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1.  The Infectious Diseases BioBank at King's College London: archiving samples from patients infected with HIV to facilitate translational research 
Retrovirology  2009;6:98.
The King's College London (KCL) Infectious Diseases BioBank opened in 2007 and collects peripheral venous blood (PVB) from individuals infected with pathogens including human immunodeficiency virus (HIV). PVBs are fractionated into plasmas, lymphocytes and DNA and are then frozen. All donations are from subjects who have given 'open consent' so samples can be used for virtually any type of biomedical research. The HIV component of the BioBank contains samples from over 400 donations from 138 HIV+ patients. Thus, the KCL Infectious Diseases BioBank - together with establishments such as the Spanish HIV BioBank - is likely to expedite translational research into this infection.
doi:10.1186/1742-4690-6-98
PMCID: PMC2779177  PMID: 19886990
2.  Variation of Peripheral Blood Mononuclear Cell RNA Quality in Archived Samples 
Biopreservation and Biobanking  2011;9(3):259-263.
The Infectious Diseases BioBank (IDB) has consistently archived peripheral blood mononuclear cell (PBMNC) RNA for transcriptome analyses. RNA is particularly labile, and hence, these samples provide a sensitive indicator for assessing the IDB's quality-assurance measures. Independent analyses of 104 PBMNC RNA specimens from 26 volunteers revealed that the mean RNA integrity number (RIN) was high (9.02), although RIN ranged between scores of 7 and 10. This variation of RIN values was not associated with ischemic time, PBMNC quality, number of samples processed per day, self-medication after immunization, freezer location, donor characteristics, differential white blood cell counts, or daily variation in RNA extractions (all P>0.05). RIN values were related to the date of collection, with those processed during mid-summer having highest RIN scores (P=0.0001). Amongst specimens with the lowest RIN scores, no common feature could be identified. Thus, no technical explanation for the variation in RNA quality could be ascertained and these may represent normal physiological variations. These data provide strong evidence that current IDB protocols for the isolation and preservation PBMNC RNA are robust.
doi:10.1089/bio.2011.0008
PMCID: PMC3178418  PMID: 21977241
3.  The Establishment of an ISO Compliant Cancer Biobank for Jordan and its Neighboring Countries Through Knowledge Transfer and Training 
Research studies aimed at advancing cancer prevention, diagnosis, and treatment depend on a number of key resources, including a ready supply of high-quality annotated biospecimens from diverse ethnic populations that can be used to test new drugs, assess the validity of prognostic biomarkers, and develop tailor-made therapies. In November 2011, KHCCBIO was established at the King Hussein Cancer Center (KHCC) with the support of Seventh Framework Programme (FP7) funding from the European Union (khccbio.khcc.jo). KHCCBIO was developed for the purpose of achieving an ISO accredited cancer biobank through the collection, processing, and preservation of high-quality, clinically annotated biospecimens from consenting cancer patients, making it the first cancer biobank of its kind in Jordan. The establishment of a state-of-the-art, standardized biospecimen repository of matched normal and lung tumor tissue, in addition to blood components such as serum, plasma, and white blood cells, was achieved through the support and experience of its European partners, Trinity College Dublin, Biostór Ireland, and accelopment AG. To date, KHCCBIO along with its partners, have worked closely in establishing an ISO Quality Management System (QMS) under which the biobank will operate. A Quality Policy Manual, Validation, and Training plan have been developed in addition to the development of standard operating procedures (SOPs) for consenting policies on ethical issues, data privacy, confidentiality, and biobanking bylaws. SOPs have also been drafted according to best international practices and implemented for the donation, procurement, processing, testing, preservation, storage, and distribution of tissues and blood samples from lung cancer patients, which will form the basis for the procurement of other cancer types. KHCCBIO will be the first ISO accredited cancer biobank from a diverse ethnic Middle Eastern and North African population. It will provide a unique and valuable resource of high-quality human biospecimens and anonymized clinicopathological data to the cancer research communities world-wide.
doi:10.1089/bio.2013.0072
PMCID: PMC3962647  PMID: 24620764
4.  Public’s attitudes on participation in a biobank for research: an Italian survey 
BMC Medical Ethics  2014;15(1):81.
Background
The creation of biobanks depends upon people’s willingness to donate their samples for research purposes and to agree to sample storage. Moreover, biobanks are a public good that requires active participation by all interested stakeholders at every stage of development. Therefore, knowing public’s attitudes towards participation in a biobank and biobank management is important and deserves investigation.
Method
A survey was conducted among family members of patients attending the outpatient department of our institute for a geriatric or neurological visit, documenting their willingness to participate in a biobank and their views on the legal-ethical aspects of biobank management. Information regarding subjects’ attitudes on biomedical research in general and genetic research in particular was also collected. Participants’ data on biobanks were compared with data previously collected from the Italian ethics committees (ECs) to evaluate the extent to which lay people and ethics committees share views and concerns regarding biobanks.
Results
One hundred forty-five subjects took part in the survey. The willingness to give biological samples for the constitution of a biobank set up for research purposes was declared by 86% of subjects and was modulated by subjects’ education. People in favour of providing biological samples for a biobank expressed a more positive view on biomedical research than did people who were not in favour; attitude towards genetic research in dementia was the strongest predictor of participation. Different from ECs that prefer specific consent (52%) and do not choose the option of broad consent (8%) for samples collection in a biobank, participants show a clear preference for broad consent (57%), followed by partially restricted consent (16%), specific consent (15%), and multi-layered consent (12%). Almost all of the subjects available to contribute to a biobank desire to receive both individual research results and research results of general value, while around fifty per cent of ECs require results communication.
Conclusion
Family members showed willingness to participate in a biobank for research and expressed a view on the ethical aspects of a biobank management that differ on several issues from the Italian ECs’ opinion. Laypersons’ views should be taken into account in developing biobank regulations.
