Biological sample collection and processing for molecular epidemiological studies

Relationships among biomarkers of one-carbon metabolism

One-carbon metabolism is a network of metabolic pathways, disruption of which has been associated with cancer and other pathological conditions. Biomarkers of these pathways include homocysteine (HCY), S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH). A better understanding of the relationships between these biomarkers is needed for their utilization in research. This study investigated the relationships between fasting concentrations of plasma HCY, SAM, SAH and the ratio of SAM:SAH, and serum folate, vitamin B(12) and creatinine in a healthy adult population. A cross-sectional study recruited 678 volunteers; only subjects with complete data (n = 581) were included in this analysis. Correlations were used to examine bivariate relationships among the biomarkers and multivariate linear regression determined independent relationships with HCY, SAM and SAH treated as dependent variables in separate models. Multivariate logistic regression examined determinants of a low SAM:SAH ratio (defined as having a SAM:SAH ratio in the bottom quartile and SAH value in the top quartile). HCY correlated inversely with folate and vitamin B(12) and weakly correlated with SAH and creatinine. Both SAM and SAH correlated with creatinine but were independent of serum folate and vitamin B(12). In multivariate analyses, folate, vitamin B(12), creatinine, sex and age were associated with HCY; age and creatinine were determinants of SAM, and sex and creatinine determinants of SAH. Finally, male sex and increasing creatinine levels were associated with having a low SAM:SAH ratio. Findings suggest that HCY, SAM and SAH are relatively independent parameters and reflect distinct aspects of one-carbon metabolism.

Translational research in pediatrics: tissue sampling and biobanking

Translational research is expanding and has become a focus of National Research funding agencies, touted as the primary avenue to improve health care practice. The use of human tissues for research on disease etiology is a pillar of translational research, particularly with innovations in research technologies to investigate the building blocks of disease. In pediatrics, translational research using human tissues has been hindered by the many practical and ethical considerations associated with tissue procurement from children and also by a limited population base for study, by the increasing complexities in conducting clinical research, and by a lack of dedicated child-health research funding. Given these obstacles, pediatric translational research can be enhanced by developing strategic and efficient biobanks that will provide scientists with quality tissue specimens to render accurate and reproducible research results. Indeed, tissue sampling and biobanking within pediatric academic settings has potential to impact child health by promoting bidirectional interaction between clinicians and scientists, helping to maximize research productivity, and providing a competitive edge for attracting and maintaining high-quality personnel. The authors of this review outline key issues and practical solutions to optimize pediatric tissue sampling and biobanking for translational research, activities that will ultimately reduce the burden of childhood disease.

Monitoring of systemic exposure to plant protection products and DNA damage in orchard workers

The systemic exposure of plum tree growers and operators to plant protection products (PPPs) and effects on DNA were assessed. Specifically, a GC-MS/MS method was developed and validated for the analysis of serum samples for the presence of seven active substances of PPPs. The analytical results verified the presence of myclobutanil, propargite, cypermethrin and deltamethrin in 7 out of 19 serum samples. The incidence of DNA damage was monitored using the single cell electrophoresis assay (comet assay). A paired Student's t-test revealed a statistically significant increase of SSBs in the blood samples collected at the end of the cropping period as compared to the samples collected from the same subjects before the start of PPPs application period. Moreover, the group of seven subjects with detectable serum pesticides levels revealed statistically significant increase of SSBs as compared to the group of subjects with no detectable PPP levels. The results of the present study demonstrate that the agriculture workers may exhibit detectable level of systemic exposure to the applied PPPs which are correlated to increased DNA damage during the cultivation period.

Clinical implementation of RNA signatures for pharmacogenomic decision-making

RNA profiling is increasingly used to predict drug response, dose, or toxicity based on analysis of drug pharmacokinetic or pharmacodynamic pathways. Before implementing multiplexed RNA arrays in clinical practice, validation studies are carried out to demonstrate sufficient evidence of analytic and clinical performance, and to establish an assay protocol with quality assurance measures. Pathologists assure quality by selecting input tissue and by interpreting results in the context of the input tissue as well as the technologies that were used and the clinical setting in which the test was ordered. A strength of RNA profiling is the array-based measurement of tens to thousands of RNAs at once, including redundant tests for critical analytes or pathways to promote confidence in test results. Instrument and reagent manufacturers are crucial for supplying reliable components of the test system. Strategies for quality assurance include careful attention to RNA preservation and quality checks at pertinent steps in the assay protocol, beginning with specimen collection and proceeding through the various phases of transport, processing, storage, analysis, interpretation, and reporting. Specimen quality is checked by probing housekeeping transcripts, while spiked and exogenous controls serve as a check on analytic performance of the test system. Software is required to manipulate abundant array data and present it for interpretation by a laboratory physician who reports results in a manner facilitating therapeutic decision-making. Maintenance of the assay requires periodic documentation of personnel competency and laboratory proficiency. These strategies are shepherding genomic arrays into clinical settings to provide added value to patients and to the larger health care system.

Influence of sample collection and preanalytical sample processing on the analyses of biological markers in the European multicentre study IDEFICS

OBJECTIVE

To evaluate the influence of a standardised sampling protocol and process quality across the different IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) centres on the results of the biochemical measurements.

DESIGN

Baseline survey within the community-based intervention study.

