Applications of Bioinformatics – and why clients use our services

Bioinformatics applications vary greatly, from agricultural applications to aiding vaccine development. At Fios Genomics, our bioinformatics services are used across a range of research areas. You will find details of these below as well as examples of how bioinformatic analyses benefit each particular research area.

Oncology Research

Bioinformatics applications for oncology research focus on analyses of cancer research datasets. Any type of cancer research dataset can benefit from bioinformatics analysis; whether it is pre-clinical, clinical, in-house data or a dataset from a publicly available database such as TCGA or DepMap.  Analysing these datasets using bioinformatics approaches can help with:

• Target and lead identification and validation
• Identifying biomarkers for measurement of drug efficacy and measurement of action
• Predicting biomarkers for stratification/classification of patient response to drug
• SNP genotype analysis & DNA sequence analysis for the detection of novel SNPs implicated in disease or response to drugs

Since over 30% of projects at Fios Genomics are oncology related we have a great deal of experience analysing oncology related data. Some previous projects we have worked on for clients include:

• Associating copy number variants with cancer cell line gene dependency
• Investigation of drug or gene knockout-induced changes to the proteome of cancer cells or tissues from various model organisms
• Single-cell RNAseq analysis of a publicly available dataset, where normal and malignant epithelial cells were identified from transcriptome profiles of ~200,000 single cells from non-small cell lung cancer (NSCLC) patients

You can also learn more about the bioinformatics applications for oncology research by browsing the many oncology research publications our work has been acknowledged in.

Environmental and Agricultural Research

Bioinformatics applications for environmental and agricultural research range from analyses of animal welfare studies to assisting with herbicide development. Since we are species agnostic at Fios Genomics, we are experienced in analysing data generated from a variety of plant and animal species. For example, our previous environmental and agricultural projects include:

• Investigation into amoebic gill disease, correlating gill infection and metabolic profiling of infected salmon to identify potential disease markers
• Time series analysis of metabolic stress response in plants
• RNA-seq analysis of flight feather-formation in avian wings

Furthermore, our bespoke bioinformatics solutions help with:

• Identification of microorganisms within a sample
• Exploration of gene expression profiles
• Linkage and association analysis of a trait within a population
• Discovery and characterisation of discriminating biomarkers for the parameter of interest

If you have an environmental or agricultural research project but are unsure if bioinformatics analysis can help, then please contact us and we will be happy to advise.

For further information about bioinformatics applications for agricultural and environmental research, browse our related publications.

Bioinformatics Applications for Gastrointestinal Research

Whether you are investigating the gut microbiome or researching the mechanisms behind Crohn’s disease, bioinformatics analyses will benefit your research. What’s more, since Fios are species agnostic, we can assist your gastrointestinal research regardless of your focus species. In fact, some of the gastrointestinal research publications we have been featured in have focused on animals such as pigs.

Our previous client projects in this area include:

• Analysis of murine gut microbiome following facility changes
• Evaluation of methylation levels at baseline against age as a continuous variable, adjusting for GI disease status
• Clinical trial analysis (Phase 2a) for a GI active drug incorporating gene expression, genotyping, PK (faecal and blood), as well as response markers and patient metadata

Learn more about our bioinformatics services for gastrointestinal research or request our sample bioinformatics report for gastrointestinal research.

.Fios genomics provide the following bioinformatics services for a range of applications

.

Bioinformatics Applications for Cardiovascular and Metabolic Research

Our bioinformatics services are popular with those researching cardiovascular and metabolic diseases. In this research area we use bioinformatics approaches to:

• Identify and validate targets and leads
• Identify biomarkers for measurement of drug efficacy and mechanism of action
• Predict biomarkers for stratification/classification of patient response to drug
• Perform systematic analysis of metabolic disorders by combining multiple ‘omics data sources

At Fios, we have experience in many types of cardiovascular and metabolic research. For example, we have helped researchers gain insight into myocardial infarction, nonalcoholic steatohepatitis (NASH), diabetes and obesity. Learn more about our bioinformatics solutions for cardiovascular and metabolic research here.

