Oncology: Somatic Variant Analysis
Bioinformatics analysis of tumour panel sequencing data, from raw FASTQ files to an annotated, tiered variant report, for research use.
Tumour tissue is profiled with a targeted gene panel.
What is Oncology Panel Data Analysis?
A bioinformatics service that turns targeted cancer panel data into an annotated variant report for research use.
It identifies alterations acquired by the tumour across the genes the panel covers, and reports each with the evidence behind it, for review by qualified professionals. It does not replace that review.
- EGFR
- KRAS
- BRAF
- ALK
- ERBB2
- TP53
Examples only; gene content depends on the panel used.
- Allele fraction
- Clinical tier
- Supporting evidence
Variant types
What a tumour panel analysis looks for, where the panel design supports it.
SNVs
Single-nucleotide changes identified within the covered genomic regions.
Indels
Insertions or deletions detected in covered regions.
Copy number changes
Changes in copy number inferred from sequencing coverage, where supported.
Our Service
From raw FASTQ we carry out quality assessment, variant calling and annotation, and return a prioritised variant list with allele fractions and supporting evidence for each call.
- Different targeted panel designs
- Commercial or custom panels
- Standard NGS-generated data
- Solid tumour applications
- Haematological applications
Subject to panel design, data quality and project requirements.
- 01
Raw FASTQ
Panel reads as supplied.
- 02
Quality assessment
Read quality, depth, uniformity.
- 03
Alignment / processing
Mapped to the reference build.
- 04
Variant calling
Candidate somatic variants called.
- 05
Annotation
Gene, consequence, cancer evidence.
- 06
Prioritisation
Ranked by evidence and relevance.
- 07
Tiered variant report
Tiers, VAFs, and evidence.
Analyses we offer
Three analysis designs, chosen by the samples and data available.
- Request this analysis→01
Screening Analysis
Focused screening of tumour panel data for a defined set of potentially actionable alterations, such as hotspot variants in EGFR, KRAS and BRAF, with the option to extend to broader analysis on the same data.
- 02
Tumour-Only Analysis
For tumour data without a matched normal. Population databases, panels of normals and other filters help separate likely somatic from inherited variation, with the basis of each call documented.
Calls are likely somatic: inferred, not experimentally confirmed.
Request this analysis→ - Request this analysis→03
Tumour–Normal Paired Analysis
Tumour data analysed alongside matched normal data from the same patient. Direct comparison adds evidence for distinguishing tumour-acquired from inherited variation.
What the Analysis Covers
Where supported by panel design and data quality
SNVs
Single nucleotide variants, with variant allele fraction for relevant calls.
Indels
Insertions and deletions, including complex or multi-nucleotide changes.
CNVs
Copy number alterations inferred from coverage.
TMB / MSI
Tumour mutational burden and microsatellite instability estimates.
Quality & coverage
Coverage and quality assessment, with detection-limit information.
Tier definitions
Each reported variant is assigned one tier. A tier summarises the strength of annotated evidence for that variant. It is not a clinical recommendation, and it depends on the evidence sources and tumour type considered.
- Tier I —
- Strong clinical significance
- Tier II —
- Potential clinical significance
- Tier III —
- Unknown clinical significance
From Inputs to Insights
Research Inputs
- FASTQ
- BAM / CRAM
- VCF
Research Outputs
- Tiered variant reportAnnotated somatic findings, tiered by evidence.
- Prioritised variant tableRanked calls, ready for review.
- Variant allele fractionsWith sequencing quality metrics per call.
- Evidence & annotationsCancer and clinical evidence for each call.
- Quality & coverage summaryDepth, uniformity, detection limits.
- Filtered VCFFor your own pipelines and records.
We analyse sequencing data generated elsewhere. Findings are provided for review by qualified clinical professionals; they are for research use, are not a diagnosis and do not determine treatment. What can be detected depends on panel design, sequencing depth and data quality.
Have tumour sequencing data to analyse?
Turn targeted oncology sequencing data into annotated and prioritised somatic variant findings for qualified clinical or research review.