HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples

There is a substantial list of pre-analytical variables that can alter the analysis of blood-derived samples. We have undertaken studies on some of these issues including choice of sample type, stability during storage, use of protease inhibitors, and clinical standardization. As there is a wide range of sample variables and a broad spectrum of analytical techniques in the HUPO PPP effort, it is not possible to define a single list of pre-analytical standards for samples or their processing. We present here a compendium of observations, drawing on actual results and sound clinical theories and practices. Based on our data, we find that (1) platelet-depleted plasma is preferable to serum for certain peptidomic studies; (2) samples should be aliquoted and stored preferably in liquid nitrogen; (3) the addition of protease inhibitors is recommended, but should be incorporated early and used judiciously, as some form non specific protein adducts and others interfere with peptide studies. Further, (4) the diligent tracking of pre-analytical variables and (5) the use of reference materials for quality control and quality assurance, are recommended. These findings help provide guidance on sample handling issues, with the overall suggestion being to be conscious of all possible pre-analytical variables as a prerequisite of any proteomic study.     

Pre-analytical factors affecting the results of laboratory blood analyses in farm animal veterinary diagnostics

The quality of the laboratory diagnostic approach in farm animals can be severely affected by pre-analytical factors of variation. They induce increase/decrease of biochemical and hematological analyte concentrations and, as a consequence, they may cause unsuitable conclusions and decisions for animal health management and research projects. The pre-analytical period covers the preparation of sampling, the sampling procedure itself, as well as all specimen handling until the beginning of the specific laboratory analysis. Pre-analytical factors may have either an animal-related or a technique-related background. Animal-related factors cover daytime/season, meals/fasting, age, gender, altitude, drugs/anesthesia, physical exercise/stress or coinfection. Technique-related factors are the choice of the tube including serum v. plasma, effects of anticoagulants/gel separators, the anticoagulant/blood ratio, the blood collection procedure itself, specimen handling, contamination, labeling, storage and serum/plasma separation, transportation of the specimen, as well as sample preparation before analysis in the laboratory. It is essential to have proper knowledge about the importance and source of pre-analytical factors to alter the entire diagnostic process. Utmost efforts should be made to minimize controllable factors. Analytical results have to be evaluated with care considering that pre-analytical factors of variation are possible causes of misinterpretation.     

Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC

The European Prospective Investigation into Cancer and nutrition (EPIC) is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS) and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88%) performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.     

Pre-analytical Factors Influence Accuracy of Urine Spot Iodine Assessment in Epidemiological Surveys

Urinary iodine concentration (UIC) is commonly used to assess iodine status of subjects in epidemiological surveys. As pre-analytical factors are an important source of measurement error and studies about this phase are scarce, our objective was to assess the influence of urine sampling conditions on UIC, i.e., whether the child ate breakfast or not, urine void rank of the day, and time span between last meal and urine collection. A nationwide, two-stage, stratified, cross-sectional study including 1560 children (6–12 years) was performed in 2012. UIC was determined by the Sandell-Kolthoff method. Pre-analytical factors were assessed from children’s mothers by using a questionnaire. Association between iodine status and pre-analytical factors were adjusted for one another and socio-economic characteristics by multivariate linear and multinomial regression models (RPR: relative prevalence ratios). Skipping breakfast prior to morning urine sampling decreased UIC by 40 to 50 μg/L and the proportion of UIC?<?100 μg/L was higher among children having those skipped breakfast (RPR?=?3.2[1.0–10.4]). In unadjusted analyses, UIC was less among children sampled more than 5 h from their last meal. UIC decreased with rank of urine void (e.g., first vs. second, P?<?0.001); also, the proportion of UIC?<?100 μg/L was greater among 4th rank samples (vs. second RPR?=?2.1[1.1–4.0]). Subjects’ breakfast status and urine void rank should be accounted for when assessing iodine status. Providing recommendations to standardize pre-analytical factors is a key step toward improving accuracy and comparability of survey results for assessing iodine status from spot urine samples. These recommendations have to be evaluated by future research.     

