables. For this article, we examine two major categories of approaches for integrated data analysis, give examples of their use in experimental and in silico datasets, and assess the limitations of each method.