In-house Reference Research Articles

Accurate in situ oxygen isotopic analysis at high resolution by secondary ion mass spectrometry shows the potential of aragonite as a reference material

Matrix effect in SIMS aragonite oxygen isotopic analysis.

Development and characterization of a new in-house reference material for stable carbon and oxygen isotopes analyses

We describe the characterization of a newly produced reference material, the SHP2L. It is made of virtually pure calcite and of uniform isotopic composition, suitable for stable carbon and oxygen isotope analyses.

Optimising a 6-plex tetanus-diphtheria-pertussis fluorescent bead-based immunoassay

Small volume assays are required for large-scale research studies and in particular paediatric trials, where multiple measures are required from a single sample. Fluorescent bead-based technology (Bioplex/Luminex) allows high through-put and simultaneous quantification of multiple analytes in a single test. This technology uses sets of microspheres, each with a unique spectral address that can be coated with a different antigen of interest. Following the addition of a detector antibody, specific for the isotype of interest and labelled with R-Phycoerythrin, the bioplex reader determines the amounts of antigen-specific antibodies in each test sample relative to a reference standard.Here we outline the optimisations undertaken to establish a 6-plex fluorescent bead-based immunoassay that can accurately measure human IgG to individual tetanus-diphtheria-acellular pertussis (Tdap) antigens from 2 to 4 ul of human serum/ plasma. This protocol was adapted from previously published methods and aligns with current recommendations for developing pertussis-serological assays. To our knowledge, this is the first Tdap-specific multiplex immunoassay (MIA) established in Australia. All components were optimised and validated in-house including: microsphere preparation conditions, reference serum and QC development, and assay running.•Determining optimal antigen coating dose and conjugation method.•Optimising an in-house reference serum with clinically relevant titres.•Determining assay specificity and reproducibility.

Development of competitive inhibition ELISA as an effective potency test to analyze human rabies vaccines and assessment of the antigenic epitope of rabies glycoprotein

The potency of all modern tissue culture human rabies vaccines is measured based on the National Institute of Health (NIH) potency test that is laborious, time-consuming, involves large test variations and requires sacrifice of large number of animals. To circumvent these limitations, several researchers and WHO expert working groups have discussed development of alternative in vitro methods to replace the NIH potency test. Although several immunochemical methods have been proposed to quantify rabies glycoprotein (G-protein) using multiple murine monoclonal antibodies, we report an In vitro competitive inhibition ELISA (CIA) method based on the use of a neutralizing rabies glycoprotein site III directed novel therapeutic human rabies monoclonal antibody (RAB1) that shows equivalence to the mice NIH potency test in recognition of neutralization site of the glycoprotein. In vitro potency testing of WHO 7th International Standard for rabies vaccine (IS) by CIA using RAB1 and In-house reference standard (IHRS) as a standard to assess its suitability for the assessment of validation parameters showed accurate and precise values with <15% coefficient variance. The method was validated using 5PL standard curve with linearity r2 > 0.98 and LLOQ of 0.125 IU/mL indicating sensitivity of the method. The method was found to be precise, robust and accurate to quantitate intact rabies glycoprotein in final vaccine and showed a strong correlation (Pearson's r = 0.81) with the NIH potency values of licensed Vero cell rabies vaccine. The CIA test using RAB1 was able to accurately quantitate degradation of rabies vaccine and assess loss in antigenicity of lyophilized and reconstituted liquid rabies vaccine under thermal stress conditions. The method was able to differentiate between potent and reduced potency vaccine samples. The new in vitro competitive inhibition ELISA method using RAB1 thus can be a valid alternative to the NIH test.

MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks

Brucellosis is one of the most common bacterial zoonoses worldwide affecting not only livestock and wildlife but also pets. Canine brucellosis is characterized by reproductive failure in dogs. Human Brucella canis infections are rarely reported but probably underestimated due to insufficient diagnostic surveillance. To improve diagnostics, we investigated dogs in a breeding kennel that showed clinical manifestations of brucellosis and revealed positive blood cultures. As an alternative to the time-consuming and hazardous classical identification procedures, a newly developed species-specific intact-cell matrix-assisted laser desorption/ionization–time of flight mass spectrometry analysis was applied, which allowed for rapid identification of B. canis and differentiation from closely related B. suis biovar 1. High-throughput sequencing and comparative genomics using single nucleotide polymorphism analysis clustered our isolates together with canine and human strains from various Central and South American countries in a distinct sub-lineage. Hence, molecular epidemiology clearly defined the outbreak cluster and demonstrated the endemic situation in South America. Our study illustrates that MALDI-TOF MS analysis using a validated in-house reference database facilitates rapid B. canis identification at species level. Additional whole genome sequencing provides more detailed outbreak information and leads to a deeper understanding of the epidemiology of canine brucellosis.