SUBJECTS

A total of 16,224 children, aged 2-8 years, enrolled in the IDEFICS baseline survey in 8 European countries. Venous or capillary blood samples were collected from 12,430 children, urine samples from 13,890 children and saliva samples from 14,019 children.

METHODS

A set of quality indicators was recorded for the biological blood, urine and saliva samples collected during the IDEFICS study. Results of blood and urine measurements were analysed and stratified by selected quality indicators.

RESULTS

Concentrations of biological markers in blood and urine measured during the IDEFICS baseline survey are associated with several quality indicators assessed in this study. Between-country variations of these biomarkers are described. It was confirmed that fasting has a big influence on the concentration of certain biomarkers. Biomarkers in morning urine samples may be erroneous if the study subjects void during the night or if samples are not taken from the very first morning urine.

CONCLUSIONS

The analysed data underline that a standardised sampling protocol is of major importance, especially in multicentre studies, but non-compliance is ever present in spite of well-defined standard operation procedures. Deviations from the protocol should therefore always be documented to avoid error pertaining to the concentration of biological markers.

Collection of human genomic DNA from neonates: a comparison between umbilical cord blood and buccal swabs

OBJECTIVE

To compare DNA yield from neonatal umbilical cord blood and buccal swab specimens.

STUDY DESIGN

Umbilical cord blood was obtained at birth in a cohort of women enrolled in a preterm labor study. If cord blood was not obtained, neonatal buccal samples were obtained using the Oragene saliva kits. DNA was extracted from all samples using the QIAamp extraction kits. DNA concentration and yield were compared between umbilical cord blood and buccal swabs.

RESULTS

DNA concentrations from umbilical cord blood (n = 35) was greater than that obtained from buccal swabs (n = 20) (total sample: 209.0 ± 110.7 ng/μL vs 6.9 ± 6.7 ng/μL respectively, P < .001; partial sample: n = 30 cord blood vs n = 11 buccal, 70.0 ± 51.4 ng/μL vs 11.3 ± 6.7 ng/μL, respectively, P < .001) and produced more total DNA (total sample: 116.5 ± 70.8 μg vs 4.2 ± 4.0 μg, P < .001; partial:14.0 ± 10.3 μg vs 1.1 ± 0.7 μg, respectively, P < .001).

CONCLUSION

Buccal swabs yield less neonatal DNA than umbilical cord blood specimens.

Measurable impact of RNA quality on gene expression results from quantitative PCR

Compromised RNA quality is suggested to lead to unreliable results in gene expression studies. Therefore, assessment of RNA integrity and purity is deemed essential prior to including samples in the analytical pipeline. This may be of particular importance when diagnostic, prognostic or therapeutic conclusions depend on such analyses. In this study, the comparative value of six RNA quality parameters was determined using a large panel of 740 primary tumour samples for which real-time quantitative PCR gene expression results were available. The tested parameters comprise of microfluidic capillary electrophoresis based 18S/28S rRNA ratio and RNA Quality Index value, HPRT1 5′–3′ difference in quantification cycle (Cq) and HPRT1 3′ Cq value based on a 5′/3′ ratio mRNA integrity assay, the Cq value of expressed Alu repeat sequences and a normalization factor based on the mean expression level of four reference genes. Upon establishment of an innovative analytical framework to assess impact of RNA quality, we observed a measurable impact of RNA quality on the variation of the reference genes, on the significance of differential expression of prognostic marker genes between two cancer patient risk groups, and on risk classification performance using a multigene signature. This study forms the basis for further rational assessment of reverse transcription quantitative PCR based results in relation to RNA quality.

Collection and handling of blood specimens for peptidomics

Pre-analytical variables can alter the analysis of blood-derived samples. In particular, sample collection and specimen preparation can alter the validity of results obtained by modern multiplex assays (e.g., LC-MS). Low-molecular weight proteins (peptides) as products of proteolytic cleavage events exhibit a close connection to protease activity and function. Altered proteolytic activity during sample collection, preparation, handling, and storage is mirrored by alterations in abundance of specific peptides. Awareness of clinical practices in medical laboratories allows for the identification of specific variables that may affect the results of a peptidomic study. Knowledge of pre-analytical variables is a prerequisite to understand and control their impact.

[Development of indicators to assess the stability of remnant blood samples stored in a biobank: experience at one institution]

BACKGROUND

One of the major concerns with biobanking is the absence of standard operating procedures to eliminate pre-analytical variation arising from sample collection, preparation, and storage. Currently, there is a lack of tools to carry out quality control procedures for stored blood samples. The aim of this study is to assess the quality of stored blood samples in our biobank and to suggest appropriate indicators for their quality control.

METHODS

The stored blood samples that we tested have been registered into our biobank since 2003. These were transferred to our biobank after carrying out routine requested tests, because the samples would have otherwise been discarded. For the purpose of quality control, we analyzed the concentrations and the integrity of DNA and RNA extracted from the stored samples and tested the levels of several serum proteins; the results were compared with the corresponding pre-storage levels.

RESULTS

A total of 19 samples were stored from 2006 to 2009. Of the 22 samples stored between 2003 and 2005, 50% showed complete DNA integrity. However, sufficient RNA integrity was noted in only 1 sample stored as recently as 2009. High blood urea nitrogen levels were also noted in the stored sera, but the increase did not correlate to the duration of storage.

