Bioanalytical ServicesWhat we do
PROTEIN BIOMARKER DISCOVERY
Laboratory service for protein biomarker discovery to validation
BioXpedia offers bioanalytical service for targeted proteomics and protein quantification. Our laboratory analyses support projects from large-scale biomarker discovery to low-plex and single-assay absolute protein quantification or biomarker validation. All projects are initiated with a discussion of the optimal technology and analysis strategy to tailor the ideal solution for your project.
Technologies for protein biomarker screening and protein quantification:
All our analytical services are performed by skilled and trained professionals and no samples are shipped for analysis outside Denmark.
Sample types for protein analysis
The majority of protein biomarkers are low abundant proteins found in minimally invasive sample types such as serum, plasma, urine, saliva and other easily accessible body fluids. However, understanding disease pathology often requires more insight, therefore we offer protein analysis and quantification on a wealth of sample types, for example tissue and tumour biopsies, cerebrospinal fluid (CSF), extracellular vesicles, tear, exosomes, cell lysates, supernatants etc. Protein extraction and sample preparation for down-stream protein analysis can also be performed. The protein analyses we offer are predominantly antibody assays developed and validated for human and murine samples. However, immunoassays for other species are also available.
Protein biomarkers versus genomic biomarkers
Biomarkers for early diagnosis, prognosis, patient stratification or monitoring treatment response is increasingly in demand with the focus on personalised medical treatment. Protein markers offer a significantly higher degree of differentiated information compared to genomic markers. In addition, proteins represent the direct functionality which makes them essential in understanding disease pathology and associated biological processes. For a short presentation of selected publications presenting biomarker research within oncology, cardiovascular disease, inflammatory and neuroinflammatory diseases, click here.
Using Proximity Extension Assay (Olink Proteomics) we can provide disease-focused screening of 92 protein biomarkers measured simultaneously using only 1µL sample. Each panel of 92 biomarkers is targeted at a specific disease or key biological process. The panels cover a total of 1165 clinically relevant proteins, divided into 15 focused biomarker panels, e.g. oncology, immuno-oncology, inflammation, immune response, cardiovascular disease, neurology, cell regulation, development, metabolism, organ damage and a translational mouse panel (see protein lists of all biomarker panels here).
Absolute protein quantification
Using the Meso Scale Discovery (MSD) technology we can provide absolute quantitation of proteins using electrochemiluminescence immunoassays providing high sensitivity and multiplex functionality. The analysis method is highly flexible offering ultra-sensitive and thoroughly fit-for-purpose validated assay panels and customized assay combinations of your own choice (more about customized assays). The immunoassays are provided as single analyte or multiplex protein assays up to 10-plex in each well. The MSD protein panels are focused on measuring proteins associated to for example inflammation, oncology, neurodegeneration, immunology, intracellular signalling, cardiovascular disease and metabolism.
miRNA expression profiling
Laboratory service for miRNA expression analysis
At BioXpedia we offer various miRNA expression services ranging from quantification studies of specific miRNAs to global microRNA expression profiling. The technologies we offer require little sample material and support various species and sample types.
What are microRNAs?
MicroRNAs (miRNAs) are a group of small non-coding RNAs involved in transcriptional regulation of a range of developmental and physiological processes, such as neurological development, spermiogenesis and in the immune system. miRNAs are typically found and exert their mechanism within the cells, however circulating miRNAs and exosomal miRNAs have also emerged as signalling molecules in the extracellular matrix. For an example of investigation of a specific miRNA signature in serum of bladder cancer patients, see more here.
MicroRNAs as diagnostic biomarkers
miRNA expression profiling is targeted for the investigation of regulatory functions related to processes such as cell growth, development and differentiation, as dysregulation of certain miRNAs has been associated with development of diseases. Thus, miRNA profiling can aid in the discovery of predictive or prognostic biomarkers for clinical disease stages or as important players in specific pathways.
Technologies for miRNA expression profiling
Tailored multiplex miRNA profiling using Fluidigm
Using the Fluidigm Biomark HD system we can provide miRNA expression profiling and experimental validation in a variety of sample types in a flexible setup. The Biomark system ensures efficient, high-throughput processing of miRNA samples with increased speed and reproducibility. The technology is fast and only requires small sample volumes in the nanolitre scale, making it ideal for miRNA profiling.