Development of a multiplex microsphere immunoassay for the detection of antibodies against highly pathogenic viruses in human and animal serum samples.

Surveillance of highly pathogenic viruses circulating in both human and animal populations is crucial to unveil endemic infections and potential zoonotic reservoirs. Monitoring the burden of disease by serological assay could be used as an early warning system for imminent outbreaks as an increased seroprevalance often precedes larger outbreaks. However, the multitude of highly pathogenic viruses necessitates the need to identify specific antibodies against several targets from both humans as well as from potential reservoir animals such as bats. In order to address this, we have developed a broadly reactive multiplex microsphere immunoassay (MMIA) for the detection of antibodies against several highly pathogenic viruses from both humans and animals. To this aim, nucleoproteins (NP) of Ebola virus (EBOV), Marburg virus (MARV) and nucleocapsid proteins (NP) of Crimean-Congo haemorrhagic fever virus, Rift Valley fever virus and Dobrava-Belgrade hantavirus were employed in a 5-plex assay for IgG detection. After optimisation, specific binding to each respective NP was shown by testing sera from humans and non-human primates with known infection status. The usefulness of our assay for serosurveillance was shown by determining the immune response against the NP antigens in a panel of 129 human serum samples collected in Guinea between 2011 and 2012 in comparison to a panel of 88 sera from the German blood bank. We found good agreement between our MMIA and commercial or in-house reference methods by ELISA or IIFT with statistically significant higher binding to both EBOV NP and MARV NP coupled microspheres in the Guinea panel. Finally, the MMIA was successfully adapted to detect antibodies from bats that had been inoculated with EBOV- and MARV- virus-like particles, highlighting the versatility of this technique and potentially enabling the monitoring of wildlife as well as human populations with this assay. We were thus able to develop and validate a sensitive and broadly reactive high-throughput serological assay which could be used as a screening tool to detect antibodies against several highly pathogenic viruses.

Viral Abundance and Diversity of Production Fluids in Oil Reservoirs.

Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 108 mL−1 and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 108 mL−1) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir’s ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment.

Critical Review of Processing and Classification Techniques for Images and Spectra in Microplastic Research.

Microplastic research is a rapidly developing field, with urgent needs for high throughput and automated analysis techniques. We conducted a review covering image analysis from optical microscopy, scanning electron microscopy, fluorescence microscopy, and spectral analysis from Fourier transform infrared (FT-IR) spectroscopy, Raman spectroscopy, pyrolysis gas-chromatography mass-spectrometry, and energy dispersive X-ray spectroscopy. These techniques were commonly used to collect, process, and interpret data from microplastic samples. This review outlined and critiques current approaches for analysis steps in image processing (color, thresholding, particle quantification), spectral processing (background and baseline subtraction, smoothing and noise reduction, data transformation), image classification (reference libraries, morphology, color, and fluorescence intensity), and spectral classification (reference libraries, matching procedures, and best practices for developing in-house reference tools). We highlighted opportunities to advance microplastic data analysis and interpretation by (i) quantifying colors, shapes, sizes, and surface topologies with image analysis software, (ii) identifying threshold values of particle characteristics in images that distinguish plastic particles from other particles, (iii) advancing spectral processing and classification routines, (iv) creating and sharing robust spectral libraries, (v) conducting double blind and negative controls, (vi) sharing raw data and analysis code, and (vii) leveraging readily available data to develop machine learning classification models. We identified analytical needs that we could fill and developed supplementary information for a reference library of plastic images and spectra, a tutorial for basic image analysis, and a code to download images from peer reviewed literature. Our major findings were that research on microplastics was progressing toward the use of multiple analytical methods and increasingly incorporating chemical classification. We suggest that new and repurposed methods need to be developed for high throughput screening using a diversity of approaches and highlight machine learning as one potential avenue toward this capability.

Summary of the WHO hearing on the development of product-specific reference materials for coagulation factor VIII and factor IX products

In recent years, several modified recombinant factor (F) VIII and FIX therapeutics with extended half-life have been licensed internationally for the treatment of haemophilia. Safe and effective use of these products requires monitoring of factor activity in patient plasma. The potency of all FVIII and FIX products is currently assigned in International Units (IU) which anchors the relationship between potency labelling, dosing and clinical monitoring. However, varying degrees of discrepancies in factor activity assays are observed between and within the factor activity analytical methods (one-stage clotting and chromogenic), when measuring these modified products against plasma and plasma-derived (concentrate) International Standards (IS) or in-house reference standard traceable to the IS. Availability of product-specific reference reagents would mitigate assay discrepancies, facilitate independent testing of assay methods and reagents, and ensure long-term continuity of the IU related to each product. A hearing meeting was organised by the WHO to discuss the requirements for product-specific reference materials for these products and whether these reference materials should be produced by the WHO. Advantages and disadvantages of product-specific reference materials were identified and discussed.

