Biobanking: The Melding of Research with Clinical Care

Studying the impact of translational genomic research: Lessons from eMERGE

Two major goals of the Electronic Medical Record and Genomics (eMERGE) Network are to learn how best to return research results to patient/participants and the clinicians who care for them and also to assess the impact of placing these results in clinical care. Yet since its inception, the Network has confronted a host of challenges in achieving these goals, many of which had ethical, legal, or social implications (ELSIs) that required consideration. Here, we share impediments we encountered in recruiting participants, returning results, and assessing their impact, all of which affected our ability to achieve the goals of eMERGE, as well as the steps we took to attempt to address these obstacles. We divide the domains in which we experienced challenges into four broad categories: (1) study design, including recruitment of more diverse groups; (2) consent; (3) returning results to participants and their health care providers (HCPs); and (4) assessment of follow-up care of participants and measuring the impact of research on participants and their families. Since most phases of eMERGE have included children as well as adults, we also address the particular ELSI posed by including pediatric populations in this research. We make specific suggestions for improving translational genomic research to ensure that future projects can effectively return results and assess their impact on patient/participants and providers if the goals of genomic-informed medicine are to be achieved.

A Preliminary Study to Explore the Informed Consent Approach and the Ethical Challenges in the Malaysian Biobanking for Research

Since 2005, Malaysia has established several biobanks to keep in line with the advancement of biomedical research and development of biobanks in other countries such as the UK and the USA. Despite the establishment of several biobanks in Malaysia, little is known about the informed consent approach in biobanking research and its ethical challenges. This study aims to identify the approach in obtaining informed consent in the Malaysian biobanking for research and explore its ethical challenges. Using non-probability purposive sampling, an in-depth interview with the key informants was conducted in Klang Valley. Based on the interviews, broad consent is the main approach used in obtaining informed consent in biobanking for research in Malaysia and five major ethical challenges were identified. These challenges include the informants’ opinion on the current informed consent approach, understanding participants’ rights, the role of the research ethics committee, biobanking governance in Malaysia, and informants’ knowledge and awareness. In summary, there is a lack of understanding among those involved in biobanking on the ethical, legal, and social aspects of biobanking for research in Malaysia.

The Evolution of a Large Biobank at Mass General Brigham

The Mass General Brigham Biobank (formerly Partners HealthCare Biobank) is a large repository of biospecimens and data linked to extensive electronic health record data and survey data. Its objective is to support and enable translational research focused on genomic, environmental, biomarker and family history associations with disease phenotypes. The Biobank has enrolled more than 135,000 participants, generated genomic data on more than 65,000 of its participants, distributed approximately 153,000 biospecimens, and served close to 450 institutional studies with biospecimens or data. Although the Biobank has been successful, based on some measures of output, this has required substantial institutional investment. In addition, several challenges are ongoing, including: (1) developing a sustainable cost model that doesn’t rely as heavily on institutional funding; (2) integrating Biobank operations into clinical workflows; and (3) building a research resource that is diverse and promotes equity in research. Here, we describe the evolution of the Biobank and highlight key lessons learned that may inform other efforts to build biobanking efforts in health system contexts.

Metformin for pregnancy and beyond: the pros and cons

CONTEXT AND AIM

Metformin has been used in pregnancy since the 1970s. It is cheap, widely available and is acceptable to women. Despite its increasing use, controversy remains surrounding its benefits and risks. Metformin effectively reduces hyperglycaemia for the mother during pregnancy and it reduces rates of macrosomia and neonatal hypoglycaemia. However, concern exists surrounding an increase in the rate of SGA births and obesity in childhood. We aim to review the evidence and expert opinion behind metformin in pregnancy through to the post-partum period.

METHODS

We performed a literature review of relevant studies from online databases using a combination of keywords. We also searched the references of retrieved articles for pertinent studies.

RESULTS

There is strong evidence that metformin is safe in early pregnancy with no risk of congenital malformations. If used throughout pregnancy, it is likely to lead to reduced maternal weight gain and reduced insulin dose in women with type 2 diabetes. In infants, metformin reduces hypoglycaemia and macrosomia but may increase the rate of infants born SGA. There is some evidence of an increased risk of obesity and altered fat distribution in offspring. Metformin appears well tolerated in pregnancy and is more acceptable to women than insulin therapy.