Digital detection and quantification of miRNA
With the nCounter® miRNA Expression assays from NanoString Technologies we perform highly multiplexed, direct digital detection and quantification of hundreds of miRNAs in a single reaction. The assays are optimized for robust performance across a variety of sample types including FFPE and plasma samples with high reproducibility. The nCounter® technology allows simultaneous measurement of miRNA and mRNA from the same sample, making it ideal to study the impact of miRNAs on their target mRNAs in a custom manner.
SNP variation analysis
BioXpedia offers SNP genotyping analysis for investigation of genetic associations, loss of heterozygosity (LOH) or copy number variations. Additionally, we provide SNP tracing for standardized authentication and quality control check of biobank samples and cell lines. We offer different genotyping technologies depending on the application and the purpose of the analysis, the number of SNPs per sample, and the number of samples in the study.
What is Single Nucleotide Polymorphism (SNP) variation?
SNPs (single nucleotide polymorphisms) or point mutations are the most common type of genetic variation determining a major part of the phenotypic diversity between individuals. Causal point mutations may change the amino acid sequence of the encoded protein, and hence such SNPs can be used as markers for development of companion diagnostics and stratification of patients.
Technologies for SNP genotyping:
SNP genotyping using Fluidigm Biomark
We provide targeted SNP genotyping, in a flexible set-up using the Fluidigm Biomark HD platfrom. SNP analysis are performed on 192×24 or 96×96 chips (samples versus assays) with pre-designed or custom designed assays using TaqMan® probes, SNP Type assays or IDT rhAmp® SNP assays.
The Fluidigm System enables efficient, high-throughput processing of SNP genotyping of samples with increased speed and reproducibility. The system requires small quantities of DNA, which makes it ideal for precious sample analysis. For more information see HT qPCR.
DNA analysis – high quality performance on FFPE samples
Especially suited to FFPE samples is the nCounter® Assays from NanoString Technologies to investigate Copy Number Variation (CNV). The NanoString system provides high sensitivity and reproducibility, making it ideal for routine screening applications. For Gene Fusion Panels and custom design options, please enquire here.
GENE EXPRESSION PROFILING
Laboratory Service for Gene Expression Profiling
BioXpedia offers RNA analyses of samples, using technologies that are time-, cost-, and sample-effective, allowing profiling of RNA from different tissues and cells.
RNA expression analysis to study molecular regulation
Analysis of changes in gene expression is the first level of exploration for any regulation at the molecular and cellular levels. Transcription of genes is a very dynamic process, allowing cells to adapt rapidly to external, environmental or physiological changes. Therefore, gene expression profiling is a very powerful way of identifying RNA biomarkers that describe a given physiological state, disease or exposure to drugs.
Technologies for RNA expression profiling:
High multiplex level and low sample requirement
With the Fluidigm BioMark HD technology, HT QPCR, rapid and reproducible results are ensured with an automated workflow on Integrated Fluidic Circuits (IFC chips) with reaction chambers of less than 10nl. The high capacity and multiplex level system enables simultaneous detection of 96 assays in 96 samples creating 9.216 data points in a single run. The technology offers a flexible set-up, production scale throughput and high sensitivity for expressed genes in specific tissues or cells. For more information, please contact us.
Targeted direct digital gene expression detection
Using the nCounter® Gene Expression Panels from NanoString Technologies, with 250-770 gene expression assays in each panel, we perform direct digital detection and quantification of mRNA molecules in a single reaction. The panels from NanoString cover relevant topics in clinical and pre-clinical research: Inflammation, immunology, Pan Cancer, Cancer Immune Profiling, Cancer Progression profiling, Cancer Pathways, CAR-T Characterization, Metabolism, Fibrosis, Autoimmunity, Neuroinflammation, Neurological Diseases like Parkinsons and Alzheimer Disease, Gene Fusion and the option for addition of custom designed assays.
The gene expression assays from NanoString are optimized for robust performance across a variety of samples like RNA extracted from tissues, cells or FFPE samples. With the NanoString technology target molecules as small as 100 base pairs are detected with less than 100 ng of input material. NanoString Technologies, nCounter® panels
EXTRACTION AND SAMPLE PREPARATION
DNA, RNA and protein extraction service
BioXpedia offers sample preparation and high-quality extraction of the molecules of interest – DNA, RNA species and proteins – for any downstream analysis.
Sample types for extraction
We provide extraction from plasma, serum, whole blood, tissue biopsies and FFPE tissue along with any other biofluid sample such as urine, cerebrospinal fluid, saliva, and tear fluid. Furthermore, cultured cells and medium from cell cultures can be used as a source for extraction of the molecules of interest.