Abstract 5963: NGS-based murine pan-cancer gene expression panel for immuno-oncology and tumor microenvironment studies

Abstract INTRODUCTION: Cancer is a heterogeneous disease and highly related to the immunological system. The significance of fully understanding the interactions between cancer and immunity in cancer therapeutics has been broadly noted, particularly for immunotherapies. Experimental murine models derived from a variety of biological technologies are essential preclinical model systems utilized before clinical studies. Molecular pathology techniques, such as gene expression biomarkers, are widely used to systematically profile and characterize these models. So far, however, there has been no robust and cost-effective assay designed for murine clinical immuno-oncology (I/O) research to characterize tumor-immune interactions at a gene expression level. METHODS: Marker genes were identified by combining public and in-house reference genomic data for non-tumor bearing mice as well as tumor mouse models. Oligonucleotide-based hybridization/capture techniques analogous to exome sequencing, targeting specific regions are well established on Illumina Novaseq and BGI MGIseq platforms. These methods were applied to the murine I/O panel assay, with accuracy and reproducibility verified across these two sequencing platforms. The results were further qualified using a PCR array platform. RESULTS: A mouse gene panel involving 1080 genes that encompass surface markers and transcriptomic biomarkers for the immune system, key pathways at the interface of the tumor, tumor microenvironment (TME), and immune response, as well as internal reference genes for data normalization has been established. By combining advanced NGS technologies and specific bioinformatic pipelines, we were able to detect and distinguish various immune and stromal cells involved in the complex interaction between the tumor and its microenvironment, allowing for a multifaceted characterization of disease biology and the interrogation of immune response and evasion. We validated the sensitivity, specificity, and repeatability of the panel by qPCR experiments. CONCLUSIONS: We have established a murine-I/O NGS panel involving 1080 genes to characterize tumor-immune interactions more efficiently and in a cost-effective manner for preclinical studies. This provides an enhanced insight into the TME, with high-content data that has the potential to translate more effectively to the clinic as well as for early identification of immunotherapy companion diagnostics. Citation Format: Xiaobo Chen, Jia Xue, Qixiang Li, Sheng Guo. NGS-based murine pan-cancer gene expression panel for immuno-oncology and tumor microenvironment studies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5963.

Use of data mining in the establishment of age-adjusted reference intervals for parathyroid hormone

Background-AimAppropriately defined reference values are of vital importance for the correct interpretation of laboratory results. However, the implementation of in-house reference intervals by traditional methods is rare due to difficulties in the selection of reference individuals, so indirect methods are often alternatively used.Parathyroid hormone (PTH) is a crucial hormone for the metabolism of calcium and phosphorus whose result can lead to erroneous diagnoses and medical actions if adequate reference intervals are not readily available.Our goal was to obtain reference values ​​for adult population for PTH by using data mining. Based on possible new reference intervals, we also aimed to perform a retrospective evaluation of the individuals mistakenly classified. MethodsRetrospective observational study between 2014 and 2019. All requests from individuals aged ≥ 18 years were considered if PTH was requested together with serum creatinine, 25-hydroxyvitamin D, calcium, albumin and phosphate (within their respective reference intervals). PTH was measured on the Cobas e411 platform (Roche).Requests were grouped by age and sex. Differences among partitions were assessed by the Harris-Boyd’s test and reference intervals were determined by the non-parametrical calculation of percentiles 2.5 and 97.5. ResultsA total of 2279 laboratory requests were included. Reference intervals for PTH were seen to be sex-independent, but age-dependent reference intervals were needed: 18–39, 40–59 and >60 years.Based on the reference intervals obtained, up to 20.1% of individuals were misclassified. ConclusionsAppropriateness of PTH reference intervals would lead to a reduction in the number of additional tests and avoid wrong medical actions, thus improving not only patient safety, but also the healthcare system as a whole.

Optimisation and standardisation of a multiplex immunoassay of diverse Plasmodium falciparum antigens to assess changes in malaria transmission using sero-epidemiology.