Electronic supplementary material
The online version of this article (doi:10.1186/1472-6939-15-81) contains supplementary material, which is available to authorized users.
doi:10.1186/1472-6939-15-81
PMCID: PMC4258254  PMID: 25425352
Public attitudes; Biobanks; Genetic research; Bioethics; Ethical policy
5.  Biomarker Profiling by Nuclear Magnetic Resonance Spectroscopy for the Prediction of All-Cause Mortality: An Observational Study of 17,345 Persons 
PLoS Medicine  2014;11(2):e1001606.
In this study, Würtz and colleagues conducted high-throughput profiling of blood specimens in two large population-based cohorts in order to identify biomarkers for all-cause mortality and enhance risk prediction. The authors found that biomarker profiling improved prediction of the short-term risk of death from all causes above established risk factors. However, further investigations are needed to clarify the biological mechanisms and the utility of these biomarkers to guide screening and prevention.
Please see later in the article for the Editors' Summary
Background
Early identification of ambulatory persons at high short-term risk of death could benefit targeted prevention. To identify biomarkers for all-cause mortality and enhance risk prediction, we conducted high-throughput profiling of blood specimens in two large population-based cohorts.
Methods and Findings
106 candidate biomarkers were quantified by nuclear magnetic resonance spectroscopy of non-fasting plasma samples from a random subset of the Estonian Biobank (n = 9,842; age range 18–103 y; 508 deaths during a median of 5.4 y of follow-up). Biomarkers for all-cause mortality were examined using stepwise proportional hazards models. Significant biomarkers were validated and incremental predictive utility assessed in a population-based cohort from Finland (n = 7,503; 176 deaths during 5 y of follow-up). Four circulating biomarkers predicted the risk of all-cause mortality among participants from the Estonian Biobank after adjusting for conventional risk factors: alpha-1-acid glycoprotein (hazard ratio [HR] 1.67 per 1–standard deviation increment, 95% CI 1.53–1.82, p = 5×10−31), albumin (HR 0.70, 95% CI 0.65–0.76, p = 2×10−18), very-low-density lipoprotein particle size (HR 0.69, 95% CI 0.62–0.77, p = 3×10−12), and citrate (HR 1.33, 95% CI 1.21–1.45, p = 5×10−10). All four biomarkers were predictive of cardiovascular mortality, as well as death from cancer and other nonvascular diseases. One in five participants in the Estonian Biobank cohort with a biomarker summary score within the highest percentile died during the first year of follow-up, indicating prominent systemic reflections of frailty. The biomarker associations all replicated in the Finnish validation cohort. Including the four biomarkers in a risk prediction score improved risk assessment for 5-y mortality (increase in C-statistics 0.031, p = 0.01; continuous reclassification improvement 26.3%, p = 0.001).
Conclusions
Biomarker associations with cardiovascular, nonvascular, and cancer mortality suggest novel systemic connectivities across seemingly disparate morbidities. The biomarker profiling improved prediction of the short-term risk of death from all causes above established risk factors. Further investigations are needed to clarify the biological mechanisms and the utility of these biomarkers for guiding screening and prevention.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
A biomarker is a biological molecule found in blood, body fluids, or tissues that may signal an abnormal process, a condition, or a disease. The level of a particular biomarker may indicate a patient's risk of disease, or likely response to a treatment. For example, cholesterol levels are measured to assess the risk of heart disease. Most current biomarkers are used to test an individual's risk of developing a specific condition. There are none that accurately assess whether a person is at risk of ill health generally, or likely to die soon from a disease. Early and accurate identification of people who appear healthy but in fact have an underlying serious illness would provide valuable opportunities for preventative treatment.
While most tests measure the levels of a specific biomarker, there are some technologies that allow blood samples to be screened for a wide range of biomarkers. These include nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. These tools have the potential to be used to screen the general population for a range of different biomarkers.
Why Was This Study Done?
Identifying new biomarkers that provide insight into the risk of death from all causes could be an important step in linking different diseases and assessing patient risk. The authors in this study screened patient samples using NMR spectroscopy for biomarkers that accurately predict the risk of death particularly amongst the general population, rather than amongst people already known to be ill.
What Did the Researchers Do and Find?
The researchers studied two large groups of people, one in Estonia and one in Finland. Both countries have set up health registries that collect and store blood samples and health records over many years. The registries include large numbers of people who are representative of the wider population.
The researchers first tested blood samples from a representative subset of the Estonian group, testing 9,842 samples in total. They looked at 106 different biomarkers in each sample using NMR spectroscopy. They also looked at the health records of this group and found that 508 people died during the follow-up period after the blood sample was taken, the majority from heart disease, cancer, and other diseases. Using statistical analysis, they looked for any links between the levels of different biomarkers in the blood and people's short-term risk of dying. They found that the levels of four biomarkers—plasma albumin, alpha-1-acid glycoprotein, very-low-density lipoprotein (VLDL) particle size, and citrate—appeared to accurately predict short-term risk of death. They repeated this study with the Finnish group, this time with 7,503 individuals (176 of whom died during the five-year follow-up period after giving a blood sample) and found similar results.
The researchers carried out further statistical analyses to take into account other known factors that might have contributed to the risk of life-threatening illness. These included factors such as age, weight, tobacco and alcohol use, cholesterol levels, and pre-existing illness, such as diabetes and cancer. The association between the four biomarkers and short-term risk of death remained the same even when controlling for these other factors.
The analysis also showed that combining the test results for all four biomarkers, to produce a biomarker score, provided a more accurate measure of risk than any of the biomarkers individually. This biomarker score also proved to be the strongest predictor of short-term risk of dying in the Estonian group. Individuals with a biomarker score in the top 20% had a risk of dying within five years that was 19 times greater than that of individuals with a score in the bottom 20% (288 versus 15 deaths).
What Do These Findings Mean?