CONCLUSION

Due to increasing rates of maternal obesity, GDM and type 2 diabetes, metformin use in pregnancy is increasing. Overall, it appears safe and effective but further research is needed to examine mechanisms linking metformin to obesity reported during childhood in some follow-up studies.

Research participant understanding and engagement in an institutional, self-consent biobank model

The number of institutional and governmental biobanks and the target enrollment sizes of modern biobanks are increasing, affording more opportunities for the public to participate in biobanking efforts. In parallel with these expansions are pressures to increase the efficiency of obtaining informed consent using shorter consent forms that cover a broader scope of research and increasingly include provisions for return of research or clinical genetic test results to participants. Given these changes, how well these participants understand genetics, their level of understanding of what they are consenting to, and their wishes to engage longitudinally and receive biobank results are not well understood. We surveyed participants in a large, medical system-based biobank who had enrolled through a two-page, self-consent process about their baseline knowledge of genetics, understanding and recall of the consent process, wishes for future contact and engagement, and level of interest in receiving clinical genetic testing results. A total of 856 consented persons participated in the survey (67% women; 67% white). Participants' general reported genetics knowledge was relatively high (mean 11.60 of 15 questions answered correctly) as was recall of key elements from the two-page consent form. Overall participant enthusiasm for future contact by the biobank and for receiving clinical genetic testing results was high. The use of a two-page, self-consent process in a large, institutional biobank resulted in high levels of consent recall and enthusiasm for future ongoing engagement and receipt of genetic testing results by participants.

Archival May-Grünwald-Giemsa-Stained Bone Marrow Smears Are an Eligible Source for Molecular DNA Research

Biobanking is increasingly important in studying complex heterogeneous diseases. Therefore, it is essential to ensure the sample quality after long-term storage for reliable downstream analyses. The Clinical Biobank of the Jessa Hospital and the University Biobank Limburg (UBiLim) hold a continuously growing collection of hematological samples, including May-Grünwald-Giemsa (MGG)- and Perls' Prussian Blue (PPB)-stained bone marrow (BM) smears, stored at room temperature (RT) for up to 20 years. In this study, we investigated the effect of short- and long-term storage on the quality of DNA and RNA extracted from these BM smears to assess their fitness-for-purpose in downstream molecular applications, including agarose gel electrophoresis, bio-analyzer analysis, quantitative polymerase chain reaction (qPCR), and targeted next-generation sequencing (NGS). The RNA quality was very low for all samples, independent of storage time or staining method. The DNA from PPB-stained BM smears was already degraded after 1 year of storage and correspondingly could not be used for reliable downstream molecular analysis. In contrast, DNA extracted from MGG-stained BM smears stored for up to 10 years was able to generate high-quality data in qPCR and targeted NGS analyses. Longer storage periods (>15 years) of these samples revealed a high degree of degradation and a significant amount of DNA transitions and transversions. In conclusion, the DNA extracted from archival MGG-stained BM smears with a storage time up to at least 10 years was qualitatively good and fit for downstream analysis, including targeted NGS. This indicates that these samples are an eligible source for molecular DNA research and for studying complex diseases.

Equitable Participation in Biobanks: The Risks and Benefits of a "Dynamic Consent" Approach

Participation in biobanks tends to favor certain groups—white, middle-class, more highly-educated—often to the exclusion of others, such as indigenous people, the socially-disadvantaged and the culturally and linguistically diverse. Barriers to participation, which include age, location, cultural sensitivities around human tissue, and issues of literacy and language, can influence the diversity of samples found in biobanks. This has implications for the generalizability of research findings from biobanks being able to be translated into the clinic. Dynamic Consent, which is a digital decision-support tool, could improve participants' recruitment to, and engagement with, biobanks over time and help to overcome some of the barriers to participation. However, there are also risks that it may deepen the “digital divide” by favoring those with knowledge and access to digital technologies, with the potential to decrease participant engagement in research. When applying a Dynamic Consent approach in biobanking, researchers should give particular attention to adaptations that can improve participant inclusivity, and evaluate the tool empirically, with a focus on equity-relevant outcome measures. This may help biobanks to fulfill their promise of enabling translational research that is relevant to all.