Quantification of mitochondrial DNA copy number: Pre-analytical factors

Mitochondrial DNA (mtDNA) content is important for understanding many cellular processes. Several pre-analytical factors, from sample collection to DNA extraction can affect measurement of mtDNA copy number. In the present study, whole blood samples yielded a higher mtDNA copy number than buffy coat samples. mtDNA content is affected by the cell separation method used and the time between blood withdrawal and cell separation. Thus, reference values must be established with the same type of sample. As to the DNA isolation and purification method, the manual phenol method can give randomly false high values. The QIAamp DNA Mini Kit provided the most highly reproducible mtDNA/nDNA yield.     

Pre-analytical requirements

Correct test selection: a test must have the potential to alter patient management and have the specificity and sensitivity appropriate to the pretest probability of disease. Correct dynamic test procedure: dynamic tests may assist diagnosis and protocols must be readily available. Correct patient preparation: fasting, or other patient preparation, may reduce variability. Clear communication, to both patients and staff, of any such requirements is essential. Correct sample collection: the tube type (for blood) or container (for urine) must be appropriate for the analyte; there must be sufficient volume, avoidance of venous stasis, contaminants and haemolysis; and adequate labelling. Correct sample handling: the time and temperature before and after separation, and the centrifugation and separation procedures, must be suitable for the analyte. Accept/reject criteria must be defined. Methods require thorough evaluation of patient-related pre-analytical factors, and quantification of the effects of time, temperature, haemolysis, anticoagulant type and minimum allowable volume on sample suitability.     

Recent methodological advances in the analysis of nitrite in the human circulation: nitrite as a biochemical parameter of the L-arginine/NO pathway

Nitric oxide (NO) plays a pivotal role in the modulation of multiple physiological processes. It acts as a messenger molecule within the cardiovascular system. NO is a highly unstable free radical in circulating blood and is oxidized rapidly to nitrite and nitrate. Recent studies suggest that nitrite has the potential to function as a surrogate of NO production under physiological and pathophysiological conditions and could therefore be of high relevance as a biochemical parameter in experimental and clinical studies. Under hypoxic conditions nitrite is reduced to bioactive NO by deoxyhemoglobin. This mechanism may represent a dynamic cycle of NO generation to adapt the demand and supply for the vascular system. Because of these potential biological functions the concentration of nitrite in blood is thought to be of particular importance. The determination of nitrite in biological matrices represents a considerable analytical challenge. Methodological problems often arise from pre-analytical sample preparation, sample contamination due to the ubiquity of nitrite, and from lack of selectivity and sensitivity. These analytical difficulties may be a plausible explanation for reported highly diverging concentrations of nitrite in the human circulation. The aim of this article is to review the methods of quantitative analysis of nitrite in the human circulation, notably in plasma and blood, and to discuss pre-analytical and analytical factors potentially affecting accurate quantification of nitrite in these human fluids.     

Quality indicators to detect pre-analytical errors in laboratory testing

Pre-analytical steps, the major source of mistakes in laboratory diagnostics, arise during patient preparation, sample collection, sample transportation, sample preparation, and sample storage. However, while it has been reported that the pre-analytical phase is error-prone, only recently has it been demonstrated that most errors occur in the 'pre-pre-analytical phase'. This comprises the initial procedures of the testing process performed by healthcare personnel outside the laboratory walls and outside the direct control of the clinical laboratory. Quality indicators (QIs) should therefore cover all steps in the pre-analytical phase, from test requesting to sample storage. In the present paper, the state-of-the-art of QIs in laboratory testing is described. The focus is on the experience of a working group of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) in developing a model of QIs, 16 of which concern the pre-analytical phase.     