Background: Antibody responses have been used to characterise transmission and exposure history in malaria-endemic settings for over a decade. Such studies have typically been conducted on well-standardised enzyme-linked immunosorbent assays (ELISAs). However, recently developed quantitative suspension array technologies (qSAT) are now capable of high-throughput and multiplexed screening of up to hundreds of analytes at a time. This study presents a customised protocol for the Luminex MAGPIX © qSAT using a diverse set of malaria antigens. The aim is to develop a standardised assay for routine serological surveillance that is implementable across laboratories and epidemiological settings. Methods: A panel of eight Plasmodiumfalciparumrecombinant antigens, associated with long- and short-lived antibody responses, was designed for the Luminex MAGPIX © platform. The assay was optimised for key steps in the protocol: antigen-bead coupling concentration, buffer composition, serum sample dilution, and bead storage conditions. Quality control procedures and data normalisation methods were developed to address high-throughput assay processing. Antigen-specific limits of quantification (LOQs) were also estimated using both in-house and WHO reference serum as positive controls. Results: Antigen-specific bead coupling was optimised across five serum dilutions and two positive controls, resulting in concentrations operational within stable analytical ranges. Coupled beads were stable after storage at room temperature (22⁰C) for up to eight weeks. High sensitivity and specificity for distinguishing positive and negative controls at serum sample dilutions of 1:500 (AUC 0.94 95%CI 0.91-0.96) and 1:1000 (AUC 0.96 95%CI 0.94-0.98) were observed. LOQs were also successfully estimated for all analytes but varied by antigen and positive control. Conclusions: This study demonstrates that developing a standardised malaria-specific qSAT protocol for a diverse set of antigens is achievable, though further optimisations may be required. Quality control and data standardisation methods may also be useful for future analysis of large sero-epidemiological surveys.

An evolved fluorimetric determination of uranium in rock/mineral sample solutions containing hydrolysable elements such as Nb, Ta, Zr and Ti sequestered by bi-fluoride

The aim of the present paper is to develop a novel method for fluorimetric determination of uranium in rock/mineral solutions containing hydrolysable elements such as Nb, Ta, Zr and Ti sequestered by bi-fluoride. These rocks/minerals are decomposed with ammonium bi-fluoride (NH4HF2) and sulfuric acid (H2SO4) mixture. Uranium in such mineral solutions is selectively extracted into ethyl acetate with 2,3-dihydroxynaphthalene at pH 10–12 in the presence of cetyltrimethylammonium bromide, prior to its pellet fluorimetric determination. Optimizations of certain parameters such as the effects of fluoride fluxes, mineral acids, masking agents and diverse ions are discussed in detail. This method is applied for the determination of uranium in synthetic mixtures and a set of in-house reference refractory minerals including certified reference material X1807 with a high degree of accuracy and precision. The results for the refractory minerals using the proposed method are in excellent agreement with results obtained by other standard methods.The novelty of the proposed method is that the decomposition mixture (NH4HF2/H2SO4) inhibits the hydrolysis of hydrolysable elements by formation of their soluble fluoro complexes, and the separation of uranium using the complexing agent 2,3-dihydroxynaphthalene is more eco-friendly compared to existing the conventional solvent extraction system using aluminum nitrate as the salting out agent.

Application of PIGE method for quantification of total boron in neutron absorbers and shielding materials and isotopic composition in in-house prepared enriched boron carbide samples

The in situ current normalized particle induced gamma-ray emission method using 4 MeV proton beam was utilized for total boron concentrations in boron based neutron absorbers and borated wood based neutron shielding materials. Boron carbide samples with varying masses were analyzed to examine the effect of matrix as well as the efficacy of the in situ current normalized method. Isotopic composition of boron (10B/11B atom ratio) has been determined in natural and 10B enriched boron carbide samples as well as in four synthetically prepared enriched boron carbide samples to serve as in-house reference standard for isotopic composition.

In-house age-specific reference ranges for free light chains measured on the SPAPlus® analyser

Background The measurement of monoclonal free light chains is being increasingly utilized since the introduction of serum-based assays. It is important for laboratories to determine their own reference ranges in order to reflect the local population. The aim of this study was to determine if age-adjusted reference ranges for serum free light chains would have implications for demand management of further laboratory investigations including immunofixation. Methods After certain exclusions, 4293 samples from individuals seen in primary care across Oxfordshire between 2014 and 2016 were identified for analysis of patient characteristics, serum free light chain results and estimated glomerular filtration rate. Results We found age to be an independent variable when considering serum free light chain concentrations, ratio and estimated glomerular filtration rate. The reference ranges derived from our data differ markedly from the original Binding Site ranges. When the age-specific ranges are retrospectively applied to our population, there is a 38% decrease in follow-up testing with no loss of specificity. Conclusion We feel confident implementing new age-specific serum free light chain reference ranges in our laboratory. We have developed a simple algorithm for evaluating serum free light chains based on age and estimated glomerular filtration rate. We encourage laboratories to establish their own local reference ranges using large cohorts and their chosen serum free light chain assay platform.