Our extraction services
Our extraction methods are suitable for mRNA extraction and small RNA species such as miRNA. Additionally, we offer isolation of RNA and miRNA from extracellular vesicles like exosomes derived from plasma, serum and other biofluid samples. Extraction of protein is optimized for the specific sample type, for example cells or tissue, to ensure extraction of native proteins and avoid degradation of proteins prior to analysis and quantification.
Quantification and integrity analysis of extracted RNA and DNA
The concentration and quality of extracted DNA and RNA is assessed by state-of-the-art technologies (4200 TapeStation and QIAxpert) to assure high quality input material for our downstream analyses. Automated workflow and robotic pipetting (QIASymphony) is used whenever possible to ensure maximum reproducibility and efficiency.
If your research is specifically focused on a sample type not mentioned above, please do not hesitate to contact us for a discussion – Contact.
Statistics and bioinformatic analysis
Analysing multi-marker data often requires advanced biostatistical methods to translate raw output data into credible and substantiated interpretation and biological knowledge.
BioXpedia offer statistical analysis of your data, for example gene expression or protein screening data. We can provide a standard statistical service, or you can choose a customized biostatistical analysis for more complex project designs and analyses. The biostatistical analyses are performed by bioinformatic professionals experienced in handling data output from the technologies that BioXpedia offers. Our biostatistical analysis and consultancy ensure that you acquire the maximal value and information output from the bioanalytical data of your project.
Standard biostatistical service
The standard statistical service includes an investigation of which biomarkers are significantly different between groups of interest, for example between a disease and control group of patients. A fast and reliable way to get the most out of your experiment!
The standard biostatistical service includes:
- Test for normal distribution of data to investigate assumptions for statistical tests.
- Hierarchical cluster analysis or Principal Component Analysis (PCA) to investigate how the profile of all samples group together.
- Identification of significant differential markers between groups, either by parametric or non-parametric tests. Correction for multiple testing is performed using false discovery rate.
- Visual presentation of all significant markers and fold change in a Volcano plot for each group comparison.
- Standard report including detailed description of statistical analysis, boxplots of significant markers and a table listing significance and fold change of all markers.
Tailored biostatistical service
If you have a project with a more complex experimental design, for example time-series data, or need additional statistical analyses and bioinformatics, we can tailor our biostatistical service targeted specifically to your project.
We also offer analyses to support decision on project and experimental design, for example power analysis and sample size calculation.
Customized biostatistical analysis is for:
- Univariate and multivariate statistical analyses, for example ANOVA, T-test, Principal Component Analysis (PCA), Partial Least Squares etc.
- Cluster analysis, for example heat-map, K-means clustering for response profile clustering to identify markers that respond similar for example during a time course.
- Network analysis forvisualization of the correlation, interaction or association among markers in a complex biological system.
- Gene Ontology annotation and enrichment analysis for example of KEGG pathways
- Model development and fitting for identification of predictive markers and validation of discovered markers.
Open Olink Proteomic panels
Each Olink Proteomic protein biomarker panel (PEA technology) provide disease-focused screening of 92 protein biomarkers. The PEA technology is run using Fluidigm 96.96 IFC chip, thus each run (chip) has space for 90 patient samples plus assay controls.
However, if you have a small project or need to run a pilot project before initiating a large-scale study including many clinical samples, it is possible to team up with other researchers to share costs.
Pilot projects running on shared chips will await a sufficient number of samples for the panel, thus a longer delivery time can be expected. We will of course keep you updated on the timeline for your project.
More information on the Proximity Extension Assay from Olink Proteomics here
Joint R&D projects – Scientific excellence together
BioXpedia is eager to participate in national and international biomarker research and development projects. We may contribute to innovative research as service provider or as SME-partner in grant proposals or research consortia. BioXpedia is ready to establish true research collaboration by exchanging knowledge, data and research expertise for shared research projects, developing scientific and commercial innovations.
BioXpedia participates actively in international funding programs such as H2020 and Eureka-Eurostars and Danish research programs run by Innovation Fund Denmark, the Lundbeck Foundation and the Novo Nordisk Foundation.
A background with many years of scientific research and experience from several successful R&D projects, makes BioXpedia the ideal partner for establishing partnerships for biomarker discovery and validation.
If you are interested in exploring collaboration opportunities, please contact us
BioXpedia is in all aspects committed to operate under controlled conditions and under the highest level of quality.