Biobanking and international interoperability: samples

In terms of sample exchange, international collaborations between biobanks, or between biobanks and their research partners, have two important aspects. First, the donors’ consent usually implies that the scope and purpose of any sample transfer to third parties is subject to major constraints. Since the legal, ethical and political framework of biobanking may differ substantially, even between countries of comparable jurisdictional systems, general rules for the international sharing of biomaterial are difficult, if not impossible, to define. Issues of uncertainty include the right to transfer the material, the scope of research allowed, and intellectual property rights. Since suitable means of international law enforcement may not be available in the context of biobanking, collaborators are advised to clarify any residual uncertainty by means of bilateral contracts, for example, in the form of material transfer agreements. Second, biobank partners may rightly expect that the biomaterial they receive for further analysis attains a certain level of quality. This implies that a biobank has to implement stringent quality control measures covering, in addition to the material transfer itself, the whole process of material acquisition, transport, pre-analytical handling and storage. Again, it may be advisable for biobank partners to claim contractual warranties for the type and quality of the biomaterial they wish to acquire.     

Towards proteome standards: The use of absolute quantitation in high-throughput biomarker discovery

The use of proteomics to profile biological fluids and identify therein biomarkers for cancer and other diseases was initially received with considerable excitement. However, results have fallen short of the expectations. Traditionally, protein biomarkers have been identified by measurement of relative expression changes between case and control samples from which differentially expressed proteins are then considered to represent biomarker candidates.We argue that current individual proteomics-based biomarker discovery studies lack the statistical strength for the identification of high-confidence biomarkers. Instead, multi-group efforts are necessary to facilitate the generation of sufficient sample sizes. This is contingent on the ability to collate and cross-compare data from different studies, which will require the use of a common metric or standards.Though profound, the technical challenges for absolute protein quantification can be overcome. The use of matrix specific, shared standards for absolute quantitation presents an opportunity to facilitate the much needed, but currently impossible, comparisons of different studies. In addition to community-wide approaches to standardize pre-analytical biomarker research studies, it is also important to establish means to integrate experimental data from different studies in order to assess the usefulness of proposed biomarkers with sufficient statistical certainty.     

SELDI-TOF-MS of saliva: methodology and pre-treatment effects

Interest in saliva as a diagnostic fluid for monitoring general health and for early diagnosis of disease has increased in the last few years. In particular, efforts have focused on the generation of protein maps of saliva using advanced proteomics technology. Surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is a novel high throughput and extremely sensitive proteomic approach that allows protein expression profiling of large sets of complex biological specimens. In this study, large scale profiling of salivary proteins and peptides, ranging from 2 to 100kDa was demonstrated using SELDI-TOF-MS. Various methodological aspects and pre-analytical variables were analysed with respect to their effects on saliva SELDI-TOF-MS profiling. Results show that chip surface type and sample type (unstimulated versus stimulated) critically affect the amount and composition of detected salivary proteins. Factors that influenced normal saliva protein profiling were matrix composition, sample dilution and binding buffer properties. Delayed processing time experiments show certain new peptides evolving 3h post-saliva donation, and quantitative analyses indicate relative intensity of other proteins and peptides changing with time. The addition of protease inhibitors partly counteracted the destabilization of certain protein/peptide mass spectra over time suggesting that some proteins in saliva are subject to digestion by intrinsic salivary proteases. SELDI-TOF-MS profiles also changed by varying storage time and storage temperature whereas centrifugation speed and freeze-thaw cycles had minimal impact. In conclusion, SELDI-TOF-MS offers a high throughput platform for saliva protein and peptide profiling, however, (pre-)analytical conditions must be taken into account for valid interpretation of the acquired data.     

Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC)

Introduction

Non-invasive mutation testing using circulating tumour DNA (ctDNA) is an attractive premise. This could enable patients without available tumour sample to access more treatment options.