CONCLUSIONS

The amount and integrity of nucleic acids extracted from stored blood samples are potential indicators that can be used for quality control. A guideline for the quality assessment of stored blood samples in a biobank is urgently needed.

Comparison of two PCR systems for the rapid detection of Leptospira spp. from kidney tissue

In this study we compared two routine PCR systems for the detection of Leptospira spp. and assessed their performance when directly applied to kidney samples from small mammals. Although the kappa value of 0.9 indicated a high level of agreement between the tests, the outer membrane lipoprotein gene lipl32 based PCR was more robust and showed a higher number of positive kidney samples.

From clinical sites to biorepositories: effectiveness in blood sample management

Today's biobanks must work to take full advantage of collected samples, while maximizing sample quality and minimizing costs to sustain operations for a long period of time. This is a tall order that will require collaboration and compromise for both end-users and collection sites. This article discusses the efforts of the Génome Québec-Centre Hospitalier Affilié Universitaire Régional de Chicoutimi Biobank to fractionate blood samples for the simultaneous preservation of plasma and DNA-containing layers while minimizing resources required for shipping and transport. This article also describes methods for successful reproducible application of the plasma-depleted blood sample to GenPlates (GenVault, Carlsbad, CA).

Before you analyze a human specimen, think quality, variability, and bias

Personalized medicine requires capabilities to detect and measure health-associated biomarkers with increasingly specific and sensitive methods, putting analytical chemists at the front lines of translational research. Analytical scientists must be upstream in the experimental design process because the analysis of a biospecimen (tissue, blood, etc.) presents technical and experimental design complexities. (To listen to a podcast about this feature, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html.).

Lung infections in cystic fibrosis: deriving clinical insight from microbial complexity

Lower respiratory tract bacterial infections, such as those associated with cystic fibrosis lung disease, represent a major healthcare burden. Treatment strategies are currently informed by culture-based routine diagnostics whose limitations, including an inability to isolate all potentially clinically significant bacterial species present in a sample, are well documented. Some advances have resulted from the introduction of culture-independent molecular assays for the detection of specific pathogens. However, the application of bacterial community profiling techniques to the characterization of these infections has revealed much higher levels of microbial diversity than previously recognized. These findings are leading to a fundamental shift in the way such infections are considered. Increasingly, polymicrobial infections are being viewed as complex communities of interacting organisms, with dynamic processes key to their pathogenicity. Such a model requires an analytical strategy that provides insight into the interactions of all members of the infective community. The rapid advance in sequencing technology, along with protocols that limit analysis to viable bacterial cells, are for the first time providing an opportunity to gain such insight.

Quality management for the collection of biological samples in multicentre studies

Large scale international multicentre studies require sophisticated quality management for the collection, processing and logistics of biological samples to ensure a maximum degree of standardisation across different environmental conditions and settings. This paper describes a quality management system for the collection of biological samples (QMS-BS) which was applied during IDEFICS, a large European multicentre study. The application was evaluated by several criteria like response rates for the different types of biological samples, measures of sample quality, compliance with the QMS-BS and efficiency of the document and sample control and of the quality assurance system. Response rates varied from 56.6% for venous blood collection to 90.1% for saliva collection. All sample types were associated with problems of sample quality (e.g. haemolysis of blood samples, lack of cooling for urine samples or desiccation of saliva samples). Overall compliance with the QMS-BS was good, with some exceptions mainly related to sample control. In conclusion the QMS-BS is a valuable tool for the management of biological sample collection in epidemiological multicentre studies.

Stability and reproducibility of simultaneously detected plasma and serum cytokine levels in asymptomatic subjects

Blood levels of cyto- and chemokines might reflect immune deregulations which might be related to lymphomagenesis. Potential utility of stored blood samples of a prospective cohort was evaluated by the effect of different blood sample types and freeze-thaw cycles on analyte levels. Bead-based immunoassays were performed on two fresh samples (serum, citrate and heparin plasma) of 10 asymptomatic adults collected 14 days apart and on aliquots of the first samples which were put through one to three freeze-thaw cycles to measure 11 cytokines, four chemokines and two adhesion molecules. Median coefficients of variation (CVs) of the measured analytes were 20%, 24% and 32% in serum, citrate and heparin plasma, respectively. Strong correlations (rank correlation coefficient 0.74-0.98) were observed between sample types, although small differences in analyte levels were observed for most analytes. Freeze-thaw cycles did not markedly change analyte levels. Our study supports the use of this assay among asymptomatic subjects in epidemiological studies.

New biomarkers for lung cancer

IMPORTANCE OF THE FIELD

Despite many efforts to improve early detection, lung cancer remains the leading cause of cancer deaths. Stage is the main determinant of prognosis and the basis for deciding treatment options. Screening tests for lung cancer have not been successful so far.

AREAS COVERED IN THE REVIEW

The article reviews the available literature related to biomarkers in use at present and those that could be used for early diagnosis, staging, prognosis, response to therapy and prediction of recurrence. The single biomarkers are analysed, divided according to the technological methods used and the locations of sampling.

WHAT THE READER WILL GAIN

The reader will gain knowledge on biomarkers in use and those now under study. The reader will also gain insights into the difficulties pertaining to the development of biomarkers, results reproducibility and clinical application.

