The Second International Standard for somatropin (recombinant DNA-derived human growth hormone): preparation and calibration in an international collaborative study.

A preparation of somatropin (recombinant DNA-derived human growth hormone) was prepared as lyophilised ampoules according to WHO procedures for international biological standards. The candidate preparation (98/574) was evaluated in an international collaborative study (16 laboratories, nine countries), with the following aims: (i) to determine the suitability of the preparation to serve as the International Standard for somatropin by studying its performance in the current range of physico-chemical and biological assay methods employed for somatropin; (ii) to assign a content in terms of the existing (first) International Standard for somatropin, using the currently recognised assay procedure (Size Exclusion High Performance Liquid Chromatography, SE HPLC); (iii) to confirm the specific biological activity of the candidate preparation; (iv) to confirm the stability of the candidate preparation. On the basis of the collaborative study WHO agreed that: the preparation in ampoules coded 98/574 is suitable to serve as the next WHO International Standard for somatropin; the preparation in ampoules coded 98/574 should be established as the second International Standard for somatropin, with a defined ampoule content of 1.95 mg total somatropin plus somatropin-related proteins per ampoule; the specific activity of the preparation should be defined as 3.0 IU/mg somatropin.     

Measurement of cytokines by bioassays: theory and application

A large number of cytokines have been characterized, of which several have proved successful in the clinic as biotherapeutic agents for malignant, infectious or autoimmune diseases. As biologically active proteins, they cannot be fully characterized by physicochemical methods alone. Thus, biological assays (bioassays) have become increasingly important for their biological characterization and potency determinations. Since cytokines exert various biological activities in vitro, cultured cell line-based bioassay methods have mainly been developed to quantify potency. Such bioassays, like all biological systems, are inherently variable. Thus, measurement of potency of a particular cytokine must be made relative to a common, stable, reference preparation of the same cytokine to permit valid inter-assay and inter-laboratory comparisons. The development and establishment of appropriate primary reference preparations as World Health Organization (WHO) International standards (IS) and reference reagents (RR) is essential for the standardization of bioassays. This review addresses the practical and statistical considerations for the development of valid bioassays, the preparation and use of WHO IS and RR and, in brief, the types of bioassay methods applicable to potency measurements of individual cytokines. More extensive details for the potency determinations of tumor necrosis factor-alpha (TNF-alpha), related cytokines, and biotherapeutic anti-TNF-alpha products are provided.     

Fibrinolysis standards: A review of the current status

Biological standards are used to calibrate measurements of components of the fibrinolytic system, either for assigning potency values to therapeutic products, or to determine levels in human plasma as an indicator of thrombotic risk. Traditionally WHO International Standards are calibrated in International Units based on consensus values from collaborative studies. The International Unit is defined by the response activity of a given amount of the standard in a bioassay, independent of the method used. Assay validity is based on the assumption that both standard and test preparation contain the same analyte, and the response in an assay is a true function of this analyte. This principle is reflected in the diversity of source materials used to prepare fibrinolysis standards, which has depended on the contemporary preparations they were employed to measure. With advancing recombinant technology, and improved analytical techniques, a reference system based on reference materials and associated reference methods has been recommended for future fibrinolysis standards. Careful consideration and scientific judgement must however be applied when deciding on an approach to develop a new standard, with decisions based on the suitability of a standard to serve its purpose, and not just to satisfy a metrological ideal.     

Application of deglycosylation to SDS PAGE analysis improves calibration of influenza antigen standards

Each year the production of seasonal influenza vaccines requires antigen standards to be available for the potency assessment of vaccine batches. These are calibrated and assigned a value for haemagglutinin (HA) content. The calibration of an antigen standard is carried out in a collaborative study amongst a small number of national regulatory laboratories which are designated by WHO as Essential Regulatory Laboratories (ERLs) for the purposes of influenza vaccine standardisation. The calibration involves two steps; first the determination of HA protein in a primary liquid standard by measurement of total protein in a purified influenza virus preparation followed by determination of the proportion of HA as determined by PAGE analysis of the sample; and second, the calibration of the freeze-dried reference antigen against the primary standard by single radial immunodiffusion (SRD) assay. Here we describe a collaborative study to assess the effect of adding a deglycosylation step prior to the SDS-PAGE analysis for the assessment of relative HA content. We found that while the final agreed HA value of the samples tested was not significantly different with or without deglycosylation, the deglycosylation step greatly improved between-laboratory agreement.     

