Biomarkers help pharmaceutical R&D teams stratify patients and understand drug response. We integrate genome resequencing, epigenomic and mass-spectrometry proteomics data to help identify molecular signatures associated with drug response in complex cohorts.
Data analysis is carried out by our bioinformatics team and reviewed by senior bioinformatics experts before delivery; see custom analysis for details.
1. Broad candidate screening: molecular profiles of response groups are compared using DIA proteomics, WGS/WES or epigenomic data.
2. Feature selection: Co-expression networks and feature selection models (LASSO, random forest) filter background redundancy and shortlist candidate markers.
3. Data support for targeted validation: statistical input on validation plans for selected markers, and analysis of the validation data.
Typical turnaround: agreed in writing per project.
Deliverables include marker heatmaps, PCA plots, differential abundance results and ROC curves.
| Analysis stage | Deliverables | Purpose |
|---|---|---|
| Initial screening | Differential protein/variant heatmaps, PCA scatter plots | Identify significant molecular differences between control and responder groups |
| Feature selection | LASSO regression curves, random forest importance ranking | Distil a marker panel from many candidates |
| Marker performance | ROC curves (AUC) | Assess how well markers predict efficacy or toxicity |
Samples are tested by a qualified partner laboratory; please collect and ship them according to that laboratory's requirements. Typical requirements for reference:
| Sample type | Minimum amount | Quality criteria | Shipping/storage |
|---|---|---|---|
| Fresh frozen tissue | > 50 mg | Necrosis < 10%, tumour cell purity > 50% | Snap-frozen in liquid nitrogen, stored at -80°C, shipped on dry ice |
| EDTA whole blood | 5 - 10 mL | Dedicated cfDNA / RNA preservation tubes | Room temperature or 4°C cold chain, do not freeze |
| Plasma / serum | > 1 mL | No haemolysis; high-speed centrifugation to remove debris | Frozen in sterile tubes, shipped on dry ice |
Testing of clinical-trial samples is performed by partner laboratories holding the required accreditation. We are responsible for the data side of the test plan: data quality control, analysis, statistics and result reports. We do not issue clinical diagnostic reports; test plans and quality requirements are agreed in writing per project.
Data analysis is carried out by our bioinformatics team and reviewed by senior bioinformatics experts before delivery; see custom analysis for details.
1. Data support for enrolment stratification: Quality control, aggregation and stratified statistics of genotype data produced by the partner laboratory, delivered as tables for enrolment discussions.
2. Pharmacogenomics (PGx) data analysis: Annotation of common drug-metabolism genes (e.g. CYP2D6, CYP2C19) against PharmGKB and similar resources; the gene list is agreed per project.
3. Statistical analysis of efficacy-related data: Longitudinal statistics and visualisation of follow-up test data according to the plan, delivered as a reproducible analysis report.
Typical turnaround: agreed in writing per project.
Data QC reports, analysis reports and statistical figures are provided; test items, the testing laboratory and limits follow the written plan.
| Item | Support available |
|---|---|
| Enrolment genotyping data | Tested by the partner laboratory; we perform QC, aggregation and stratified statistics |
| Pharmacogenomics (PGx) | PharmGKB-based annotation of common drug-metabolism genes; gene list agreed per project |
| Follow-up test data | Longitudinal statistics, visualisation and reporting; metrics agreed in the plan |
Clinical-trial samples are collected and shipped according to the partner laboratory and the project plan. Common types for reference:
| Sample type | Specification | Tube | Shipping and turnaround |
|---|---|---|---|
| Peripheral blood | 5 mL | Dedicated cfDNA / EDTA tubes | Ship at 4°C, arrival within 48 hours; turnaround as agreed in the plan |
| FFPE tissue sections | 8 - 10 slides | Slide box, protected from light | Room temperature or cold pack; turnaround as agreed in the plan |
Companion diagnostics are developed alongside targeted therapies. For pharma CDx programmes we provide data analysis: evidence compilation for candidate targets, data-level input on assay plans and statistical analysis of validation data. Testing is performed by qualified partner laboratories. We do not design assays, manufacture reagents or prepare regulatory submissions, and we do not issue clinical diagnostic reports; the scope is agreed in writing per project.
Data analysis is carried out by our bioinformatics team and reviewed by senior bioinformatics experts before delivery; see custom analysis for details.
1. Target and marker selection: Evidence and population frequencies of candidate targets compiled from cohort data and public databases.
2. Data-level input on assay plans: comments on target regions and analytical performance metrics from a data perspective; assay design remains with the client and its laboratory.
3. Analysis of validation data: Statistical analysis and documentation of precision, sensitivity, specificity and stability experiments.
Typical turnaround: agreed in writing per project.
Target evidence summaries, data-level comments on assay plans and statistical reports on analytical-validation data; scope agreed per project.
| Support | Deliverable | Notes |
|---|---|---|
| Target and marker evidence | Candidate list, evidence table, population frequency annotation | Data sources and criteria are written into the plan |
| Assay plan input | Written data-level comments on target regions and performance metrics | Assay design is decided by the pharma company and its laboratory |
| Validation data analysis | Statistical reports on precision, sensitivity, specificity and stability | Experiments run by an accredited laboratory; we handle the data |
Companion diagnostic data analysis is set up as a custom project; any testing is carried out by a qualified partner laboratory according to its own requirements. The process:
| Step | Content |
|---|---|
| 1. Technical discussion | Mechanism of action, target information and the expected analytical performance requirements. |
| 2. Data and materials | Raw validation data, de-identified reference material information and any existing Sanger or qPCR results. |
| 3. Scope confirmation | Work starts after both sides confirm scope, deliverables and timeline in writing. |