TAKE HOME MESSAGE

Although some markers seem to be promising, at present there is no consensus on the proven value of their clinical use in lung cancer. The future lies probably in a panel of biomarkers instead of individual assays, or in predictive models derived from the integration of clinical variables and gene expression profiles.

Ensuring quality in studies linking cancer registries and biobanks

The Nordic countries have a long tradition of providing comparable and high quality cancer data through the national population-based cancer registries and the capability to link the diverse large-scale biobanks currently in operation. The joining of these two infrastructural resources can provide a study base for large-scale studies of etiology, treatment and early detection of cancer. Research projects based on combined data from cancer registries and biobanks provides great opportunities, but also presents major challenges. Biorepositories have become an important resource in molecular epidemiology, and the increased interest in performing etiological, clinical and gene-environment-interaction studies, involving information from biological samples linked to population-based cancer registries, warrants a joint evaluation of the quality aspects of the two resources, as well as an assessment of whether the resources can be successfully combined into a high quality study. While the quality of biospecimen handling and analysis is commonly considered in different studies, the logistics of data handling including the linkage of the biobank with the cancer registry is an overlooked aspect of a biobank-based study. It is thus the aim of this paper to describe recommendations on data handling, in particular the linkage of biobank material to cancer registry data and the quality aspects thereof, based on the experience of Nordic collaborative projects combining data from cancer registries and biobanks. We propose a standard documentation with respect to the following topics: the quality control aspects of cancer registration, the identification of cases and controls, the identification and use of data confounders, the stability of serum components, historical storage conditions, aliquoting history, the number of freeze/thaw cycles and available volumes.

Guidelines for the development and incorporation of biomarker studies in early clinical trials of novel agents

The National Cancer Institute (NCI) Investigational Drug Steering Committee (IDSC) charged the Biomarker Task Force to develop recommendations to improve the decisions about incorporation of biomarker studies in early investigational drug trials. The Task Force members reviewed biomarker trials, the peer-reviewed literature, NCI and U.S. Food and Drug Administration (FDA) guidance documents, and conducted a survey of investigators to determine practices and challenges to executing biomarker studies in clinical trials of new drugs in early development. This document provides standard definitions and categories of biomarkers, and lists recommendations to sponsors and investigators for biomarker incorporation into such trials. Our recommendations for sponsors focus on the identification and prioritization of biomarkers and assays, the coordination of activities for the development and use of assays, and for operational activities. We also provide recommendations for investigators developing clinical trials with biomarker studies for scientific rationale, assay criteria, trial design, and analysis. The incorporation of biomarker studies into early drug trials is complex. Thus the decision to proceed with studies of biomarkers should be based on balancing the strength of science, assay robustness, feasibility, and resources with the burden of proper sample collection on the patient and potential impact of the results on drug development. The Task Force provides these guidelines in the hopes that improvements in biomarker studies will enhance the efficiency of investigational drug development.

Mass spectrometry imaging of pharmacological compounds in tissue sections

The use of MS imaging (MSI) to resolve the spatial and pharmacodynamic distributions of compounds in tissues is emerging as a powerful tool for pharmacological research. Unlike established imaging techniques, only limited a priori knowledge is required and no extensive manipulation (e.g., radiolabeling) of drugs is necessary prior to dosing. MS provides highly multiplexed detection, making it possible to identify compounds, their metabolites and other changes in biomolecular abundances directly off tissue sections in a single pass. This can be employed to obtain near cellular, or potentially subcellular, resolution images. Consideration of technical limitations that affect the process is required, from sample preparation through to analyte ionization and detection. The techniques have only recently been adapted for imaging and novel variations to the established MSI methodologies will further enhance the application of MSI for pharmacological research.

Opening up the "Black Box": metabolic phenotyping and metabolome-wide association studies in epidemiology

BACKGROUND

Metabolic phenotyping of humans allows information to be captured on the interactions between dietary, xenobiotic, other lifestyle and environmental exposures, and genetic variation, which together influence the balance between health and disease risks at both individual and population levels.

OBJECTIVES

We describe here the main procedures in large-scale metabolic phenotyping and their application to metabolome-wide association (MWA) studies.

METHODS

By use of high-throughput technologies and advanced spectroscopic methods, application of metabolic profiling to large-scale epidemiologic sample collections, including metabolome-wide association (MWA) studies for biomarker discovery and identification.

DISCUSSION

Metabolic profiling at epidemiologic scale requires optimization of experimental protocol to maximize reproducibility, sensitivity, and quantitative reliability, and to reduce analytical drift. Customized multivariate statistical modeling approaches are needed for effective data visualization and biomarker discovery with control for false-positive associations since 100s or 1,000s of complex metabolic spectra are being processed.

CONCLUSION

Metabolic profiling is an exciting addition to the armamentarium of the epidemiologist for the discovery of new disease-risk biomarkers and diagnostics, and to provide novel insights into etiology, biological mechanisms, and pathways.

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.

