Lab type
Molecular and genomics
Variants, QC and interpretation in one traceable genomic report.
Who it is for
Molecular pathology and genomics laboratories running somatic tumour testing, germline panels, rapid prenatal tests or cytogenetics, from a single-room PCR service to a laboratory with an NGS pipeline. It suits teams who already have bioinformatics tools and need a dependable case record and report around them.
Genomic reports carry a lot of context: why the test was requested, which block and how much tumour, what the assay could and could not detect, and how each variant was classified. VipLIMS gives each of those its own report section, so reports are consistent across scientists and easy to check before sign-off.
A day with VipLIMS
- The lung cancer team requests a panel through the referrer portal and quotes the parent histology number. The case is received, numbered, for example
MOL26-00871, and the TAT clock starts. - A pathologist marks the tumour area and records tumour content. After extraction, DNA concentration and purity are entered against the case and checked against your acceptance criteria.
- Sequencing and analysis run in your existing pipeline. The scientist enters reportable variants in HGVS nomenclature, with gene, transcript, allele frequency and tier.
- The clinical scientist writes the interpretation and recommendations, states the method and its limitations, and sends the case for authorisation.
- A senior scientist reviews and authorises the report. The PDF is released to the requesting team in the portal and the TAT closes.
- If a reanalysis later changes a classification, an amended report is issued as a new version and the earlier report stays on file.
What the pack sets up
Ready on day one, editable afterwards
Case types and numbering
| Case type | Example number | Routine target | Urgent target |
|---|---|---|---|
| Somatic tumour NGS panel | MOL26-00042 | 14 days | 7 days |
| Somatic single-gene or hotspot test | MP26-00042 | 7 days | 3 days |
| Germline genetic test | GL26-00042 | 42 days | 14 days |
| Rapid prenatal aneuploidy (QF-PCR) | PN26-00042 | 3 days | 2 days |
| Cytogenetics (karyotype, array, FISH) | CG26-00042 | 21 days | 7 days |
Example tests
| Test | Unit (UCUM) | Example reference range |
|---|---|---|
| Tumour cell content | % | |
| DNA concentration | ng/uL | ≥ 2 ng/µL |
| DNA purity (A260/A280) | {ratio} | 1.7–2 {ratio} |
| Target regions above minimum depth | % | ≥ 95 % |
| Variant allele frequency (main variant) | % |
Acceptance thresholds for DNA quantity and purity in this pack are illustrative examples only. Every laboratory must verify and replace them with the criteria validated for its own methods before reporting.
Report sections
- Indication required
- Sample and quality required
- Method, coverage and limitations required
- Results required
- Interpretation required
- Recommendations
Specimen types
- FFPE tumour block
- FFPE sections or curls
- Blood for cell-free DNA
- Whole blood, EDTA
- Saliva
- Whole blood, lithium heparin
- Amniotic fluid
- Chorionic villus sample
- Bone marrow aspirate
- Extracted DNA
- Fresh tissue
Starter synoptic templates
- Generic reportable variant (starter)
Written by VipLIMS; not RCPath, ICCR or CAP datasets. Build forms for the datasets your laboratory is licensed to use.
Words your team will see
- Reporter
- Clinical scientist
- Sender
- Hospital
- Work item
- Case
- Subject
- Patient
- Specimen
- Sample
- Output
- Report
Good practice built in
- Report sections for indication, sample quality, method and limitations, results, interpretation and recommendations.
- HGNC gene symbols and HPO phenotype terms available as coded terminology.
- Turnaround targets that match real practice, from rapid prenatal results in days to germline panels in weeks.
- Versioned reports and a full audit trail, which matter when classifications change over time.
- Supports workflows that laboratories accredited to ISO 15189 need, including traceable QC results and authorisation.
- Mandatory two-factor sign-in, encryption at rest and a full export of your data at any time. Genetic data is special-category data, so these are not optional extras.
Questions labs ask
Can we upload VCF files and have variants imported?
Not yet. Variants are entered on the case. File attachments and VCF import are on our roadmap.
Does VipLIMS classify variants for us?
No. Classification is your scientists' decision. VipLIMS records the class you assign and who assigned it; it does not run classification rules or query variant databases.
Can it track runs, libraries and barcodes on the sequencer?
Run and library management is limited today. You can record run and barcode identifiers on the case, but there is no instrument integration.
How is consent recorded for germline tests?
Consent is recorded on the request and in the clinical details. A dedicated consent register with withdrawal handling is planned.
Try the molecular and genomics pack
Create your laboratory, choose this pack, load the sample cases and see how it fits your work. Free, with no card.