Improved reporting of DNA methylation data derived from studies of the human placenta

Epigenetic variation is increasingly hypothesized as a mechanism underlying the effect of the in utero environment on long-term postnatal health; however, there is currently little clear data to support this in humans. A number of biological and technical factors provide challenges for the design of clinical epigenetic studies: from the type of cells or tissues that are available to the large range of predicted confounders that may impact findings. The human placenta, in addition to other neonatal tissues and whole blood, is commonly sampled for the study of epigenetic modifications. However there is little conformity for the most appropriate methods for study design, data analysis, and importantly, data interpretation. Here we present general recommendations for the reporting of DNA methylation in biological samples, with specific focus on the placenta. We outline key guidelines for: (1) placental sampling, (2) data analysis and presentation, and (3) interpretation of DNA methylation data. We emphasize the need to consider methodological noise, increase statistical power and to ensure appropriate adjustment for biological covariates. Finally, we highlight that epigenetic changes may be non-pathological and not necessarily translate into disease-associated changes. Improved reporting of DNA methylation data will be critical to identify epigenetic-based effects and to better understand the full phenotypic impact of these widely-reported epigenomic changes.     

Evaluation of Fourth International Standard for Whole Cell Pertussis Vaccine

Whole cell pertussis vaccine is still widely used in many countries. An International Standard is needed for its potency control. The Third International Standard for Pertussis Vaccine was prepared about 40 years ago and its replacement was recommended by the Expert Committee for Biological Standardisation (ECBS) of the WHO. Material in ampoules coded 94/532 was prepared as a candidate replacement and has been evaluated in international collaborative studies which consisted of two parts. The first part, to assess the suitability of the candidate standard by comparing it with the Second International Standard for Pertussis Vaccine (IS2) involved 14 laboratories in 11 countries. The second part to compare the candidate standard with the Third International Standard for Pertussis Vaccine (IS3) involved 16 laboratories in 14 countries. Since 1995 various other studies have included the international standards and the results of these are also considered in assessing likely continuity of the IU for potency of whole cell pertussis vaccine. The preparation in ampoules coded 94/532 was adopted by the WHO ECBS in October 2006 as the 4th International Standard for whole cell pertussis vaccine and assigned an activity of 40 IU per ampoule on the basis of the studies reported here.     

Calibration of replacement international standards of diphtheria and tetanus toxoids for use in flocculation test

The 1st International Reference Reagents (IRR) of Diphtheria and Tetanus Toxoids for Flocculation Test (DIFT and TEFT) were established by the WHO in 1988. These reagents are essential for the standardization of assays used to calculate Lf units of toxoids. Candidate replacement materials were provided by several European vaccine manufacturers and were formulated and freeze-dried at NIBSC. This paper provides a summary of the results of an international collaborative study including 18 laboratories from 16 countries, which examined the candidate replacement materials in a variety of methods. Materials 02/176 and 04/150 were proposed and adopted by the Expert Committee on Biological Standardization of WHO in October 2007 as 2nd WHO International Standards of Diphtheria and Tetanus Toxoid for use in Flocculation Test. The replacement standards were assigned the value of 1100 and 690Lf/ampoule, respectively, based on results of flocculation tests carried out using provided reagents. Material coded 02/176 fully complied with the WHO specifications for stability, residual moisture content, precision of fill and sterility. Stability of material coded 04/150 was slightly lower than expected but predictions were based only on 2-year data and were to be further monitored, post-adoption.     

Improving the analysis of designed studies by combining statistical modelling with study design information

Background  

In the fields of life sciences, so-called designed studies are used for studying complex biological systems. The data derived from these studies comply with a study design aimed at generating relevant information while diminishing unwanted variation (noise). Knowledge about the study design can be used to decompose the total data into data blocks that are associated with specific effects. Subsequent statistical analysis can be improved by this decomposition if these are applied on selected combinations of effects.     