Impact of blood collection devices on clinical chemistry assays

Blood collection devices interact with blood to alter blood composition, serum, or plasma fractions and in some cases adversely affect laboratory tests. Vascular access devices may release coating substances and exert shear forces that lyse cells. Blood-dissolving tube additives can affect blood constituent stability and analytical systems. Blood tube stoppers, stopper lubricants, tube walls, surfactants, clot activators, and separator gels may add materials, adsorb blood components, or interact with protein and cellular components. Thus, collection devices can be a major source of preanalytical error in laboratory testing. Device manufacturers, laboratory test vendors, and clinical laboratory personnel must understand these interactions as potential sources of error during preanalytical laboratory testing. Although the effects of endogenous blood substances have received attention, the effects of exogenous substances on assay results have not been well described. This review will identify sources of exogenous substances in blood specimens and propose methods to minimize their impact on clinical chemistry assays.

Analytical and statistical approaches to metabolomics research

Metabolomics, the global profiling of metabolites in different living systems, has experienced a rekindling of interest partially due to the improved detection capabilities of the instrumental techniques currently being used in this area of biomedical research. The analytical methods of choice for the analysis of metabolites in search of disease biomarkers in biological specimens, and for the study of various low molecular weight metabolic pathways include NMR spectroscopy, GC/MS, CE/MS, and HPLC/MS. Global metabolite analysis and profiling of two different sets of data results in a plethora of data that is difficult to manage or interpret manually because of their subtle differences. Multivariate statistical methods and pattern-recognition programs were developed to handle the acquired data and to search for the discriminating features between data acquired from two sample sets, healthy and diseased. Metabolomics have been used in toxicology, plant physiology, and biomedical research. In this paper, we discuss various aspects of metabolomic research including sample collection, handling, storage, requirements for sample analysis, peak alignment, data interpretation using statistical approaches, metabolite identification, and finally recommendations for successful analysis.

The Henry Ford production system: LEAN process redesign improves service in the molecular diagnostic laboratory: a paper from the 2008 William Beaumont hospital symposium on molecular pathology

Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here, we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN production. Our goal was to complete greater than 90% of the molecular tests in less than 3 days. The project required cooperation from different laboratory disciplines as well as individuals outside of the laboratory. The redesigned processes involved defining and standardizing the protocols and approaching blood and tissue specimens as analytes for molecular testing. The LEAN process resulted in fewer steps, approaching the ideal of a one-piece flow for specimens through collection/retrieval, transport, and different aspects of the testing process. The outcome of introducing the LEAN process has been a 44% reduction in molecular test turnaround time for tissue specimens, from an average of 2.7 to 1.5 days. In addition, extending LEAN work principles to the clinician suppliers has resulted in a markedly increased number of properly collected and shipped blood specimens (from 50 to 87%). These continuous quality improvements were accomplished by empowered workers in a blame-free environment and are now being sustained with minimal management involvement.

Testing protocols: care of biological samples in a rural setting

The purpose of this study is to evaluate collection, transport, and storage protocols of urine and air allergen samples from infants in a rural setting. Infant urine and aeroallergen samples (n = 21) are collected in the home setting in rural areas where time and distance to the central laboratory is a consideration. Urine samples are analyzed using ELISA tests after being transported using three different techniques: (a) ambient temperature, (b) dry ice, and (c) packaged on dry ice and shipped commercially. Following initial ELISA testing for levels of cytokines, urine samples are frozen at -70 degrees Celsius for 6 months. Samples are then reanalyzed for levels of cytokines. Dust samples are analyzed for levels of aeroallergens, stored at 4 degrees for 6 months, and reanalyzed. The integrity of samples varies by biomarker, shipment temperature, and storage time, creating a high degree of variability in results.

Metabonomics: a useful tool for the future surgeon

BACKGROUND

In the past decade or so, a range of technologies have emerged that have shown promise in increasing our understanding of disease processes and progression. These advances are referred to as the "omics" technologies; genomics, transcriptomics, and proteomics. More recently, another "omics" approach has come to the fore: metabonomics, and this technology has the potential for significant clinical impact. Metabonomics refers to the analysis of the metabolome, that is, the metabolic profile of a system. The advantage of studying the metabolome is that the end points of biological events are elucidated.

RESULTS

Although still in its infancy, the metabonomics approach has shown immense promise in areas as diverse as toxicology studies to the discovery of biomarkers of disease. It has also been applied to studies of both renal and hepatic transplants. Metabolome analysis may be conducted on a variety of biological fluids and tissue types and may utilize a number of different technology platforms, mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being the most popular. In this review, we cover the background to the evolution of metabonomics and its applications with particular emphasis on clinical applications.

CONCLUSIONS

We conclude with the suggestion that metabonomics offers a platform for further biomarker development, drug development, and in the field of medicine.

[Biological safety in the storage and transport of biological specimens from patients with respiratory diseases used in research settings]

Major advances in genomics and proteomics have prompted the creation of biological specimen collections and biobanks for use in biomedical research. These specimen collections and the wealth of data they generate will allow longitudinal studies to be conducted and subproducts such as DNA or RNA to be obtained. They may even be used in future studies. To ensure specimen integrity, from the outset it is necessary to define procedures for sampling, transport and storage, the subproducts to be obtained, and the end purpose, as well as to address biosafety issues and arrange for suitable equipment monitoring. Strict control of these conditions will confer added value on the specimens, as quality and traceability would be assured. This article aims to provide a general overview of the recommendations concerning biological safety, transport, and storage of biological specimens for biomedical research into respiratory diseases in accordance with current legislation.