This study suggests that there are four biomarkers in the blood—alpha-1-acid glycoprotein, albumin, VLDL particle size, and citrate—that can be measured by NMR spectroscopy to assess whether otherwise healthy people are at short-term risk of dying from heart disease, cancer, and other illnesses. However, further validation of these findings is still required, and additional studies should examine the biomarker specificity and associations in settings closer to clinical practice. The combined biomarker score appears to be a more accurate predictor of risk than tests for more commonly known risk factors. Identifying individuals who are at high risk using these biomarkers might help to target preventative medical treatments to those with the greatest need.
However, there are several limitations to this study. As an observational study, it provides evidence of only a correlation between a biomarker score and ill health. It does not identify any underlying causes. Other factors, not detectable by NMR spectroscopy, might be the true cause of serious health problems and would provide a more accurate assessment of risk. Nor does this study identify what kinds of treatment might prove successful in reducing the risks. Therefore, more research is needed to determine whether testing for these biomarkers would provide any clinical benefit.
There were also some technical limitations to the study. NMR spectroscopy does not detect as many biomarkers as mass spectrometry, which might therefore identify further biomarkers for a more accurate risk assessment. In addition, because both study groups were northern European, it is not yet known whether the results would be the same in other ethnic groups or populations with different lifestyles.
In spite of these limitations, the fact that the same four biomarkers are associated with a short-term risk of death from a variety of diseases does suggest that similar underlying mechanisms are taking place. This observation points to some potentially valuable areas of research to understand precisely what's contributing to the increased risk.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001606
The US National Institute of Environmental Health Sciences has information on biomarkers
The US Food and Drug Administration has a Biomarker Qualification Program to help researchers in identifying and evaluating new biomarkers
Further information on the Estonian Biobank is available
The Computational Medicine Research Team of the University of Oulu and the University of Bristol have a webpage that provides further information on high-throughput biomarker profiling by NMR spectroscopy
doi:10.1371/journal.pmed.1001606
PMCID: PMC3934819  PMID: 24586121
6.  A Strategic Plan for the Second Phase (2013–2015) of the Korea Biobank Project 
The Korea Biobank Project (KBP) was led by the Ministry of Health and Welfare to establish a network between the National Biobank of Korea and biobanks run by university-affiliated general hospitals (regional biobanks). The Ministry of Health and Welfare started the project to enhance medical and health technology by collecting, managing, and providing researchers with high-quality human bioresources. The National Biobank of Korea, under the leadership of the Ministry of Health and Welfare, collects specimens through various cohorts and regional biobanks within university hospitals gather specimens from patients. The project began in 2008, and the first phase ended in 2012, which meant that there needed to be a plan for the second phase that begins in 2013. Consequently, professionals from within and outside the project were gathered to develop a plan for the second phase. Under the leadership of the planning committee, six working groups were formed to formulate a practical plan. By conducting two workshops with experts in the six working groups and the planning committee and three forums in 2011 and 2012, they have developed a strategic plan for the second phase of the KBP. This document presents a brief report of the second phase of the project based on a discussion with them.
During the first phase of the project (2008–2012), a network was set up between the National Biobank of Korea and 17 biobanks at university-affiliated hospitals in an effort to unify informatics and governance among the participating biobanks. The biobanks within the network manage data on their biospecimens with a unified Biobank Information Management System. Continuous efforts are being made to develop a common standard operating procedure for resource collection, management, distribution, and personal information security, and currently, management of these data is carried out in a somewhat unified manner. In addition, the KBP has trained and educated professionals to work within the biobanks, and has also carried out various publicity promotions to the public and researchers. During the first phase, biospecimens from more than 300,000 participants through various cohorts and biospecimens from more than 200,000 patients from hospitals were collected, which were distributed to approximately 600 research projects.
The planning committee for the second phase evaluated that the first phase of the KBP was successful. However, the first phase of the project was meant to allow autonomy to the individual biobanks. The biobanks were able to choose the kind of specimens they were going to collect and the amount of specimen they would set as a goal, as well as being allowed to choose their own methods to manage their biobanks (autonomy). Therefore, some biobanks collected resources that were easy to collect and the resources needed by researchers were not strategically collected. In addition, there was also a low distribution rate to researchers outside of hospitals, who do not have as much access to specimens and cases as those in hospitals. There were also many cases in which researchers were not aware of the KBP, and the distribution processes were not set up to be convenient to the demands of researchers.
Accordingly, the second phase of the KBP will be focused on increasing the integration and cooperation between the biobanks within the network. The KBP plans to set goals for the strategic collection of the needed human bioresources. Although the main principle of the first phase was to establish infrastructure and resource collection, the key objective of the second phase is the efficient utilization of gathered resources. In order to fully utilize the gathered resources in an efficient way, distribution systems and policies must be improved. Vitalization of distribution, securing of high-value resource and related clinical and laboratory information, international standardization of resource management systems, and establishment of a virtuous cycle between research and development (R&D) and biobanks are the four main strategies. Based on these strategies, 12 related objectives have been set and are planned to be executed.
doi:10.1016/j.phrp.2013.03.006
PMCID: PMC3767092  PMID: 24159540
biobank; biobank network; biospecimen; Korea Biobank Project; National Biobank of Korea
7.  Research understanding, attitude and awareness towards biobanking: a survey among Italian twin participants to a genetic epidemiological study 
BMC Medical Ethics  2009;10:4.
Background
The Italian Twin Registry (ITR) has been carrying out several genetic-epidemiological studies. Collection and storage of biological material from study participants has recently increased in the light of biobanking development. Within this scenario, we aimed at investigating understanding, awareness and attitude towards blood/DNA donation of research participants. About these quite unknown dimensions more knowledge is needed from ethical and social perspectives.
Methods
Cross-sectional mail survey to explore three dimensions: (i) understanding of aims and method of a specific study, (ii) attitude (three ideas for donation: "moral duty", "pragmatism", "spontaneity") and (iii) awareness (i.e. the recall of having been asked to donate) towards blood/DNA donation for research, among all the Italian twins who had participated in Euroclot (n = 181), a large international genetic-epidemiological study. Multivariate models were applied to investigate the association of sex, age, education and modality of Euroclot recruitment (twins enrolled in the ITR and volunteers) with the targeted dimensions. Pair-wise twin concordance for the "pragmatic" attitude was estimated in monozygotic and dizygotic pairs.
