Cancer Genomics Analysis Services

Cancer genomics analysis, end to end

Cancer is a disease of the genome. Tumour sequencing reveals the somatic mutations, copy-number changes and structural rearrangements that drove a cancer to develop and that determine how it may respond to treatment. Turning raw tumour sequencing into that picture is a demanding analysis, and the difference between a careful pipeline and a careless one is the difference between real drivers and a list of artefacts.

We analyse tumour whole-genome, whole-exome and targeted panel data from raw reads through to an interpreted report, using tumour-normal designs wherever paired material exists and clearly flagging the added uncertainty when it does not.

Our Services

• Somatic single-nucleotide variant and indel calling, with tumour-normal pairing where available
• Copy-number alteration analysis, including focal amplifications and deletions
• Structural variant and gene fusion detection
• Tumour purity and ploidy estimation, and subclonal architecture
• Mutational signature analysis against the COSMIC signature catalogue
• Tumour mutational burden and microsatellite instability status
• Driver gene identification and annotation against cancer knowledge bases
• Germline variant analysis for cancer predisposition where consented
• Clinical annotation of actionable variants against OncoKB, CIViC and ClinVar

The result is a defensible account of what is driving the tumour, which alterations are actionable, and how confident each of those calls is.

What you receive

• Annotated somatic and germline variant tables with confidence and filtering rationale
• Copy-number and structural variant calls with genome-wide plots
• Mutational signature decomposition with contribution estimates
• Tumour mutational burden, MSI status and purity and ploidy estimates
• A ranked driver and actionability summary linked to the supporting evidence
• Publication-ready figures: oncoprints, signature plots, copy-number profiles and lollipop diagrams
• A written report and the complete analysis code, so results can be reproduced and extended

Why tumour-normal pairing matters so much

Every genome carries millions of germline variants that are simply inherited. Without a matched normal sample, distinguishing a somatic mutation the tumour acquired from a rare inherited variant relies on population databases, and rare germline variants are systematically misclassified as somatic.

That inflates tumour mutational burden, contaminates driver lists and distorts mutational signatures. Where a matched normal exists we always use it. Where it does not, we run a tumour-only pipeline with stricter filtering and state plainly which conclusions the design can and cannot support — rather than presenting tumour-only calls with unearned confidence.

Purity, ploidy and why they change everything

A tumour biopsy is never pure tumour. It contains stroma, immune infiltrate and normal tissue, and the tumour cells themselves may be aneuploid and genetically heterogeneous.

Low purity suppresses variant allele frequencies, so real mutations fall below detection thresholds. Ploidy changes shift what a given copy number means. Estimating both is not an optional refinement — it determines whether your variant calls, copy-number segments and subclonal reconstruction mean anything at all.

Mutational signatures: what caused this cancer

Different mutagenic processes leave characteristic patterns across the genome. Tobacco smoke, ultraviolet light, defective mismatch repair, homologous recombination deficiency and APOBEC activity each produce a recognisable signature.

Decomposing a tumour’s mutation spectrum against the COSMIC catalogue identifies which processes were active. This is more than descriptive: a homologous recombination deficiency signature is directly relevant to PARP inhibitor sensitivity, and a mismatch repair signature points toward immunotherapy.

Data we accept

Raw FASTQ, aligned BAM or CRAM, or existing VCF files, from whole-genome, whole-exome or targeted panel sequencing. Tumour-normal pairs, tumour-only, FFPE and fresh-frozen material are all supported — FFPE data receives additional filtering for the deamination artefacts that characteristically inflate C>T calls.

Questions this analysis answers

• Which somatic alterations are driving this tumour, and which are passengers?
• Are there clinically actionable variants, and what is the evidence level for each?
• What mutational processes have been active, and what do they imply for treatment?
• Is the tumour clonal, or are there subclones with different therapeutic implications?
• How do tumours differ across a cohort, and what distinguishes responders from non-responders?