Evaluation of reference genes for studies of gene expression in the bovine liver, kidney, pituitary, and thyroid

Expression patterns of candidate genes with important functions in animal metabolism can help to identify potential molecular markers for cattle production traits. Reverse transcription followed by polymerase chain reaction is a method for rapid and accurate mRNA quantification. However, for exact comparison of mRNA quantity in various samples or tissues, it is important to choose appropriate reference genes. In cattle, little information is available on the expression stability of housekeeping genes (HKGs). The aim of the present study is to develop a set of reference genes that can be used for normalization of concentrations of mRNAs of genes expressed in the bovine liver, kidney, pituitary and thyroid. The study was performed on 6-, 9-, and 12-month-old bulls of dairy and meat cattle breeds. Six HKGs were investigated: ACTB, GAPDH, HPRTI, SDHA, TBP, and YWHAZ. The most stably expressed potential reference HKGs differed among tissues/organs examined: ACTB, TBP, YWHAZ, GAPDH, HPRTI, and SDHA in the liver; GAPDH and YWHAZ in the kidney; GAPDH and SDHA in the pituitary; and TBP and HPRTI in the thyroid. The results showed that the use of a single gene for normalization may lead to relatively large errors, so it is important to use multiple control genes based on a survey of potential reference genes applied to representative samples from specific experimental conditions.

The CREST biorepository: a tool for molecular epidemiology and translational studies on malignant mesothelioma, lung cancer, and other respiratory tract diseases

OBJECTIVES

The Cancer of RESpiratory Tract (CREST) biorepository was established to investigate biological mechanisms and to develop tools and strategies for primary and secondary prevention of respiratory tract cancer. The CREST biorepository is focused on pleural malignant mesothelioma, a rare and severe cancer linked to asbestos exposure whose incidence is particularly high in the Ligurian region.

METHODS

The CREST biorepository includes biological specimens from (a) patients with pleural malignant mesothelioma and lung cancer, (b) patients with nonneoplastic respiratory conditions, and (c) control subjects. Whole blood, plasma, serum, lymphocytes, pleural fluid, saliva, and biopsies are collected, and a questionnaire is administered. Collection, transportation, and storage are done according to international standards.

RESULTS

As of January 31, 2008, the overall number of subjects recruited was 1,590 (446 lung cancer, 209 pleural malignant mesothelioma, and 935 controls). The biorepository includes a total of 10,055 aliquots (4,741 serum; 3,082 plasma; 1,599 whole blood; 633 pleural fluid; and 561 lymphocytes) and 107 biopsies. Demographic, clinical, and epidemiologic information is collected for each subject and processed in a dedicated database.

CONCLUSIONS

The CREST biorepository is a valuable tool for molecular epidemiology and translational studies. This structure relies on a network of contacts with local health districts that allows for an active search for patients. This is a particularly efficient approach, especially when the object of the study is a rare cancer type. The CREST experience suggests that the presence of limited resources can be overcome by the biorepository specialization, the high quality of the epidemiologic information, and the variety of samples.

Relative validity and reproducibility of a food-frequency questionnaire for estimating food intakes among Flemish preschoolers

The aims of this study were to assess the relative validity and reproducibility of a semi-quantitative food-frequency questionnaire (FFQ) applied in a large region-wide survey among 2.5–6.5 year-old children for estimating food group intakes. Parents/guardians were used as a proxy. Estimated diet records (3d) were used as reference method and reproducibility was measured by repeated FFQ administrations five weeks apart. In total 650 children were included in the validity analyses and 124 in the reproducibility analyses. Comparing median FFQ1 to FFQ2 intakes, almost all evaluated food groups showed median differences within a range of ± 15%. However, for median vegetables, fruit and cheese intake, FFQ1 was > 20% higher than FFQ2. For most foods a moderate correlation (0.5–0.7) was obtained between FFQ1 and FFQ2. For cheese, sugared drinks and fruit juice intakes correlations were even > 0.7. For median differences between the 3d EDR and the FFQ, six food groups (potatoes & grains; vegetables Fruit; cheese; meat, game, poultry and fish; and sugared drinks) gave a difference > 20%. The largest corrected correlations (>0.6) were found for the intake of potatoes and grains, fruit, milk products, cheese, sugared drinks, and fruit juice, while the lowest correlations (<0.4) for bread and meat products. The proportion of subjects classified within one quartile (in the same/adjacent category) by FFQ and EDR ranged from 67% (for meat products) to 88% (for fruit juice). Extreme misclassification into the opposite quartiles was for all food groups < 10%. The results indicate that our newly developed FFQ gives reproducible estimates of food group intake. Overall, moderate levels of relative validity were observed for estimates of food group intake.

Practical approaches to proteomic biomarkers within prostate cancer radiotherapy trials

INTRODUCTION

Proteomic biomarkers may be useful for monitoring therapeutic response and to triage cancer patients to best therapy.

OBJECTIVES

In this review, we highlight the importance of specimen acquisition, preparation and analysis in radiotherapy proteomic studies. We also discuss practical approaches for the design and execution of clinical proteomic studies using our recent experience based on specimens accrued during prostate cancer radiation therapy.

DISCUSSION AND CONCLUSIONS

Numerous proteomic methods are being employed, including high-throughput mass spectrometry and immunoassays, and using solid tissues, blood and urine for analysis. Given the potential complexity of cytokine and other protein responses, there is a need to assess proteomic signatures within serial samples as longitudinal studies during a course of fractionated radiotherapy (RT).