Shared reference materials harmonize lipidomics across MS-based detection platforms and laboratories

Quantitative MS of human plasma lipids is a promising technology for translation into clinical applications. Current MS-based lipidomic methods rely on either direct infusion (DI) or chromatographic lipid separation methods (including reversed phase and hydrophilic interaction LC). However, the use of lipid markers in laboratory medicine is limited by the lack of reference values, largely because of considerable differences in the concentrations measured by different laboratories worldwide. These inconsistencies can be explained by the use of different sample preparation protocols, method-specific calibration procedures, and other experimental and data-reporting parameters, even when using identical starting materials. Here, we systematically investigated the roles of some of these variables in multiple approaches to lipid analysis of plasma samples from healthy adults by considering: 1) different sample introduction methods (separation vs. DI methods); 2) different MS instruments; and 3) between-laboratory differences in comparable analytical platforms. Each of these experimental variables resulted in different quantitative results, even with the inclusion of isotope-labeled internal standards for individual lipid classes. We demonstrated that appropriate normalization to commonly available reference samples (i.e., “shared references”) can largely correct for these systematic method-specific quantitative biases. Thus, to harmonize data in the field of lipidomics, in-house long-term references should be complemented by a commonly available shared reference sample, such as NIST SRM 1950, in the case of human plasma.

Quantification of Arsenic, Cadmium, Mercury and Lead in Pineapple: Method Development, Validation and Evaluation of In-House Reference Materials

A method for quantification of arsenic, cadmium, mercury, and lead in pineapple using inductively coupled plasma-mass spectrometry (ICP-MS) was developed, validated, and used to test the homogeneity and stability of in-house reference materials. The method was tested at the regulation levels given by the Food and Agriculture Organization of the United Nations (FAO, 100 µg kg−1). The mineralization conditions of the samples, in a microwave oven, were improved throughout the study of HNO3 and H2O2 concentrations, sample weight, time, and temperatures. The calibration was made by a gravimetric standard addition method with internal standard correction. The validation parameters were accuracy (trueness as recovery, between 97-112%, and precision as repeatability, below 12%), limits of detection (As 14.2, Cd 1.5, Hg 21.9, and Pb 5.4 µg kg−1 measured in pineapple), linearity and selectivity. The in-house material was lyophilized or dried in an oven. The best way to dry it was by the oven process because it has the lowest uncertainty.

MALDI-TOF Clinical Filamentous Fungi Identification. Bead Beating Versus Acid Solvent Protein Extraction Method

Abstract In recent years, Matrix-Assisted Laser Desorption Ionization–Time-Of-Flight Mass Spectrometry (MALDI-TOF) has changed clinical microbiology, allowing filamentous fungi identification. The aim of this paper is to validate a novel protein extraction method using bead beating to identified filamentous fungi and compare the fingerprinting spectra obtain to acid solvent method. A total of 50 clinical isolates, including Trichophyton interdigitale, T.rubrum, T.tonsurans, Aspergillus terreus, Microsporum canis were analyzed in this study. The MALDI-TOF spectra scores were identified correctly at the genus and species level for all. According to our results the fingerprinting spectra obtained by acid solvent extraction have, especially for Trychophyton spp, quantitative and qualitative poorly defined protein expression because of the similarities of the species. Our bead beating protein extraction methods allows to obtain a wider variability of protein pattern and huge defined number of peaks. Bead beating protocol could in this way implement a clinical in-house reference library. Keywords Bead beating; Filamentous fungi; MALDI-TOF; Protein extraction; Spectra

Novel Method of Extraction for Radiocarbon Measurements of Atmospheric Carbon dioxide

ABSTRACTIn this paper, we present the first data from an alternative extraction method for atmospheric 14CO2 analysis, based on the direct trapping of whole air samples onto a molecular sieve zeolite (13X) trap, incorporated into a commercially available automated graphitization system. Results are presented for both inter-laboratory comparison samples and an in-house reference standard. The in-house reference was used to calculate the standard deviation of measurements (2.0‰). This newly developed method will facilitate faster sample processing and therefore lower cost per analysis, critical for scaling up such studies.

A Study to Qualify an In-house Reference Standard Batch of Sci-B-Vac™

A Study to Qualify an In-house Reference Standard Batch of Sci-B-Vac™