Enhancing Electronic Health Record Data with Geospatial Information

Electronic Health Record (EHR)-derived data is a valuable resource for research, and efforts are underway to overcome some of its limitations by using data from external sources to gain a fuller picture of patient characteristics, symptoms, and exposures. Our goal was to assess the utility of augmenting EHR data with geocoded patient addresses to identify geospatial variation of disease that is not explained by EHR-derived demographic factors. Using 2011-2014 encounter data from 27,604 University of Pennsylvania Hospital System asthma patients, we identified factors associated with asthma exacerbations: risk was higher in female, black, middle aged to elderly, and obese patients, as well as those with positive smoking history and with Medicare or Medicaid vs. private insurance. Significant geospatial variability of asthma exacerbations was found using generalized additive models, even after adjusting for demographic factors. Our work shows that geospatial data can be used to cost-effectively enhance EHR data.

Biobanks and Their Clinical Application and Informatics Challenges

Biobanks are one of the most important biomedical research resources and contribute to the development of biomarker detection, molecular diagnosis, translational medicine, and multidisciplinary disease research, as well as studies of interactions between genetic and environmental or lifestyle factors. Aiming for the wide clinical application of biobanks, biobanking efforts have recently switched from a focus on accumulating samples to both formalizing and sustaining collections in light of the rapid progress in the fields of personalized medicine and bioinformatics analysis. With the emergence of novel molecular diagnostic technologies, although the bioinformatics platform of biobanks ensures reliable bioinformatics analysis of patient samples, there are a series of challenges facing biobanks in terms of the overall harmonization of policies, integrated processes, and local informatics solutions across the network. Further, there is a controversy regarding the increased role of ethical boards, governance, and accreditation bodies in ensuring that collected samples have sufficient informatics capabilities to be used in biobanks. In this volume, we present a selection of current issues on the inevitable challenges of the clinical application of biobanks in informatics.

Uses for an HIV specimen repository: experience and lessons for other conditions

Biobanking is increasingly becoming recognized as an emerging resource for enhancing both clinical care and research. Establishing a useful repository of clinical specimens is, however, challenging. Below we discuss the barriers encountered and lessons learned while developing and using a specimen repository integrated into an HIV care program. Substantial effort, time, cost and foresight coupled with good fortune in establishing a biobank are, however, needed to improve patient care and research productivity. Disease and population selection, ethics, legal implications, costs and sustainable funding are critical areas to consider prior to initiating a repository. We discuss these topics and demonstrate some of the beneficial results achieved in HIV, which may be relevant to other conditions, from establishing even a small repository.

Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer

BACKGROUND/AIM

To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses.

MATERIALS AND METHODS

FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide's image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed.

RESULTS

High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed.

CONCLUSION

This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists' knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine.

Engaging diverse populations in biospecimen donation: results from the Hoy y Mañana study

The disproportionately lower number of certain subpopulations participating in clinical and prevention research has a significant impact on the representativeness of scientific outcomes. The Hoy y Mañana program (Today and Tomorrow) was developed as a culturally and linguistically appropriate education program to engage diverse medically underserved populations without a cancer diagnosis in biospecimen donation for cancer genomic research. Participants were recruited to in-depth community-based educational programs (∼45-60-min duration) or during open events in the community based on a convenience sampling. Programs were offered in English and Spanish. An on-site mobile lab along with phlebotomy services was provided at all programs and events to collect participant biospecimen (blood) samples to be stored at the cancer center's Data Bank and BioRepository (DBBR). The distributions for education, race/ethnicity, and gender were similar across the event types. Most of the participants were women. The analysis sample had a total of 311 participants, including 231 from the education programs and 80 participants from open events. Those with a higher education (college or more) were more likely to donate than those with a lower level of education (high school or less) (45 vs 28 %, p = 0.007). Actual donation status was not associated with age or race. Willingness to donate a biospecimen and biospecimen donation rates followed the same pattern with respect to participants with higher levels of education being more willing to donate and giving a blood donation. Prior to outreach efforts, less than 6 % of specimens donated to DBBR from healthy/non-cancer patients were from minority participants.