Results
Response rate was 56% (99 subjects); 75.8% understood the Euroclot method, only 33.3% correctly answered about the study aim. A significantly better understanding of aim and method was detected in "volunteers". Graduated subjects were more likely to understand study aim. In the overall sample, the "pragmatic" attitude to blood donation reached 76.8%, and biobanking awareness 89.9%. The latter was significantly higher among women. Monozygotic twins were more concordant than dizygotic twins for the "pragmatic" attitude towards blood/DNA donation for research.
Conclusion
Level of understanding of aims and methods of a specific research project seems to vary in relation to modalities of approaching research; most of the twins are well aware of having been asked to donate blood for biobanking activities, and seem to be motivated by a "pragmatic" attitude to blood/DNA donation. Genetic influences on this attitude were suggested. The framing of interests and concerns of healthy participants to genetic-epidemiological studies should be further pursued, since research, particularly for "common diseases", is increasingly relying on population surveys and biobanking.
doi:10.1186/1472-6939-10-4
PMCID: PMC2703640  PMID: 19531243
8.  Two Large-Scale Surveys on Community Attitudes Toward an Opt-Out Biobank 
Although US research regulations allow for de-identified biorepositories to be developed without formal informed consent from the patients whose samples are included, it is unknown whether this model will be well-received by community members. Based on early evidence that such a biobank could be successful if patients who object have the opportunity to opt-out, Vanderbilt University developed a biorepository named BioVU that follows this model. This study reports the findings from two large-scale surveys among communities important to this biorepository. In the first, a population-based phone survey of Nashville residents, we found that approval for BioVU is high (93.9%) and that this approval is similar among all population groups. A hypothetical biobank that does not obtain some form of written permission is much less well received. In the second, an online survey of Vanderbilt University faculty and staff, we found a higher level of support for BioVU (94.5%) among faculty and staff working throughout the university. In this survey, employees least likely to approve of BioVU are those employees who prefer not to receive medical care at Vanderbilt University. These surveys demonstrate the highest level of approval for a genomic biobank ever reported in the literature, even among groups traditionally cautious about such research. This high level of approval may reflect increasing comfort with genomic research over time combined with the effect that trust in a specific institution can have on approval for an operating biobank compared with approval of a hypothetical biobank.
doi:10.1002/ajmg.a.34304
PMCID: PMC3222722  PMID: 22065592
biorepository research; patient perspectives; research ethics
9.  A Data Standard for Sourcing Fit-for-Purpose Biological Samples in an Integrated Virtual Network of Biobanks 
Biopreservation and Biobanking  2014;12(3):184-191.
Human tissue biobanks are at the epicenter of clinical research, responsible for providing both clinical samples and annotated data. There is a need for large numbers of samples to provide statistical power to research studies, especially since treatment and diagnosis are becoming ever more personalized. A single biobank cannot provide sufficient numbers of samples to capture the full spectrum of any disease. Currently there is no infrastructure in the United Kingdom (UK) to integrate biobanks. Therefore the National Cancer Research Institute (NCRI) Confederation of Cancer Biobanks (CCB) Working Group 3 looked to establish a data standard to enable biobanks to communicate about the samples they hold and so facilitate the formation of an integrated national network of biobanks. The Working Group examined the existing data standards available to biobanks, such as the MIABIS standard, and compared these to the aims of the working group. The CCB-developed data standard has brought many improvements: (1) Where existing data standards have been developed, these have been incorporated, ensuring compatibility with other initiatives; (2) the standard was written with the expectation that it will be extended for specific disease areas, such as the Breast Cancer Campaign Tissue Bank (BCCTB) and the Strategic Tissue Repository Alliances Through Unified Methods (STRATUM) project; and (3) biobanks will be able to communicate about specific samples, as well as aggregated statistics.
The development of this data standard will allow all biobanks to integrate and share information about the samples they hold, facilitating the possibility of a national portal for researchers to find suitable samples for research. In addition, the data standard will allow other clinical services, such as disease registries, to communicate with biobanks in a standardized format allowing for greater cross-discipline data sharing.
doi:10.1089/bio.2013.0089
PMCID: PMC4066222  PMID: 24785371
10.  Qualitative study of knowledge and attitudes to biobanking among lay persons in Nigeria 
BMC Medical Ethics  2012;13:27.
Background
Interest in biobanking for collection of specimens for non-communicable diseases research has grown in recent times. This paper explores the perspectives of Nigerians on donation of specimen for the biobanking research.
Methods
We conducted 16 Focus Group Discussions (FGD) with individuals from different ethnic, age and socio-economic groups in Kano (North), Enugu (Southeast), Oyo States (Southwest) and Abuja, the Federal Capital Territory (Central) of Nigeria. We used topic guides and prompt statements to explore the knowledge and understanding of interviewees to general issues about biobanking of biospecimens, their use and specifically about role of biobanking in non-communicable diseases research.
Results
A total of 123 individuals participated in 16 focus group discussions in 2011. Our participants had limited knowledge of the concept of biobanking but accepted it once they were educated about it and saw it as a worthwhile venture. Half of our study participants supported use of broad consent, a quarter supported restricted consent while the remaining quarter were in favour of tiered consent. Most discussants support shipment of their samples to other countries for further research, but they prefer those collaborations to be done only with competent, ethical researchers and they would like to receive feedback about such projects. The majority preferred health care as a benefit from participation, particularly for any unexpected condition that may be discovered during the course of the research instead of financial compensation. Participants emphasized the need to ensure that donated samples were not used for research that contradicts their religious beliefs.
