Epigenetic analyses are relevant to:
- Gain insight into protein–DNA interactions
- Investigate methylation patterns
- Characterise the response of cells or tissues to epigenetic modifying agents
- Understanding the mechanisms that regulate gene expression in response to environmental stresses or during developmental processes
Understanding epigenetic processes plays an important role in developing treatments for human cancers, metabolic syndromes and brain disorders as well as various other areas. Fios Genomics can help companies and organisations to investigate disease mechanisms and also to develop therapies which target therapying the epigenome. We provide a range of analysis services and solutions specifically for epigenetic research.
ChIP-seq Analysis
Chromatin immunoprecipitation sequencing (ChIP-seq) analysis can be used to analyse DNA-protein interactions. It can also be used for both transcription factor determination and histone modification assessment.
Our ChIP-seq analysis pipeline includes:
- Quality control evaluation of raw sequencing data
- Peak calling to identify regions of ChIP-seq signal enrichment. We can assess peaks in genomic features such as genes, exons/introns/intergenic or enhancers/promoters
- Visualisation of peaks/binding sites
- Differential binding analysis
- Also, Chromatin state learning using histone ChIP-seq
We have utilized the Bioinformatics team at FIOS Genomics for many of our drug discovery projects, as they provide expertise in the analysis of complex bioinformatic datasets. This includes large scale datasets from public sources as well as internally generated datasets. In many instances, at the start of a project, we have planned our large scale transcriptomic/proteomic studies with the FIOS team, to ensure that the data generated would provide the information we need, and that our projects had the highest chance of success. We have been consistently impressed with the rigor of FIOS’ work, their communication throughout the projects, and the rapid speed at which they complete their analyses.
DNA methylation
The addition of a methyl group to the cytosine nucleotide in a cytosine-guanine (CpG) dinucleotide pairing is the most well characterised epigenetic modification and is known widely as DNA methylation. CpG sites occur throughout the genome in a non-random distribution in CpG islands, shelves, shores or seas. Although the functional effect of DNA methylation is context-dependent, it is a method used by cells to tightly and dynamically regulate gene expression in response to developmental or environmental factors – given that this can be achieved in the absence of modification of the DNA sequence. DNA methylation can be measured directly at targeted sites by array (for example Illumina EPIC arrays) or more widely through bisulphite sequencing.
ATAC-seq Analysis
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) allows investigation into genome-wide chromatin changes as well as chromatin-accessibility signatures.
Our ATAC-seq analysis pipeline includes:
- Quality control evaluation of raw sequencing data
- Peak calling to identify regions of ATAC-seq signal enrichment. We can assess peaks in genomic features such as genes, exons/introns/intergenic or enhancers/promoters
- Visualisation of peaks/accessible regions
- Integration with other epigenetics data types such as ChIP-seq
CLIP-seq analysis
Cross-linking immunoprecipitation sequencing (CLIP-seq) can be used to analyse protein-RNA interaction and binding sites or locate RNA modification sites on a genome-wide scale.
Our CLIP-seq analysis pipeline includes:
- Quality control evaluation of raw sequencing data
- Peak calling to identify regions of CLIP-seq signal enrichment and visualisation of these peaks
- Integration with other data types
- Assessment of binding sites in genomic features such as genes, exons/introns/intergenic or enhancers/promoters
We also provide similar pipelines for methylation analysis including data generated from both arrays and bisulfite sequencing.
Every time our clients work with us, they benefit from:
- A dedicated analyst backed by an experienced team to curate all data, identify the most appropriate statistical approach to take and provide a biological interpretation of results
- An interactive data analysis report, internally peer-reviewed, including all analysis methods and results
- Post-report follow ups: upon receipt of our data analysis report, we arrange a teleconference so that our lead analyst can talk through the results
- As well as access to large capacity computing and secure data storage facilities
What we have helped with
Below is a small selection of gene expression projects where we have successfully helped our clients:
- Methylation analysis (Illumina 450k and 850k arrays and bisulfite sequencing)
- ChIP-seq analysis to identify DNA-protein interaction sites.
- Evaluation of methylation levels at baseline against age as a continuous variable, adjusting for disease status
- Metanalysis of disease vs healthy samples using methylation data generated from multiple studies
- Assessing sites of interest in human fibroblast cells following UV exposure and application of treatments.
WHAT YOU WILL GET
Transparency
All methods and analysis tools utilised are detailed in the final report. This means no blackbox of analysis.
Fast Turnaround
We help you to achieve your research goals in a quick and timely manner.
Rigorous QC
We always perform Quality Control as part of an analysis project.
Getting Your Data Ready for Analysis
We can analyse:
- Recent data, generated within your own laboratory or that of a 3rd party provider
- In-house historic data
- Data sourced from the public domain and database (data mining).
While we prefer to receive data in the raw format (e.g. CEL files) we can also receive pre-normalised files.
However, If you have yet to generate the data, we can help by arranging for the generation of your data. We have a list of providers for this purpose who are located worldwide and can take care of data generation. Generally this service is only available as part of a data analysis contract.
Alternatively, we are able to source and mine data from available databases. We are happy to work with you at every stage of your study to ensure the best outcome for your research.
Our Reports
We provide all Fios analysis reports via an HTML link hosted on our secure server. The secure link leads the user to a password-protected HTML document which is clickable, searchable and dynamic. This format therefore allows you to easily interrogate and explore your data (as demonstrated in this report walkthrough). Additionally, all methods, tools and thresholds are fully documented within the report.
We Can Help With Different NGS Data Types
We can help with data from all of the major technology platforms (eg Illumina, PacBio) for a wide range of applications such as:
- Genome-wide association studies (GWAS), whole genome sequencing (WGS) analysis, SNP detection and haplotype analysis to facilitate the discovery and/or typing of SNPs implicated in disease
- RNA-Seq data analysis: whole transcriptome analysis for differential gene analysis
- ChIP-Seq data analysis, for analysing interactions in DNA-protein
- Methyl-Seq data analysis: Bisulfite sequencing analysis for epigenetic studies
- Exome analysis for the identification of known and novel SNPs and indels etc.
- CNV analysis
Our Expertise
Watch our video where our team of bioinformaticians talk about extracting biological insight from NGS data and the challenges in doing this.
We offer a wide range of services:
Discovery
Selecting the correct targets and/or the correct indication is essential for development success. We help support the process with robust analysis of historic or new data.
Preclinical Research
We help in experimental design and statistical analysis while guiding our clients in making informed decisions during the preclinical stage.
Clinical
Research
We offer a comprehensive analysis approach for augmenting clinical trial outcomes, ensuring you get the most information out of your research.
Drug Repurposing
We have strong experience with identifying in silico new potential indications for existing drugs, reducing the cost and time of downstream wet lab validation.