Optimization of the formulation for a candidate lyophilised tetanus toxoid reference preparation

Tetanus toxoid is a vital primary reference material used for standardization of assays required to establish the antigenic purity of tetanus toxoid for vaccine production. Several formulations were assessed and ampouled fills of each formulation lyophilised. The relative Lf content determined by Ramon flocculation, SRD, and ELISA assays was measured. The stability of the tetanus toxoid activity in each formulation was assessed by accelerated degradation studies. Formulations containing glycine were not suitable in flocculation tests but both sorbitol and trehalose formulations were. The trehalose/sodium chloride formulation had a good appearance, showed good activity in all assays and maintained its activity best under stress conditions. This formulation has been applied to a large scale batch of ampoules prepared as a WHO candidate replacement standard, evaluated in a collaborative study and accepted as a replacement WHO IS for use in flocculation test (WHO ECBS, October 2007, ref no BS/07.2061). The stability of this formulation was also excellent for the large scale batch. The benefits of using thermal analysis and freeze drying microscopy coupled with small scale lyophilisation trials in order to screen formulations for the preparation of batches of biological reference materials are demonstrated.     

The Second International Standard for anti-poliovirus sera types 1, 2 and 3.

The Second International Standard for anti-poliovirus sera types 1, 2 and 3 was established by the WHO Expert Committee on Biological Standardization in 1991 on the basis of an extensive collaborative study. Nine laboratories from eight countries participated and all used neutralizing antibody assays. The standard is a human serum pool which contains antibodies to all three poliovirus types and replaces the three previously established monovalent standards which were all hyperimmune monkey sera. The standard was assigned an activity of 25 IU of anti-poliovirus serum (type 1) human: 50 IU of anti-poliovirus serum (type 2) human; and 5 IU of anti-poliovirus serum (type 3) human. The study also showed significant interlaboratory differences in relative potency are observed when human sera are compared to hyperimmune monkey sera. It was therefore recommended that National laboratory references are established from human sera.     

Health-related monitoring and assessment of airborne particulate matter

Since 1992, the International Atomic Energy Agency (IAEA) has been promoting studies of air pollution using a standard design of air sampler that provides separation on filters into two size fractions with cutoffs of 2.5 and 10 Μm (approximately). These are the size ranges presently considered to have the most important health consequences. Such filter samples are highly amenable to analysis using nuclear and related techniques. After reviewing some of the health effects of airborne particulate matter and current air quality standards and guidelines, this article provides an overview of current and recent IAEA programs in this area, which involve collaborative activities with participants in more than 40 countries.     

WHO technical workshop on stability of reference materials for biological medicines and in vitro diagnostics, Geneva, Switzerland, 28–29 November 2005

In November 2005, the World Health Organization convened an informal technical workshop on the stability of reference materials for biological medicines and in vitro diagnostics. The meeting was attended by experts from WHO collaborating centres in the area of biological standardization, national control laboratories, industries and other relevant organizations. The consultation group discussed current practices and approaches to predicting and monitoring the stability of biological reference materials. The group agreed to the need for establishing a working group (i) to continue dialogue on potential issues encompassing the principles, strategies and practicality for assuring the stability of WHO international reference standards for biological medicines and in vitro diagnostics and (ii) to develop more detailed guidance for assessment of the stability of WHO international biological reference materials.     

Collaborative study for the calibration of a replacement International Standard for Tetanus Toxoid Adsorbed

We present the results of a collaborative study for the establishment of a replacement International Standard (IS) for Tetanus Toxoid Adsorbed. Two candidate preparations were included in the study, one of which was established as the 4th IS for Tetanus Toxoid Adsorbed at the WHO Expert Committee on Biological Standardization meeting in October 2010. This preparation was found to have a unitage of 490 IU/ampoule, based on calibration in guinea pig challenge assays. Results from mouse challenge assays suggest that the relative performance of two candidate preparations may differ significantly between guinea pigs and mice. The authors note that the number of laboratories that performed guinea pig challenge assays, which are used to calibrate and assign IU, is much lower than in previous collaborative studies and this may have implications for calibration of replacement standards in the future. The issue of assigning separate units to the IS for guinea pig and mouse assays is discussed. The study also assessed performance of the replacement standard in serological assays which are used as alternative procedures to challenge assays for tetanus potency testing. Results suggest that the replacement standard is suitable for use as the reference vaccine in serological assays.     

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.     

