Biobank literature update week 30 (2015)
[1] The Cryoprotectant Effect of Polysaccharides from Plants and Microalgae on Human White Blood
Cells. Khudyakov AN, Polezhaeva TV, Zaitseva OO et al. Biopreserv Biobank 2015. The use of
carbohydrates as cryoprotectants is increasing. In this study the effects of incorporating polysaccharides
extracted from plants and microalgae originating in northern Russia, into cryoprotectant solutions used
to preserve human white blood cells were investigated. Cells in the presence of the polysaccharides were
cooled to either -40 degrees C or -80 degrees C, using a two-step cooling process. The morphological and
functional indicators of the cryopreserved leukocytes were assessed by light microscopy. When
combined with glycerol, the pectin-polysaccharides Lemnan from common duckweed (Lemna minor L.)
and Comaruman from marsh cinquefoil (Comarum palustre L), were capable of lowering the freezing
point of the cryoprotectant solution and helped to preserve the integrity of the human white blood cell
membranes at temperatures below zero. In addition, the increase in phagocytic activity of neutrophils
was confirmed. In the context of the contemporary search for effective cell cryoprotectants, the results
of this research demonstrate that the cryopreservation of biospecimens in a polysaccharide environment
is a promising trend in applied medicine, which can be considered an alternative to traditional cryogenic
nitrogen techniques.
[2] Tube Polypropylene: A Neglected Critical Parameter for Protein Adsorption During Biospecimen
Storage. Kofanova OA, Mommaerts K, Betsou F. Biopreserv Biobank 2015. This biospecimen research
case study illustrates the importance of a neglected pre-analytical factor, the polypropylene type of
storage tubes. We measured amyloid beta1-42 peptide and showed that a non-irradiated, homopolymer
type of polypropylene has the lowest adsorption properties.
[3] DogMATIC-A Remote Biospecimen Collection Kit for Biobanking. Milley KM, Nimmo JS, Bacci B et al.
Biopreserv Biobank 2015. Canine tumors are valuable comparative oncology models. This research was
designed to create a sustainable biobank of canine mammary tumors for breast cancer research. The aim
was to provide a well-characterized sample cohort for specimen sharing, data mining, and long-term
research aims. Canine mammary tumors are most frequently managed at a local veterinary clinic or
hospital. We adopted a biobank framework based on a large number of participating veterinary hospitals
and clinics acting as collection centers that were serviced by a centralized storage facility. Recruitment
was targeted at rural veterinary clinics. A tailored, stable collection kit (DogMATIC) was designed that
was used by veterinarians in remote or rural locations to collect both fresh and fixed tissue for
submission to the biobank. To validate this methodology the kit design, collection rate, and sample
quality were analyzed. The Australian Veterinary Cancer Biobank was established as a network of 47
veterinary clinics and three veterinary pathology laboratories spanning over 200,000 km2. In the first 12
months, 30 canine mammary tumor cases were submitted via the DogMATIC kit. Pure intact RNA was
isolated in over 80% of samples with an average yield of 14.49 mug. A large network biobank, utilizing
off-site collection with the DogMATIC kit, was successfully coordinated. The creation of the Australian
Veterinary Cancer Biobank has established a long-term, sustainable, comparative oncology research
resource in Australia. There are broader implications for biobanking with this very different form of
collection and banking.
[4] Impact of in Vivo Ischemic Time on RNA Quality-Experiences from a Colon Cancer Biobank. Olsen J,
Kirkeby LT, Eiholm S et al. Biopreserv Biobank 2015. Considerable effort has been made to improve
differentiated diagnostics as well as personalized treatment for colorectal cancer patients. High-quality
fresh frozen tissue is often required to investigate relevant molecular signatures in these patients. In
RNA expression studies, the "RNA integrity number" is widely accepted as a reliable marker of RNA
Biobank literature update week 30 (2015)
quality. Here, we investigate the feasibility of obtaining high-quality tissue from a colon cancer biobank
and the impact of in vivo ischemic time and various technical and clinicopathological factors on RNA
quality. Biopsies were obtained immediately following the tumor removal. The time from clamping the
main arterial supply to resection and removal of the tumor was used to estimate the in vivo ischemic
time. We did not observe a significant difference in RNA quality between normal tissue and tumor tissue.
We observed a significant correlation between in vivo ischemic time and RNA quality in normal tissue (r =
-0.24, p<0.001) but not in tumor tissue. Male gender and laparoscopic procedure were also significantly
associated with lower RNA quality in normal tissue only. In tumor tissue, poor differentiation was
associated with low RNA quality. In conclusion, in vivo ischemic time, surgical procedure, and gender
have minor but significant effects on the quality of RNA from normal colon tissue but not tumor tissue.
Poorly differentiated tumors are associated with lower RNA quality. Although its impact is low, it can still
be considered to note in vivo ischemic time in colon cancer specimen procurement.
[5] Sharing and Reuse of Sensitive Data and Samples: Supporting Researchers in Identifying Ethical and
Legal Requirements. Sariyar M, Schluender I, Smee C, Suhr S. Biopreserv Biobank 2015. Availability of
and access to data and biosamples are essential in medical and translational research, where their reuse
and repurposing by the wider research community can maximize their value and accelerate discovery.
However, sharing human-related data or samples is complicated by ethical, legal, and social sensitivities.
