We offer a range of services to interrogate genetic variation and association with clinical outcomes or phenotype including:
- WGS/WES sequence analysis to call SNPs or mutations
- Copy number variation (CNV) calling and analysis
- Somatic vs germline mutation detection
- GWAS studies
Genetic variation at the DNA sequence level can be associated with phenotypic differences observed between individuals in terms of disease, trait status or response to treatment. Where associations between these measures are performed across variants at the genomic scale, this is generally termed a genome-wide association study (GWAS). Markers that are found to be associated with a phenotype or outcome of interest may consequently be used to build predictive polygenic risk scores to predict outcome for a given genotype.
Alternatively, markers can help highlight new disease-associated genes or cellular pathways as well as identify therapeutic targets for intervention. In oncology particularly, mapping genetic variation in exomes using whole exome sequencing (WES) rather than the whole genome can be preferred. WES balances cost of data generation while retaining the ability to identify genetic variants with direct functional impact in coding regions of genes.
Genetic Variation Analysis:
What We Offer
Whole exome or whole genome sequencing (WES or WGS) or SNP arrays can be used to profile genetic variation across many sites in the genome simultaneously. However, sequence data is often generated on the scale of terabytes which makes the data challenging to handle, process and analyse.
At Fios, we have workflows and compute resources that can process data generated from most next generation sequencing (NGS) and array-based technologies at scale. Where necessary, we can also leverage cloud computing for high throughput of large data sets.
Our Genetic Variation Services
We offer a range of services to interrogate genetic variation and association with clinical outcomes or phenotype, including:
- WGS/WES sequence analysis to call SNPs or mutations
- Copy number variation (CNV genetics) calling and analysis
- Somatic vs germline mutation detection
- Genome-wide association studies (GWAS) and haplotype analysis to facilitate the discovery and/or typing of SNPs implicated in disease
Every time our clients work with us, they benefit from:
- A dedicated analyst, backed by an experienced team, to curate all data and identify the most appropriate statistical approach to take before providing 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.
- Access to large capacity computing and secure data storage facilities
A typical genetic variation analysis pipeline includes:
- SNP calling (where necessary) and quality control (e.g. filtering low quality calls, low frequency alleles and those that depart from Hardy-Weinberg equilibrium)
- Somatic variation calling and quality control including, for example, evaluation of sequence data, alignment to the genome and sample uniformity
- Unsupervised analysis to detect and attribute, for example, demographic clustering within the data
- Association testing, correcting for population stratification as necessary, e.g. using PLINK
- Computation of a polygenic risk score (PRS) if required
Previous Genetic Variation Projects
We have helped our clients with the following types of projects:
- Identifying genomic loci associated with disease status
- Identifying SNPs associated with poorer drug response and survival
- Assessment of tumour mutational burden and its association with response to immunotherapy and survival
- Associating copy number variants with cancer cell line gene dependency (CNV Genetics)
- Investigating associations between pharmacokinetic data and genetic variation
- Multivariate analysis across RNAseq and SNP/CNV data, alongside efficacy data from over 800 CRISPR screens.
- Association of gene expression or mutations that confer sensitivity to CRISPR gene knockout in cell lines of interest.
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.
Transparency
We detail all methods and anlysis tools we have used 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.
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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
- As well as data sourced from the public domain and database (data mining).
While we prefer to receive data in the raw format (eg .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 located worldwide which can take care of data generation. Generally this service is only available as part of an 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
Our analysis reports at Fios are provided as 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. Therefore, this format allows you to easily interrogate and explore your data. Additionally, all methods, tools and thresholds are fully documented within the report. See what our data analysis reports look like in this video.
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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 and guide 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.