Conclusions
Our study demonstrates that our participants accepted biobanking once they understand it but there were different attitudes to elements of biobanking such as type of consent. Our study highlights the need to carefully document population attitudes to elements of modern scientific research and the consenting process.
doi:10.1186/1472-6939-13-27
PMCID: PMC3507723  PMID: 23072321
Biobanking; Non-communicable diseases; Public perspectives; Nigeria
11.  Public support and consent preference for biomedical research and biobanking in Jordan 
The success of any biobank depends on a number of factors including public's view of research and the extent to which it is willing to participate in research. As a prototype of surrounding countries, public interest in research and biobanking in addition to the influence and type of informed consent for biobanking were investigated in Jordan. Data were collected as part of a national survey of 3196 individuals representing the Jordanian population. The majority of respondents (88.6%) had a positive perception of the level of research in Jordan and they overwhelmingly (98.2%) agreed to the concept of investing as a country in research. When respondents were asked if the presence of an informed consent would influence their decision to participate in biobanking, more individuals (19.8%) considered having an informed consent mechanism as a positive factor than those who considered it to have negative connotations (13.1%). However, a substantial portion (65%) did not feel it affected their decision. The majority of survey participants (64%) expressed willingness to participate in biobanking and over 90% of them preferred an opt-in consent form whether general (75.2%) or specific for disease or treatment (16.9%). These results indicate a promising ground for research and biobanking in Jordan. Educational programs or mass awareness campaigns to promote participation in biobanking and increase awareness about informed consent and individual rights in research will benefit both the scientific community as well as the public.
doi:10.1038/ejhg.2012.213
PMCID: PMC3641386  PMID: 22968133
biobanking; informed consent; public opinion; Jordan; Middle East; research participation
12.  ‘Cool! and creepy’: engaging with college student stakeholders in Michigan’s biobank 
Journal of Community Genetics  2014;5(4):349-362.
Large population biobanks, important resources for genomic research, also present ethical challenges. The Michigan BioTrust for Health makes dried bloodspots (DBS) leftover from newborn screening, including ~4.5 million collected before 2010 without written consent, available for health research. Absent prospectively gathered consent and/or current engagement with 18- to 29-year olds, little is known about opinions and beliefs from this age group about use of the bloodspots for research. We engaged 2,101 students—BioTrust participants and their peers—at information booths at 20 college campuses across the state to educate youth about the BioTrust and gather information about consent preferences and about hopes and concerns about this public health program. We surveyed student stakeholder DBS research consent preferences and fielded a “postengagement” survey to gauge the attitudes of participants and to evaluate the campus engagement. The most prevalent themes in open-ended comments were support for biobank research and concern that Michiganders are not aware of their participation. While 78 % of students said they would, if asked, opt in to the BioTrust, half of these preferred to be contacted each time a researcher sought to use their DBS. Students reported great interest in the topic and strong likelihood to share what they had learned. BioTrust participants are interested in learning about their role in an initiative whose goals they widely support. Public engagement is particularly important to biobank participants who, absent traditional consent practices, are unaware of their participation. Health-fair style engagements were effective for targeting college-aged stakeholders, communicating complex messages, and likely increasing knowledge. Retrospective biobanks and biobanks that collect proxy consent need policies to respect those who would opt out and will need resources to educate participants and conduct community outreach that is a safeguard to public trust.
Electronic supplementary material
The online version of this article (doi:10.1007/s12687-014-0190-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s12687-014-0190-4
PMCID: PMC4159476  PMID: 24916145
Biobank; Public health; Informed consent; Newborn screening; Public attitudes; Community engagement; Public health education
13.  Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database 
PLoS ONE  2010;5(3):e9598.
Background
In the last decade, the inhibition of protein-protein interactions (PPIs) has emerged from both academic and private research as a new way to modulate the activity of proteins. Inhibitors of these original interactions are certainly the next generation of highly innovative drugs that will reach the market in the next decade. However, in silico design of such compounds still remains challenging.
Methodology/Principal Findings
Here we describe this particular PPI chemical space through the presentation of 2P2IDB, a hand-curated database dedicated to the structure of PPIs with known inhibitors. We have analyzed protein/protein and protein/inhibitor interfaces in terms of geometrical parameters, atom and residue properties, buried accessible surface area and other biophysical parameters. The interfaces found in 2P2IDB were then compared to those of representative datasets of heterodimeric complexes. We propose a new classification of PPIs with known inhibitors into two classes depending on the number of segments present at the interface and corresponding to either a single secondary structure element or to a more globular interacting domain. 2P2IDB complexes share global shape properties with standard transient heterodimer complexes, but their accessible surface areas are significantly smaller. No major conformational changes are seen between the different states of the proteins. The interfaces are more hydrophobic than general PPI's interfaces, with less charged residues and more non-polar atoms. Finally, fifty percent of the complexes in the 2P2IDB dataset possess more hydrogen bonds than typical protein-protein complexes. Potential areas of study for the future are proposed, which include a new classification system consisting of specific families and the identification of PPI targets with high druggability potential based on key descriptors of the interaction.
Conclusions
2P2I database stores structural information about PPIs with known inhibitors and provides a useful tool for biologists to assess the potential druggability of their interfaces. The database can be accessed at http://2p2idb.cnrs-mrs.fr.
doi:10.1371/journal.pone.0009598
PMCID: PMC2834754  PMID: 20231898
14.  Evolutionary concepts in biobanking - the BC BioLibrary 
Background
Medical research to improve health care faces a major problem in the relatively limited availability of adequately annotated and collected biospecimens. This limitation is creating a growing gap between the pace of scientific advances and successful exploitation of this knowledge. Biobanks are an important conduit for transfer of biospecimens (tissues, blood, body fluids) and related health data to research. They have evolved outside of the historical source of tissue biospecimens, clinical pathology archives. Research biobanks have developed advanced standards, protocols, databases, and mechanisms to interface with researchers seeking biospecimens. However, biobanks are often limited in their capacity and ability to ensure quality in the face of increasing demand. Our strategy to enhance both capacity and quality in research biobanking is to create a new framework that repatriates the activity of biospecimen accrual for biobanks to clinical pathology.
