ReviewBiological sample collection and processing for molecular epidemiological studies
Introduction
In recent years, epidemiology has been enriched tremendously with tools from molecular biology. It has branched into a complex field, named molecular epidemiology, incorporating the principles and methods of traditional epidemiology and the new, expanding knowledge of molecular events that lead to disease [1], [2], [3], [4], [5], [6]. The concept of biomarkers has been introduced to describe the molecular events characteristic for various stages between exposure and disease [7], [8], [9]. Molecular epidemiology offers insights into specific mechanisms underlying the causation of disease, including the interaction of genetic and environmental factors, which may determine individual susceptibility to toxic exposures [10]. Thus, developments in molecular epidemiology allow researchers to better understand mechanisms of toxicity, evaluate whether there is a causal relationship between specific hazards and biological effects, more accurately assess the risk from exposures to certain hazards, differentiate between groups of higher or lower susceptibility, and provide solid scientific support to policy makers toward intervention strategies [11].
Knowledge and appreciation of the continually developing biological/biochemical tools must be incorporated into study designs and procedures. In this light, certain provisions must be made for the preparation, preservation, and storage of biological samples collected for epidemiological, and other monitoring, studies. Hundreds of thousands of samples are currently being collected in many ongoing studies. New proposed projects will result in even more collected and banked biological specimens [12]. Despite the importance of biological sample collection and banking, very little has been published on selection and validation of these procedures and how they can affect the outcome of molecular epidemiology studies [13], [14].
The purpose of this paper is to discuss the challenges and potential pitfalls of sample collection, processing, and banking, based on our experience with large epidemiological studies of genetic endpoints, in the Superfund Basic Research Program and Children’s Environmental Health Center, at the University of California, Berkeley. The factors affecting the quality and the potential future use of biological samples are discussed and some of the provisions that must be made during collection, processing, and storage of samples are also addressed.
Section snippets
Challenges of molecular epidemiology
Fig. 1 presents the components of a molecular epidemiologic study that includes collection of biological samples for future analysis of various biomarkers. This review focuses on the components of the figure highlighted in bold, specifically the sample collection, processing and banking. The other components are mentioned briefly.
The main challenges that molecular epidemiologists face are: (a) obtaining a large amount of information from limited samples; (b) making provisions for evaluation of
Study design
In many epidemiologic studies, the collection of biological samples has been often limited to serum and urine [18]. However, many of the new molecular tools use other types of biological samples and, thus, require different more extensive and careful collection and processing procedures [19]. For example, in studies of environmental epidemiology, the target tissue of an exposure and its metabolic route are important considerations. As shown in cases of exposure to formaldehyde via inhalation,
Informed consent
The rapidly expanding potential of biotechnology and the growing public concern about undisclosed use of participants’ biologic materials has led to complex ethical issues, and the issue of informed consent acquires a new dimension. Ethical concerns arise that challenge the traditional process of obtaining informed consent [26]. Until recently, participants were asked to give consent in order to inform them of immediate potential risks inherent in the study. Now, study scientists need to obtain
Interaction between study subjects, field personnel and researchers
For a reliable and consistent sample collection, it is essential to establish clear communication between scientists, staff, and study subjects. The collection process depends as much on the nurse or technical staff who collect the specimens, as on the study subject. Special collection procedures may be necessary if collecting specimens from a special population, such as children. For example, blood collection from children often requires a pediatric phlebotomist. Whenever possible, collection
Sample processing
Whether the original biological sample is whole blood, urine, buccal cells, bronchial lavage, or other tissue (e.g. biopsies), the processing can produce a variety of banked specimens for future purposes. The sooner the samples are processed the better the quality of the extracted components of interest. Processing may be extremely simple, for example, aliquoting and freezing, or separation of blood into clot and serum. Efficient and effective processing ensures that the appropriate components
Sample banking
Large epidemiological studies produce tens of thousands of valuable samples that may be stored for years. It becomes apparent from the descriptions above that making provisions for future studies can lead to a wide variety of processed samples originating from a single tube of blood. Adequate physical storage, and an effective labeling and inventory management system are essential.
Labeling of samples so that they are efficiently tracked and retrieved can be done with electronic data management
Sample analysis
A broad spectrum of analytical methods with equally broad applications is available today: simple toxic substance detection (e.g. lead, mercury, benzene metabolites); immunological methods (ELISA, RIA, flow-cytometry) to detect levels of antibodies, cytokines, protein or DNA adducts, etc.; classical cytogenetic methods that detect chromosomal aberrations, SCE, MN formation; or more sophisticated multicolor FISH; or finally, advanced genetic analysis, based on the TaqMan®, or microarray
Laboratory core
Our experience in meeting needs of sample collection and processing has led to the formation of Laboratory Cores responsible for several large epidemiological projects for the Superfund Basic Research Program and for the Center for Children’s Environmental Health Research at UC Berkeley. The Specific goals of the Laboratory Cores include: (a) development of sample collection and processing protocols (SOPs) and QA/QC procedures; (b) coordination of sample handling with the field offices and/or
Summary
We have presented a series of issues related to sample collection, processing, and banking. The advances in molecular genetics can only be taken advantage of if sample quality is assured for already available and future biomarkers. High-throughput technology offers enormous power to the analysis of large number of samples in a time efficient manner, along with increased sensitivity, accuracy and reproducibility. Proper handling of biological samples from the time of collection to the analysis
Acknowledgements
We appreciate commitment and outstanding work of all laboratory assistants and field staff of the CHAMACOS and Superfund Laboratory Cores, especially Kelly Birch, Selene Jaramillo, Terri Manzur, Amanda Kemper, Paurene Duramad, Jin Bae, Sean Swearingen, Dan Golden, Yen-yin Wu, Ephraim Woldesalassie and Alan Ho. Our special thanks to Dr. Errol Zeiger for his helpful comments and suggestions during preparation of this manuscript. This work was supported by NIEHS grants P42 ES04705, P30 ES01896,
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