The specific ethical and legal requirements linked to sensitive data are often unfamiliar to life science
researchers who, faced with vast amounts of complex, fragmented, and sometimes even contradictory
information, may not feel competent to navigate through it. In this case, the impulse may be not to
share the data in order to safeguard against unintentional misuse. Consequently, helping data providers
to identify relevant ethical and legal requirements and how they might address them is an essential and
frequently neglected step in removing possible hurdles to data and sample sharing in the life sciences.
Here, we describe the complex regulatory context and discuss relevant online tools-one which the
authors co-developed-targeted at assisting providers of sensitive data or biosamples with ethical and
legal questions. The main results are (1) that the different approaches of the tools assume different user
needs and prior knowledge of ethical and legal requirements, affecting how a service is designed and its
usefulness, (2) that there is much potential for collaboration between tool providers, and (3) that
enriched annotations of services (e.g., update status, completeness of information, and disclaimers)
would increase their value and facilitate quick assessment by users. Further, there is still work to do with
respect to providing researchers using sensitive data or samples with truly 'useful' tools that do not
require pre-existing, in-depth knowledge of legal and ethical requirements or time to delve into the
details. Ultimately, separate resources, maintained by experts familiar with the respective fields of
research, may be needed while-in the longer term-harmonization and increase in ease of use will be very
desirable.
[6] The Social Value of Knowledge and International Clinical Research. Wenner DM. Dev World Bioeth
2015; 15:76-84. In light of the growth in the conduct of international clinical research in developing
populations, this paper seeks to explore what is owed to developing world communities who host
international clinical research. Although existing paradigms for assigning and assessing benefits to host
communities offer valuable insight, I criticize their failure to distinguish between those benefits which
can justify the conduct of research in a developing world setting and those which cannot. I argue that the
justification for human subjects research is fundamentally grounded in the social value of knowledge,
and that this value is context-dependent in a manner which should inform our ethical evaluation of the
conduct of research in specific settings. I propose a new framework for the assessment of research
Biobank literature update week 30 (2015)
benefits assigned to developing world host communities, a natural implication of which is to limit the
types of research projects which may permissibly be conducted in developing world settings.
[7] Epigenome data release: a participant-centered approach to privacy protection. Dyke SO, Cheung
WA, Joly Y et al. Genome Biol 2015; 16:142. Large-scale epigenome mapping by the NIH Roadmap
Epigenomics Project, the ENCODE Consortium and the International Human Epigenome Consortium
(IHEC) produces genome-wide DNA methylation data at one base-pair resolution. We examine how such
data can be made open-access while balancing appropriate interpretation and genomic privacy. We
propose guidelines for data release that both reduce ambiguity in the interpretation of open-access data
and limit immediate access to genetic variation data that are made available through controlled access.
[8] Leveraging Epidemiologic and Clinical Collections for Genomic Studies of Complex Traits. Crawford
DC, Goodloe R, Farber-Eger E et al. Hum Hered 2015; 79:137-146. BACKGROUND/AIMS: Present-day
limited resources demand DNA and phenotyping alternatives to the traditional prospective populationbased epidemiologic collections. METHODS: To accelerate genomic discovery with an emphasis on
diverse populations, we - as part of the Epidemiologic Architecture for Genes Linked to Environment
(EAGLE) study - accessed all non-European American samples (n = 15,863) available in BioVU, the
Vanderbilt University biorepository linked to de-identified electronic medical records, for genomic
studies as part of the larger Population Architecture using Genomics and Epidemiology (PAGE) I study.
Given previous studies have cautioned against the secondary use of clinically collected data compared
with epidemiologically collected data, we present here a characterization of EAGLE BioVU, including the
billing and diagnostic (ICD-9) code distributions for adult and pediatric patients as well as comparisons
made for select health metrics (body mass index, glucose, HbA1c, HDL-C, LDL-C, and triglycerides) with
the population-based National Health and Nutrition Examination Surveys (NHANES) linked to DNA
samples (NHANES III, n = 7,159; NHANES 1999-2002, n = 7,839). RESULTS: Overall, the distributions of
billing and diagnostic codes suggest this clinical sample is a mixture of healthy and sick patients like that
expected for a contemporary American population. CONCLUSION: Little bias is observed among health
metrics, suggesting this clinical collection is suitable for genomic studies along with traditional
epidemiologic cohorts. (c) 2015 S. Karger AG, Basel.
[9] Constructing populations in biobanking. Tupasela A, Snell K, Canada JA. Life Sci Soc Policy 2015;
11:24. This article poses the question of whether biobanking practices and standards are giving rise to
the construction of populations from which various biobanking initiatives increasingly draw on for
legitimacy? We argue that although recent biobanking policies encourage various forms of engagement
with publics to ensure legitimacy, different biobanks conceptualize their engagement strategies very
differently. We suggest that biobanks undertake a broad range of different strategies with regard to
engagement. We argue that these different approaches to engagement strategies are contributing to the
construction of populations, whereby specific nationalities, communities, societies, patient groups and
political systems become imbued or bio-objectified with particular characteristics, such as compliant,
distant, positive, commercialized or authoritarian. This bio-objectification process is problematic in
relation to policy aspirations ascribed to biobanking engagement since it gives rise to reified notions of
different populations.
[10] Optimizing sharing of hospital biobank samples. Riegman PH, de Jong B, Daidone MG et al. Sci
Transl Med 2015; 7:297fs231. Implementing technical guidelines and standards as well as ways to boost
cooperation should facilitate sharing of hospital biobank samples.
Biobank literature update week 30 (2015)