Replication, Variation and Normalisation in Microarray Experiments

INTRODUCTION: Microarray experiments often have complex designs that include sample pooling, biological and technical replication, sample pairing and dye-swapping. This article demonstrates how statistical modelling can illuminate issues in the design and analysis of microarray experiments, and this information can then be used to plan effective studies. METHODS: A very detailed statistical model for microarray data is introduced, to show the possible sources of variation that are present in even the simplest microarray experiments. Based on this model, the efficacy of common experimental designs, normalisation methodologies and analyses is determined. RESULTS: When the cost of the arrays is high compared with the cost of samples, sample pooling and spot replication are shown to be efficient variance reduction methods, whereas technical replication of whole arrays is demonstrated to be very inefficient. Dye-swap designs can use biological replicates rather than technical replicates to improve efficiency and simplify analysis. When the cost of samples is high and technical variation is a major portion of the error, technical replication can be cost effective. Normalisation by centreing on a small number of spots may reduce array effects, but can introduce considerable variation in the results. Centreing using the bulk of spots on the array is less variable. Similarly, normalisation methods based on regression methods can introduce variability. Except for normalisation methods based on spiking controls, all normalisation requires that most genes do not differentially express. Methods based on spatial location and/or intensity also require that the nondifferentially expressing genes are at random with respect to location and intensity. Spotting designs should be carefully done so that spot replicates are widely spaced on the array, and genes with similar expression patterns are not clustered. DISCUSSION: The tools for statistical design of experiments can be applied to microarray experiments to improve both efficiency and validity of the studies. Given the high cost of microarray experiments, the benefits of statistical input prior to running the experiment cannot be over-emphasised.     

International reference standards in coagulation

Measurement of coagulation factor activity using absolute physico-chemical techniques is not possible and estimation therefore relies on comparative bioassay relative to a reference standard with a known or assigned potency. However the inherent variability of locally prepared and calibrated reference standards can give rise to poor agreement between laboratories and methods. Harmonisation of measurement between laboratories at the international level relies on the availability of a common source of calibration for local reference standards and this is provided by the World Health Organization (WHO) International Standards which define the International Unit for the analyte. This article describes the principles, practices and problems of biological standardisation and the development and use of reference standards for assays of coagulation factors, with particular emphasis on WHO International Standards for both concentrates and plasma.     

Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology

Over the past 2 decades, there have been revolutionary developments in life science technologies characterized by high throughput, high efficiency, and rapid computation. Nutritionists now have the advanced methodologies for the analysis of DNA, RNA, protein, low-molecular-weight metabolites, as well as access to bioinformatics databases. Statistics, which can be defined as the process of making scientific inferences from data that contain variability, has historically played an integral role in advancing nutritional sciences. Currently, in the era of systems biology, statistics has become an increasingly important tool to quantitatively analyze information about biological macromolecules. This article describes general terms used in statistical analysis of large, complex experimental data. These terms include experimental design, power analysis, sample size calculation, and experimental errors (Type I and II errors) for nutritional studies at population, tissue, cellular, and molecular levels. In addition, we highlighted various sources of experimental variations in studies involving microarray gene expression, real-time polymerase chain reaction, proteomics, and other bioinformatics technologies. Moreover, we provided guidelines for nutritionists and other biomedical scientists to plan and conduct studies and to analyze the complex data. Appropriate statistical analyses are expected to make an important contribution to solving major nutrition-associated problems in humans and animals (including obesity, diabetes, cardiovascular disease, cancer, ageing, and intrauterine growth retardation).     

Integrated analysis of genome-wide genetic and epigenetic association data for identification of disease mechanisms

Many human diseases are multifactorial, involving multiple genetic and environmental factors impacting on one or more biological pathways. Much of the environmental effect is believed to be mediated through epigenetic changes. Although many genome-wide genetic and epigenetic association studies have been conducted for different diseases and traits, it is still far from clear to what extent the genomic loci and biological pathways identified in the genetic and epigenetic studies are shared. There is also a lack of statistical tools to assess these important aspects of disease mechanisms. In the present study, we describe a protocol for the integrated analysis of genome-wide genetic and epigenetic data based on permutation of a sum statistic for the combined effects in a locus or pathway. The method was then applied to published type 1 diabetes (T1D) genome-wide- and epigenome-wide-association studies data to identify genomic loci and biological pathways that are associated with T1D genetically and epigenetically. Through combined analysis, novel loci and pathways were also identified, which could add to our understanding of disease mechanisms of T1D as well as complex diseases in general.