Methods
The British Columbia (BC) BioLibrary is a framework to maximize the accrual of high-quality, annotated biospecimens into biobanks. The BC BioLibrary design primarily encompasses: 1) specialized biospecimen collection units embedded within clinical pathology and linked to a biospecimen distribution system that serves biobanks; 2) a systematic process to connect potential donors with biobanks, and to connect biobanks with consented biospecimens; and 3) interdisciplinary governance and oversight informed by public opinion.
Results
The BC BioLibrary has been embraced by biobanking leaders and translational researchers throughout BC, across multiple health authorities, institutions, and disciplines. An initial pilot network of three Biospecimen Collection Units has been successfully established. In addition, two public deliberation events have been held to obtain input from the public on the BioLibrary and on issues including consent, collection of biospecimens and governance.
Conclusion
The BC BioLibrary framework addresses common issues for clinical pathology, biobanking, and translational research across multiple institutions and clinical and research domains. We anticipate that our framework will lead to enhanced biospecimen accrual capacity and quality, reduced competition between biobanks, and a transparent process for donors that enhances public trust in biobanking.
doi:10.1186/1479-5876-7-95
PMCID: PMC2785772  PMID: 19909513
15.  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.
doi:10.1186/2001-1326-2-7
PMCID: PMC3599425  PMID: 23445834
Malignant melanoma; Protein sequencing; Proteomics; Genes; Antibodies; mRNA; Mass spectrometry; Bioinformatics
16.  Developing a semantically rich ontology for the biobank-administration domain 
Background
Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has also shown that there is a lack of data about the administrative aspects of biobanks. These data would be helpful to answer research-relevant questions such as what is the scope of specimens collected in a biobank, what is the curation status of the specimens, and what is the contact information for curators of biobanks. Our use cases include giving researchers the ability to retrieve key administrative data (e.g. contact information, contact's affiliation, etc.) about the biobanks where specific specimens of interest are stored. Thus, our goal is to provide an ontology that represents the administrative entities in biobanking and their relations. We base our ontology development on a set of 53 data attributes called MIABIS, which were in part the result of semantic integration efforts of the European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). The previous work on MIABIS provided the domain analysis for our ontology. We report on a test of our ontology against competency questions that we derived from the initial BBMRI use cases. Future work includes additional ontology development to answer additional competency questions from these use cases.
Results
We created an open-source ontology of biobank administration called Ontologized MIABIS (OMIABIS) coded in OWL 2.0 and developed according to the principles of the OBO Foundry. It re-uses pre-existing ontologies when possible in cooperation with developers of other ontologies in related domains, such as the Ontology of Biomedical Investigation. OMIABIS provides a formalized representation of biobanks and their administration. Using the ontology and a set of Description Logic queries derived from the competency questions that we identified, we were able to retrieve test data with perfect accuracy. In addition, we began development of a mapping from the ontology to pre-existing biobank data structures commonly used in the U.S.
Conclusions
In conclusion, we created OMIABIS, an ontology of biobank administration. We found that basing its development on pre-existing resources to meet the BBMRI use cases resulted in a biobanking ontology that is re-useable in environments other than BBMRI. Our ontology retrieved all true positives and no false positives when queried according to the competency questions we derived from the BBMRI use cases. Mapping OMIABIS to a data structure used for biospecimen collections in a medical center in Little Rock, AR showed adequate coverage of our ontology.
doi:10.1186/2041-1480-4-23
PMCID: PMC4021870  PMID: 24103726
17.  Population biobanking in selected European countries and proposed model for a Polish national DNA bank 
Journal of Applied Genetics  2012;53(2):159-165.
Population biobanks offer new opportunities for public health, are rudimentary for the development of its new branch called Public Health Genomics, and are important for translational research. This article presents organizational models of population biobanks in selected European countries. Review of bibliography and websites of European population biobanks (UK, Spain, Estonia). Some countries establish national genomic biobanks (DNA banks) in order to conduct research on new methods of prevention, diagnosis and treatment of the genetic and lifestyle diseases and on pharmacogenetic research. Individual countries have developed different organizational models of these institutions and specific legal regulations regarding various ways of obtaining genetic data from the inhabitants, donors’ rights, organizational and legal aspects. Population biobanks in European countries were funded in different manners. In light of these solutions, the authors discuss prospects of establishing a Polish national genomic biobank for research purpose. They propose the creation of such an institution based on the existing network of blood-donation centres and clinical biobanks in Poland.
doi:10.1007/s13353-012-0082-4
PMCID: PMC3334487  PMID: 22281780
DNA banking; Genetic epidemiology; Population biobanks; Public health genomics; Life Sciences; Human Genetics; Plant Genetics & Genomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Life Sciences, general
18.  Patients’ Willingness to Participate in a Breast Cancer Biobank at Screening Mammogram 
Purpose
To characterize patients’ willingness to donate a biospecimen for future research as part of a breast cancer-related biobank involving a general screening population.
Materials and Methods
We performed a prospective cross-sectional study of 4,217 women aged 21 to 89 years presenting to our facilities for screening mammogram between December 2010 and October 2011. This HIPAA-compliant study was approved by our institutional review board. We collected data on patients’ interest in and actual donation of a biospecimen, motivators and barriers to donating, demographic information, and personal breast cancer risk factors. A multivariate logistic regression analysis was performed to identify patient-level characteristics associated with an increased likelihood to donate.
Results
Mean patient age was 57.8 years (SD 11.1 years). While 66.0% (2785/4217) of patients were willing to donate blood or saliva during their visit, only 56.4% (2378/4217) actually donated. Women with a college education (OR=1.27, p=0.003), older age (OR=1.02, p<0.001), previous breast biopsy (OR=1.23, p=0.012), family history of breast cancer (OR=1.23, p=0.004), or a comorbidity (OR=1.22, p=0.014) were more likely to donate. Asian-American women were significantly less likely to donate (OR=0.74, p=0.005). The major reason for donating was to help all future patients (42.3%) and the major reason for declining donation was privacy concerns (22.3%).