The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine

BACKGROUND

UK Biobank is a large prospective study in the UK to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. Extensive data and biological samples are being collected from 500,000 participants aged between 40 and 69 years. The biological samples that are collected and how they are processed and stored will have a major impact on the future scientific usefulness of the UK Biobank resource.

AIMS

The aim of the UK Biobank sample handling and storage protocol is to specify methods for the collection and storage of participant samples that give maximum scientific return within the available budget. Processing or storage methods that, as far as can be predicted, will preclude current or future assays have been avoided.

METHODS

The protocol was developed through a review of the literature on sample handling and processing, wide consultation within the academic community and peer review. Protocol development addressed which samples should be collected, how and when they should be processed and how the processed samples should be stored to ensure their long-term integrity. The recommended protocol was extensively tested in a series of validation studies. UK Biobank collects about 45 ml blood and 9 ml of urine with minimal local processing from each participant using the vacutainer system. A variety of preservatives, anti-coagulants and clot accelerators is used appropriate to the expected end use of the samples. Collection of other material (hair, nails, saliva and faeces) was also considered but rejected for the full cohort. Blood and urine samples from participants are transported overnight by commercial courier to a central laboratory where they are processed and aliquots of urine, plasma, serum, white cells and red cells stored in ultra-low temperature archives. Aliquots of whole blood are also stored for potential future production of immortalized cell lines. A standard panel of haematology assays is completed on whole blood from all participants, since such assays need to be conducted on fresh samples (whereas other assays can be done on stored samples). By the end of the recruitment phase, 15 million sample aliquots will be stored in two geographically separate archives: 9.5 million in a -80 degrees C automated archive and 5.5 million in a manual liquid nitrogen archive at -180 degrees C. Because of the size of the study and the numbers of samples obtained from participants, the protocol stipulates a highly automated approach for the processing and storage of samples. Implementation of the processes, technology, systems and facilities has followed best practices used in manufacturing industry to reduce project risk and to build in quality and robustness. The data produced from sample collection, processing and storage are highly complex and are managed by a commercially available LIMS system fully integrated with the entire process.

CONCLUSION

The sample handling and storage protocol adopted by UK Biobank provides quality assured and validated methods that are feasible within the available funding and reflect the size and aims of the project. Experience from recruiting and processing the first 40,000 participants to the study demonstrates that the adopted methods and technologies are fit-for-purpose and robust.

Gene expression analysis of interferon kappa in laser capture microdissected cervical epithelium

Optimal sample handling techniques for tissue preparation and storage, RNA extraction and quantification, and target gene detection are crucial for reliable gene expression analysis. Methods for measuring low-expressing genes, such as interferons, in human cervical samples are not described in the scientific literature. To detect interferon mRNA in human cervical samples we obtained normal and dysplastic frozen and formalin-fixed cervical biopsies from colposcopy. Histopathological diagnosis was performed by one pathologist. Cervical keratinocytes were isolated using laser capture microdissection. Immortalized keratinocytes transduced with or devoid of an HPV oncogene were used for initial method development. RNA from samples was extracted and integrity tested to compare tissue storage and extraction methods. The expression of five housekeeping genes was analyzed in cell lines and patient tissue to permit normalization between samples using quantitative real-time polymerase chain reaction. The usefulness of cDNA amplification was assessed for the detection of low-expressing interferon kappa in cervical tissue. Here we report optimal tissue storage conditions, RNA extraction, sample normalization, and transcript amplification, as well as the sensitivity of quantitative real-time polymerase chain reaction and laser capture microdissection, for interferon kappa detection in cervical tissue. Without these optimized techniques, interferon kappa detection would be unattainable in cervical samples.

Consent for genetics studies among clinical trial participants: findings from Action for Health in Diabetes (Look AHEAD)

BACKGROUND

Increasingly, genetic specimens are collected to expand the value of clinical trials through study of genetic effects on disease incidence, progression or response to interventions.

PURPOSE

and methods We describe the experience obtaining IRB-approved DNA consent forms across the 19 institutions in the Action for Health in Diabetes (Look AHEAD), a clinical trial examining the effect of a lifestyle intervention for weight loss on the risk of serious cardiovascular events among individuals with type 2 diabetes. We document the rates participants provided consent for DNA research, identify participant characteristics associated with consent, and discuss implications for genetics research.

RESULTS

IRB approval to participate was obtained from 17 of 19 institutions. The overall rate of consent was 89.6% among the 15 institutions that had completed consenting at the time of our analysis, which was higher than reported for other types of cohort studies. Consent rates were associated with factors expected to be associated with weight loss and cardiovascular disease and to affect the distribution of candidate genes. Non-consent occurred more frequently among participants grouped as African-American, Hispanic, female, more highly educated or not dyslipidemic.

LIMITATIONS

The generalizabilty of results is limited by the inclusion/exclusion criteria of the trial.

CONCLUSIONS

Barriers to obtaining consent to participate in genetic studies may differ from other recruitment settings. Because of the potentially complex associations between personal characteristics related to adherence, outcomes and gene distributions, differential rates of consent may introduce biases in estimates of genetic relationships.