Materials & Methods

Peripheral blood and matched tumours were analysed from 45 NSCLC patients. We investigated the impact of pre-analytical variables on DNA yield and/or KRAS mutation detection: sample collection tube type, incubation time, centrifugation steps, plasma input volume and DNA extraction kits.

Results

2 hr incubation time and double plasma centrifugation (2000 x g) reduced overall DNA yield resulting in lowered levels of contaminating genomic DNA (gDNA). Reduced “contamination” and increased KRAS mutation detection was observed using cell-free DNA Blood Collection Tubes (cfDNA BCT) (Streck), after 72 hrs following blood draw compared to EDTA tubes. Plasma input volume and use of different DNA extraction kits impacted DNA yield.

Conclusion

This study demonstrated that successful ctDNA recovery for mutation detection in NSCLC is dependent on pre-analytical steps. Development of standardised methods for the detection of KRAS mutations from ctDNA specimens is recommended to minimise the impact of pre-analytical steps on mutation detection rates. Where rapid sample processing is not possible the use of cfDNA BCT tubes would be advantageous.     

Factors that drive the increasing use of FFPE tissue in basic and translational cancer research

The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.     

Unravelling in vitro variables of major importance for the outcome of mass spectrometry-based serum proteomics

The use of mass spectrometry (MS) for analysing low-molecular weight proteins and peptides from biological fluids has a great, yet not fully realized, potential for biomarker discovery. To prune MS-data as much as possible for non-relevant non-biological variation the development of standardized protocols for handling and processing the samples before MS and adjusting data after MS to compensate for method-induced variability are warranted. This calls for knowledge about how different variables contribute to MS-based proteome analyses. In addition, identification of the peptides involved in pre-analytical variation will be helpful in evaluating the clinical significance of predictive models derived from MS data. Using human sera, extraction by weak cation-exchange magnetic beads, and analysis by MALDI-TOF MS we here evaluated pre-analytical variation and identify peptides involved in this. The influences of humidity, temperature, and time for preparation of sera on spectral changes were evaluated. Also, the reproducibility of the methods and the effect of a baseline correction procedure were examined. Low temperatures, short handling times, and a baseline correction procedure minimize the contribution of artifacts to sample variability as observed by MS. The complement split product C3f and fragments thereof appear to be sensitive indicators of sample handling induced modifications. Other peptides that are indicative of such variability are fibrin and kininogen fragments. Using strict experimental guidelines as well as standardized sample collection procedures it is possible to obtain reproducible peak intensities and positions in serum mass profiling using magnetic bead-based fractionation and MALDI-TOF MS.     

Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures

Neurochemical Research - Gene expression studies are reported to be influenced by pre-analytical factors that can compromise RNA yield and integrity, which in turn may confound the experimental...     

Pre-analytical factors affecting ascorbic and uric acid quantification in human plasma

We have recently described a new capillary electrophoresis assay to measure serum ascorbic and uric acids in which a baseline separation of peaks was obtained in less than 4 min by using a 60.2 cm x 75 microm uncoated capillary with a 100 mmol/L sodium borate running buffer pH 8. Since during sample preparation AA is rapidly oxidized, we employed our new capillary electrophoresis method to analyze the pre-analytical factors affecting its stability. In particular we evaluated how the standard mix preparation, the blood collection (plasma EDTA or serum) and the plasma protein precipitation influence the results of analysis. Our data suggest that standard ascorbate must be dissolved in a solution containing cysteine and EDTA in order to avoid oxidation and that EDTA blood collection is better than serum for AA measurement. Moreover, the type and the quantity of the precipitating compound are critical parameters to obtain a complete recovery of analytes. We performed AA and UA analysis in 32 healthy volunteers with the optimized experimental conditions by using our capillary electrophoresis method and a reference CE assay. Obtained data were compared to Bland-Altman test to verify the accuracy of our CZE method.     