Conclusion
A large proportion of women participating in a breast cancer screening registry are willing to donate blood or saliva to a biobank. Among minority participants, Asian-American women are less likely to donate and further qualitative research is required to identify novel active recruitment strategies to ensure their involvement.
doi:10.1007/s10549-012-2324-x
PMCID: PMC3676182  PMID: 23129174
biospecimen; biobank; breast cancer; screening; patient willingness
19.  The Mayo Clinic Biobank: A building block for individualized medicine 
Mayo Clinic proceedings  2013;88(9):952-962.
OBJECTIVE
To report the design and first three years of enrollment of the Mayo Clinic Biobank.
PATIENTS AND METHODS
Preparations for this Biobank began with a 4-day Deliberative Community Engagement with local residents to obtain community input into the design and governance of the biobank. Recruitment, which began in April 2009, is ongoing with a target goal of 50,000. Any Mayo Clinic patient who is 18+ years, able to consent, and a US resident is eligible to participate. Each participant completes a health history questionnaire, provides a blood sample and allows access to existing tissue specimens and all data from their Mayo Clinic medical record (EMR). A Community Advisory Board provides ongoing advice and guidance on complex decisions.
RESULTS
After three years of recruitment, 21,736 subjects have enrolled. Participants were 58% female, 95% of European ancestry, and median age of 62 years. Seventy-four percent lived in Minnesota, 42% from Olmsted County where the Mayo Clinic Rochester is located. The five most commonly self-reported conditions were hyperlipidemia (41%), hypertension (38%), osteoarthritis (30%), any cancer (29%), and gastroesophageal reflux disease (26%). Among self-reported cancer patients, the five most common types were non-melanoma skin cancer (14%), prostate cancer (12% in men), breast cancer (4%), melanoma (3%), and cervical cancer (2% in women). Fifty-six percent of participants had at least 15 years of EMR history. To date, over sixty projects and over 69,000 samples have been approved for use.
CONCLUSION
The Mayo Clinic Biobank has quickly been established as a valuable resource for researchers.
doi:10.1016/j.mayocp.2013.06.006
PMCID: PMC4258707  PMID: 24001487
20.  Engaging diverse populations about biospecimen donation for cancer research 
Journal of Community Genetics  2014;5(4):313-327.
Clinical research increasingly relies upon the availability of appropriate genetic materials; however, the proportion of biospecimens from racial/ethnic minority patients and healthy controls are underrepresented, which preclude equitable research across all patient groups for cancer treatment. National Cancer Institute-funded Community Network Program Centers in California, Florida, and New York collaborated with local community partners to conduct three independent formative research studies with diverse (African American, Asian American, Hispanic, and White) participants to explore their knowledge, attitudes, and beliefs about biobanking, and their experiences with the donation of biospecimens. Our findings demonstrated similarities in overall low knowledge and understanding about the use of biospecimens for research. This was exacerbated for non-English speakers. Racial and ethnic groups differed with regard to a number of factors that are obstacles for participation, e.g., continuing medical mistrust (African Americans), lack of benefit (Hispanics), apprehension about the physical toll of donating (Vietnamese), usage of biospecimen for research (Hmong and Chinese), and suspicion of exploitation by corporate entities (Whites). However, participants uniformly reported general interest and willingness to participate in biobanking for altruistic purposes, particularly to benefit future generations. This interest was framed with a strong admonition that donations should be accompanied by transparency about study sponsorship and ownership, distribution and use of biospecimens, and study information that fit participants’ backgrounds and experiences. This cross-cultural regional analysis offers significant insights into the similarities and variations in opinions and perceptions about biobanking and the collection of biospecimens for use in cancer research.
doi:10.1007/s12687-014-0186-0
PMCID: PMC4159470  PMID: 24664489
Biobanking; Biospecimens; Asian Americans; African Americans; Hispanics; Medically underserved
21.  p-BioSPRE—an information and communication technology framework for transnational biomaterial sharing and access 
ecancermedicalscience  2014;8:401.
Biobanks represent key resources for clinico-genomic research and are needed to pave the way to personalised medicine. To achieve this goal, it is crucial that scientists can securely access and share high-quality biomaterial and related data. Therefore, there is a growing interest in integrating biobanks into larger biomedical information and communication technology (ICT) infrastructures. The European project p-medicine is currently building an innovative ICT infrastructure to meet this need. This platform provides tools and services for conducting research and clinical trials in personalised medicine. In this paper, we describe one of its main components, the biobank access framework p-BioSPRE (p-medicine Biospecimen Search and Project Request Engine). This generic framework enables and simplifies access to existing biobanks, but also to offer own biomaterial collections to research communities, and to manage biobank specimens and related clinical data over the ObTiMA Trial Biomaterial Manager. p-BioSPRE takes into consideration all relevant ethical and legal standards, e.g., safeguarding donors’ personal rights and enabling biobanks to keep control over the donated material and related data. The framework thus enables secure sharing of biomaterial within open and closed research communities, while flexibly integrating related clinical and omics data. Although the development of the framework is mainly driven by user scenarios from the cancer domain, in this case, acute lymphoblastic leukaemia and Wilms tumour, it can be extended to further disease entities.
doi:10.3332/ecancer.2014.401
PMCID: PMC3922646  PMID: 24567758
biobank access; specimen management; p-BioSPRE; ObTiMA; Trial Biomaterial Manager; IDB; p-biobank wrapper
22.  Newspaper coverage of biobanks 
PeerJ  2014;2:e500.
Background. Biobanks are an important research resource that provides researchers with biological samples, tools and data, but have also been associated with a range of ethical, legal and policy issues and concerns. Although there have been studies examining the views of different stakeholders, such as donors, researchers and the general public, the media portrayal of biobanks has been absent from this body of research. This study therefore examines how biobanking has been represented in major print newspapers from Australia, Canada, the United Kingdom and the United States to identify the issues and concerns surrounding biobanks that have featured most prominently in the print media discourse.