Engaging diverse populations in biospecimen donation: results from the Hoy y Mañana study

The disproportionately lower number of certain subpopulations participating in clinical and prevention research has a significant impact on the representativeness of scientific outcomes. The Hoy y Mañana program (Today and Tomorrow) was developed as a culturally and linguistically appropriate education program to engage diverse medically underserved populations without a cancer diagnosis in biospecimen donation for cancer genomic research. Participants were recruited to in-depth community-based educational programs (∼45-60-min duration) or during open events in the community based on a convenience sampling. Programs were offered in English and Spanish. An on-site mobile lab along with phlebotomy services was provided at all programs and events to collect participant biospecimen (blood) samples to be stored at the cancer center's Data Bank and BioRepository (DBBR). The distributions for education, race/ethnicity, and gender were similar across the event types. Most of the participants were women. The analysis sample had a total of 311 participants, including 231 from the education programs and 80 participants from open events. Those with a higher education (college or more) were more likely to donate than those with a lower level of education (high school or less) (45 vs 28 %, p = 0.007). Actual donation status was not associated with age or race. Willingness to donate a biospecimen and biospecimen donation rates followed the same pattern with respect to participants with higher levels of education being more willing to donate and giving a blood donation. Prior to outreach efforts, less than 6 % of specimens donated to DBBR from healthy/non-cancer patients were from minority participants.

Proceedings of the 1st Puerto Rico Biobanking Workshop

The 1st Puerto Rico Biobanking Workshop took place on August 20st, 2014 in the Auditorium of the Comprehensive Cancer Center of the University of Puerto Rico, Medical Sciences Campus in San Juan Puerto Rico. The program for this 1-day, live workshop included lectures by three biobanking experts, followed by presentations from existing biobanks in Puerto Rico and audience discussion. The need for increasing biobanking expertise in Puerto Rico stems from the fact that Hispanics in general are underrepresented in the biobanks in existence in the US, which limits the research conducted specifically to understand the molecular differences in cancer cells compared to other better studied populations. In turn, this lack of information impairs the development of better diagnostic and therapeutic approaches for our population. Dr. James Robb, M.D., F.C.A.P., consulting pathologist to the National Cancer Institute (NCI) and the Office of Biorepositories and Biospecimen Research (OBBR), opened the workshop with a discussion on the basic aspects of the science of biobanking (e.g., what is a biobank; its goals and objectives; protocols and procedures) in his talk addressing the importance of banking tissues for advancing biomedical research. Next, Dr. Gustavo Stefanoff, from the Cancer Institutes Network of Latin America (RINC by its name in Spanish), explained the mission, objectives, and structure of the Network of Latin-American and Caribbean Biobanks (REBLAC by its name in Spanish), which despite limited resources and many challenges, currently accrue high quality human tissue specimens and data to support cancer research in the region. Dr. Robert Hunter-Mellado, Professor of Internal Medicine, Universidad Central del Caribe, followed with an examination of the ethical and regulatory aspects of biobanking tissues for future research, including informed consent of subjects; protection of human subjects rights; and balancing risks and benefit ratios. In the afternoon, the directors of existing biobanks in Puerto Rico (the Puerto Rico Biobank, the Comprehensive Cancer Center biobank, and an HIV-focused biobank at Universidad Central del Caribe) presented their experiences and challenges with establishing biobanks for research in Puerto Rico. In sum, this workshop presented opportunities to share knowledge in the science of biobanking, for further training, and of networking among the participants (34 from 4 different institutions), which will strengthen the collaborative links between investigators studying cancer in Latin America, the Caribbean, and the US.

The evolution of withdrawal: negotiating research relationships in biobanking

The right to withdraw from research, along with the necessity of adequately informed consent, is at the heart of the post-Nuremburg code of ethical safeguards in biomedical research on human participants. As biomedical research moves away from direct interventional studies towards research using networks of linked human tissue samples and data, however, questions arise about what withdrawal can and should mean in these new contexts. Some of the more expansive traditional understandings, such as the right to withdraw from a study 'at any time' are limited in practice by the nature of biobank- supported research, particularly where it makes possible widespread dissemination and ongoing reuse of data. It is time for a more nuanced, granular arrangement for withdrawal, appropriate to the ongoing relationships between participants and long-term biobanking enterprises.