Effect of freeze-thaw cycles on serum measurements of AFP, CEA, CA125 and CA19-9

AFP, CEA, CA125 and CA19-9 are commonly used serum tumour markers (TMs) in clinical practice, although their quantification by immunoassay may be influenced by pre-analytical sample handling. Though the effect of repetitive freeze-thaw cycles is generally recognized, it is not clear in detail. The present study measured (CLIA) these TMs in serum samples freshly separated and after each of five freeze-thaw cycles, in which the samples were frozen at -40 degrees C for 10 months at cycle 4 and 2 h at other cycles. Statistical analysis with the General Linear Model for Repeated Measures revealed significant decreases in the measurements of the four TMs, with the least decrease of 6.8 % for CA125 and the most decrease of 18.2 % for CA19-9 after the last cycle, and an overwhelming single cycle decrease of mean 7.7 % at cycle 4 for AFP, CEA and CA125, of 7.5 % and 9.3 % at cycles 4 and 5 for CA19-9. So it seems that measurements of AFP, CEA and CA125 are more readily affected by long-term frozen storage compared with frequent freezing-thawing, while CA19-9 is relatively unstable under both conditions.

Specimen collection and handling: standardization of blood sample collection

Preanalytical variables can alter the analysis of blood-derived samples. Prior to the analysis of a blood sample, multiple steps are necessary to generate the desired specimen. The choice of blood specimens, its collection, handling, processing, and storage are important aspects since these characteristics can have a tremendous impact on the results of the analysis. The awareness of clinical practices in medical laboratories and the current knowledge allow for identification of specific variables that affect the results of a proteomic study. The knowledge of preanalytical variables is a prerequisite to understand and control their impact.

Cytokines and other immunological biomarkers in children's environmental health studies

Environmental exposures (e.g. pesticides, air pollution, and environmental tobacco smoke) during prenatal and early postnatal development have been linked to a growing number of childhood diseases including allergic disorders and leukemia. Because the immune response plays a critical role in each of these diseases, it is important to study the effects of toxicants on the developing immune system. Children's unique susceptibility to environmental toxicants has become an important focus of the field of immunotoxicology and the use of immune biomarkers in molecular epidemiology of children's environmental health is a rapidly expanding field of research. In this review, we discuss how markers of immune status and immunotoxicity are being applied to pediatric studies, with a specific focus on the various methods used to analyze T-helper-1/2 (Th1/Th2) cytokine profiles. Furthermore, we review recent data on the effects of children's environmental exposures to volatile organic compounds, metals, and pesticides on Th1/Th2 cytokine profiles and the associations of Th1/Th2 profiles with adverse health outcomes such as pediatric respiratory diseases, allergies, cancer and diabetes. Although cytokine profiles are increasingly used in children's studies, there is still a need to acquire distribution data for different ages and ethnic groups of healthy children. These data will contribute to the validation and standardization of cytokine biomarkers for future studies. Application of immunological markers in epidemiological studies will improve the understanding of mechanisms that underlie associations between environmental exposures and immune-mediated disorders.

Plasma/serum proteomics: pre-analytical issues

High-throughput proteomics technologies tend to provide highly sensitive information about living tissues and biological fluids. Analytes are characterized by intrinsic and extrinsic properties, the latter depending on each phase of their preparation, sometimes adding artifacts with crucial repercussions in result reliability and interpretation. This review aims to address some issues that can be encountered when handling plasma and serum in experimental and clinical proteomic settings.

New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies

Epidemiological studies may require noninvasive methods for off-site DNA collection. We compared the DNA yield and quality obtained using a whole-saliva collection device (Oragene DNA collection kit) to those from three established noninvasive methods (cytobrush, foam swab, and oral rinse). Each method was tested on 17 adult volunteers from our center, using a random crossover collection design and analyzed using repeated-measures statistics. DNA yield and quality were assessed via gel electrophoresis, spectophotometry, and polymerase chain reaction (PCR) amplification rate. The whole-saliva method provided a significantly greater DNA yield (mean +/- SD = 154.9 +/- 103.05 microg, median = 181.88) than the other methods (oral rinse = 54.74 +/- 41.72 microg, 36.56; swab = 11.44 +/- 7.39 microg, 10.72; cytobrush = 12.66 +/- 6.19, 13.22 microg) (all pairwise P < 0.05). Oral-rinse and whole-saliva samples provided the best DNA quality, whereas cytobrush and swab samples provided poorer quality DNA, as shown by lower OD(260)/OD(280) and OD(260)/OD(230) ratios. We conclude that both a 10-ml oral-rinse sample and 2-ml whole-saliva sample provide sufficient DNA quantity and better quality DNA for genetic epidemiological studies than do the commonly used buccal swab and brush techniques.

Effective use of microarrays in neuroendocrine research

The development of microarray technology makes it possible to simultaneously assay the expression level of hundreds to tens of thousands of mRNA transcripts in one experiment. Genome-wide transcriptional analysis has increasing importance for many areas of neuroendocrinology research. The expense and technical complexity of microarray experiments can make it difficult to navigate the terrain of rival platforms and technologies. In this review, we provide a practical view and comparison of various microarray technologies. Affymetrix arrays, high-density cDNA arrays, membrane arrays and experimental design and data analysis are all discussed by researchers currently using these techniques to study gene regulation in neuroendocrine tissues.