Methods. Using Factiva, articles published in major broadsheet newspapers in Canada, the US, the UK, and Australia were identified using specified search terms. The final sample size consisted of 163 articles.
Results. Majority of articles mentioned or discussed the benefits of biobanking, with medical research being the most prevalent benefit mentioned. Fewer articles discussed risks associated with biobanking. Researchers were the group of people most quoted in the articles, followed by biobank employees. Biobanking was portrayed as mostly neutral or positive, with few articles portraying biobanking in a negative manner.
Conclusion. Reporting on biobanks in the print media heavily favours discussions of related benefits over risks. Members of the scientific research community appear to be a primary source of this positive tone. Under-reporting of risks and a downtrend in reporting on legal and regulatory issues suggests that the print media views such matters as less newsworthy than perceived benefits of biobanking.
doi:10.7717/peerj.500
PMCID: PMC4121587  PMID: 25101229
Biobanks; Media representations; Public perceptions; ELSI; Consent; Privacy; Evidence-based policy
23.  Biobanks in the United States: How to Identify an Undefined and Rapidly Evolving Population 
Biopreservation and Biobanking  2012;10(6):511-517.
As part of a larger organizational study, we sought to survey biobanks in the United States. However, we encountered two problems with this population. First, no common definition of biobanks exists. Second, no census is available of these facilities from which to sample in order to implement a survey. In light of these problems, we employed a multifaceted approach using electronic searches of PubMed, RePORTER, and Google. In addition, we systematically searched for biobanks housed within universities that have NIH-designated Clinical and Translational Science Awards (CTSA). We expanded this part of the search by looking for biobanks among all members of the American Association of Medical Colleges (AAMC). Finally, we added banks to our database found previously by other researchers and banks found via correspondence with our colleagues. Our search strategy produced a database of 624 biobanks for which we were able to confirm contact information in order to conduct our online survey. Another 140 biobanks were identified but did not respond to our requests to confirm their existence or contact information. In order to maximize both the uniqueness of banks found and the greatest return on effort for each search, we suggest targeting resources that are already organized. In our work, these included the CTSA, AAMC, and part of the Google searches. We contend that our search provides a model for analysis of new fields of research and/or rapidly evolving industries. Furthermore, our approach demonstrates that with the appropriate tools it is possible to develop a systematic and comprehensive database to investigate undefined populations.
doi:10.1089/bio.2012.0034
PMCID: PMC4076972  PMID: 24845137
24.  Biobanking research on oncological residual material: a framework between the rights of the individual and the interest of society 
BMC Medical Ethics  2013;14:17.
Background
The tissue biobanking of specific biological residual materials, which constitutes a useful resource for medical/scientific research, has raised some ethical issues, such as the need to define which kind of consent is applicable for biological residual materials biobanks.
Discussion
Biobank research cannot be conducted without considering arguments for obtaining the donors’ consent: in this paper we discuss to what extent consent in biobank research on oncological residual materials has to be required, and what type of consent would be appropriate in this context, considering the ethical principles of donation, solidarity, protection of the donors’ rights and the requirements of scientific progress. Regarding the relationship between informed consent and tissue collection, storage and research, we have focused on two possible choices related to the treatment of data and samples in the biobank: irreversible and reversible anonymization of the samples, distinguishing between biobank research on residual materials for which obtaining consent is necessary and justified, and biobank research for which it is not. The procedures involve different approaches and possible solutions that we will seek to define. The consent for clinical research reported in the Helsinki Declaration regards research involving human beings and for this reason it is subordinate to specific and detailed information on the research projects.
Summary
An important ethical aspect in regard to the role of Biobanks is encouraging sample donation. For donors, seeing human samples being kept rather than discarded, and seeing them become useful for research highlights the importance of the human body and improves the attitude towards donation. This process might also facilitate the giving of informed consent more willingly, and with greater trust.
doi:10.1186/1472-6939-14-17
PMCID: PMC3616854  PMID: 23547565
Biobanks; Consent; Oncological residual material; Cancer biobanks; Residual materials biobanks; Informed consent; Ethics; Research; Solidarity
25.  Hospitalizations and Emergency Department Use of Mayo Clinic Biobank Participants within the Employee and Community Health Medical Home 
Mayo Clinic proceedings  2013;88(9):963-969.
Objective
To evaluate the participants in the Mayo Clinic Biobank for their representativeness to the entire Employee and Community Health (ECH) primary care population with regards to hospital utilization.
Patient and Methods
Participants enrolled in the Mayo Clinic Biobank from April 1, 2009, to December 31, 2010, were linked to ECH panels. Subjects were categorized into risk tiers (0–4) based on the number of health conditions as of December 31, 2010. Outcomes were ascertained through December 31, 2011. Hazard ratios (HR) and 95% confidence intervals (CI) for risk of hospitalization, ER visits, and 30-day re-hospitalization were estimated using Cox regression, accounting for age and sex.
Results
The 8,927 Biobank participants were part of an ECH panel (N=84,872). Compared to all of ECH, the Biobank-ECH participants were more likely to be female (64% vs 55%), older (median age of 58 years vs 47 years), and have a lower percentage in tier 0 (6% vs 24%). There were strong positive associations of tier (4 vs 0/1) with risk of hospitalization (HR=5.8; 95% CI, 4.6–7.5) and ER visits (HR=5.4; 95% CI, 4.2–6.8), among Biobank-ECH participants. Similar associations for risk of hospitalization (HR=8.5; 95% CI, 7.8–9.3) and ER visits (HR=6.9; 95%CI, 6.4–7.5) were observed for all of ECH.
Conclusion
Biobank-ECH participants were older and had more chronic conditions compared to the ECH panel. Nevertheless, the associations of risk tier with utilization outcomes were similar, supporting the use of the Biobank-ECH participants for assessing biomarkers for health care outcomes in the primary care setting.
doi:10.1016/j.mayocp.2013.06.015
PMCID: PMC4151531  PMID: 24001488

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