Delay in centrifugation and measurement of serum constituents in normal subjects

It is a fairly common practice to issue biochemical results of multichannel analysers containing many analytes, irrespective of the number of tests requested by the physician. Abnormal results in such profiles may occur from presentation of artefacted blood samples; it is sometimes not possible to differentiate the abnormality arising as a result of pathological process from that due to a poor sample quality. In this study normal volunteers were studied to examine changes occurring when centrifugation was delayed for a few hours to a few days. Analyses on stored serum samples over the same period were also studied. If haemolysis is present, lactate dehydrogenase (hydroxybutyrate dehydrogenase), aspartate transaminase, potassium, chloride, bicarbonate, phosphate and creatinine estimations are not valid. Accurate data, however, can be obtained on sodium, urea, proteins, albumin, alkaline phosphatase and gammaglutamyl transferase. The very concept of efficient and cost-effective testing by multichannel profiles may generate further unnecessary investigations with a consequent waste of health service resources if pre-analytical factors are not taken into consideration.     

Simulation exercises for environmental biology teaching

Simulation exercises are of particular relevance in the presentation of issues in environmental aspects of biology. Three examples, which require no special apparatus or materials, are described, each being presented in a different way and relating to a different aspect of the subject.

A series of prepared sheets lists basic parameters which influence the size of a population of herbivorous mammals, different combinations of factors and random events yielding a wide range of population changes in the course of a simulation during which the participants carry out simple arithmetical calculations of natality, mortality and changes in age-distribution of the population.

Pollution, arising from several industrial and agricultural sources, combines with fluctuation in flow rate to bring about changes in the biota of a river. The changes are illustrated by altering the positions of cards on a board; the events which generate the changes being brought about by drawing cards from a pack. Participants take turns to ‘sample’ the river or to bring about events. Alternatively, the board can be used by the teacher as a visual aid to demonstrate the ways in which changes may occur.

The survival of wildlife in the face of changing conditions in British farming practice is the subject of a competitive game intended to provoke discussion of the issues involved. Each player is provided with a small board representing a farm. This has to be managed with due regard for economic factors while the player attempts to manipulate habitats in order to increase the diversity of wildlife on his land.

All three simulations are intended to be used with senior classes in secondary education (16–18 age group) though they may be adapted for use with other groups.

A list of requirements for setting up each simulation is appended.     

Renal cell carcinoma: handling and treatment

The quality of samples and of pre-analytical steps are crucial in all biological tests, this is dramatically true in proteomics analysis. In renal cell carcinoma preparation for two-dimensional gel electrophoresis the time elapsed between sample collection and treatment, and the heterogeneity of tissues are considered in order to obtain high quality and reproducibility of spots. The mechanical dissection and cell separation by magnetic beads coated with anti-Ber and EP4 antibodies to minimize the contamination of nonepithelial cells are described.     

Red cell PMVs, plasma membrane-derived vesicles calling out for standards

Plasma membrane-derived vesicles (PMVs) or microparticles are vesicles (0.1-1 μm in diameter) released from the plasma membrane of all blood cell types under a variety of biochemical and pathological conditions. PMVs contain cytoskeletal elements and some surface markers from the parent cell but lack a nucleus and are unable to synthesise macromolecules. They are also defined on the basis that in most cases PMVs express varying amounts of the cytosolic leaflet lipid phosphatidylserine, which is externalised during activation on their surface. This marks the PMV as a biologically distinct entity from that of its parent cell, despite containing surface markers from the original cell, and also explains its role in events such as phagocytosis and thrombosis. There is currently a large amount of variation between investigators with regard to the pre-analytical steps employed in isolating red cell PMVs or RPMVs (which are slightly smaller than most PMVs), with key differences being centrifugation and sample storage conditions, which often leads to result variability. Unfortunately, standardization of preparation and detection methods has not yet been achieved. This review highlights and critically discusses the variables contributing to differences in results obtained by investigators, bringing to light numerous studies of which RPMVs have been analysed but have not yet been the subject of a review.