Infections and Vaccines Research

There are applications for bioinformatics throughout the drug development process for infections and vaccines. In fact, our bioinformatics solutions benefit both pre-clinical and clinical research in this area. In addition to our popular services which aid drug development (such as biomarker identification and target/lead identification and validation) we also:

• Identify mechanisms of resistance to treatment for bacterial and viral species
• Monitor mutation profiles of pathogens
• Detect novel SNPs implicated in disease or drug response

To learn more about how bioinformatics can benefit vaccine and infection research request our sample report Analysis of resistance in Mycobacterium tuberculosis. We also have further information about our services and experience in this area on our infections and vaccines page.

Respiratory Research

Our bioinformatics solutions are popular with those working in the field of respiratory research. In fact, we have analysed datasets relating to the following respiratory conditions: mesothelioma, COPD, fibrosis and lung cancer. Details of our analyses relating to these respiratory conditions are below.

• Investigation into fibrotic pathways and gene expression changes regulated by TGFβ and L-13
• Analysis of pharmacogenomics data from a Phase 2B trial in asthmatic patients
• Identification of early markers for lung cancer risk
• Individual dataset analysis of patient demographic, response, genotype and miRNA expression data from patients with COPD, and subsequent integration and congruence analysis

What’s more, our bioinformatics work for respiratory research has been acknowledged in these client publications. However, it is important to note that acknowledging our work when publishing results of your research is never a requirement of working with us.

Dermatology Research

There are many bioinformatics applications for skin disease research, such as:

• Differential profiling in skin diseases such as psoriasis and atopic dermatitis
• Methylation profiling
• Analysis of data from skin ageing experiments
• Target and lead identification and validation
• Identifying biomarkers for measurement of drug efficacy and mechanism of action
• Predicting biomarkers for stratification/classification of patient response to drug
• SNP genotype analysis & DNA sequence analysis for the detection of novel SNPs implicated in disease or response to drugs

Fios bioinformaticians have a wealth of experience in analysing dermatological data as we have provided bioinformatics analyses for several dermatology research projects. In fact, we even participated in the MAARS (Microbes in Allergy and Autoimmunity Related to the Skin) FP7 project.

For an in-depth example of how bioinformatics approaches can benefit dermatology research, request our dermatology sample report. This report features RNAseq expression profiling of psoriatic skin.

Central Nervous System Research

Researchers studying central nervous system disorders such as epilepsy, Parkinson’s and dementia can use our bioinformatics services to help answer their research questions. Indeed, our bioinformatics solutions can support each stage of the drug development process for CNS disorders, from the pre-clinical to clinical stage.

CNS projects we have provided bioinformatics solutions for include:

• RNA-Seq analysis of iPSC-derived models for understanding the effect of a compound on brain disorders
• Analysis of a high-throughput siRNA screen to identify biomarkers in Huntington’s Disease
• Data landscaping and mining of public datasets for proteomics and/or gene expression data, related to a range of disorders such as dementia, Parkinson’s disease, narcolepsy, epilepsy and Alzheimer’s disease

For further information on how we can help you meet your CNS research goals; contact us today to discuss your project and receive our CNS sample bioinformatic report.

Bioinformatics Applications for Rare Disease Research

There are various bioinformatics applications for rare disease research, such as:

• Computation of differentially expressed genes and pathways
• Analysis of immune context for specific rare diseases
• Data landscaping of publicly available data sources to assess literature for specific diseases of interest
• Data mining of publicly available datasets for diseases of interest

At Fios, we are proud to have supported important findings in the study of rare diseases such as Wilson’s disease and Prader-Willi Syndrome. You can learn more about our work in this area and the solutions we offer on our rare diseases page. However, if you have a particular project you would like to discuss then please get in touch. We are always happy to discuss new research projects in order to advise where bioinformatics analyses could help you to reach your research goals.

Author: Breige McBride, Content and Social Media Manager, Fios Genomics
Reviewed by Fios Genomics Bioinformatics Experts to ensure accuracy

You may also be interested in:

Bioinformatics and the Pharmaceutical Industry

Skin Microbiome – Analysis for Dermatology

Predictions for Bioinformatics in 2022