Clinical Area · Oncology

Tumor profiling connected to the treatment question

Oncology testing is most useful when the assay, specimen type, and report interpretation are matched to the clinical decision at hand. AC supports physicians from test selection through report review — not just sample forwarding.

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FFPE tumor profiling

DNA and DNA+RNA options for solid tumors from tissue biopsy. Covers mutations, fusions, CNVs, MSI, TMB, and HRD where applicable.

Liquid biopsy (cfDNA)

Cell-free DNA profiling from a blood draw. Useful when tissue is unavailable, repeat sampling is needed, or monitoring is required.

Hematologic panels

Molecular profiling for AML, ALL, MDS/MPN, lymphoma, and plasma-cell neoplasms through a curated NGS panel approach.

HRD testing

Homologous recombination deficiency assessment for PARP inhibitor candidacy in ovarian, breast, and other tumor types.

Clinical indications

When to consider molecular oncology testing

Pre-analytic factors — tumor content, FFPE quality, decalcification, RNA integrity, and tissue volume — should be evaluated before selecting an assay. AC can help review these before ordering.

Solid tumor — newly diagnosed, treatment selection, or disease progression

Liquid biopsy — when tissue is unavailable or repeat sampling is needed

Hematologic malignancy — AML, ALL, MDS/MPN, lymphoma, or multiple myeloma

Homologous recombination deficiency (HRD) — for PARP inhibitor eligibility

MSI/TMB — for immunotherapy candidacy assessment

Broad solid tumor profiling including hotspot mutations, full-exon coverage, CNV, RNA fusion analysis, MSI, and TMB.

Specimen: FFPE tissue

TAT: 17–21 days

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Understanding the report

What an oncology NGS report contains

Molecular oncology reports are structured around the clinical question. Understanding what each section means helps ensure findings are translated into appropriate clinical action.

Actionable variant detected

— Pathogenic or likely pathogenic variant with therapeutic or prognostic relevance

A variant in a gene with established clinical significance for the tumor type has been identified. This may indicate eligibility for a targeted therapy, clinical trial, or specific monitoring protocol. The treating oncologist should review findings in the context of current treatment guidelines and available therapies.

Variant of uncertain significance (VUS)

— Variant detected with unclear clinical impact

A variant has been identified but lacks sufficient evidence to classify it as pathogenic or benign in the current tumor context. Management decisions should not be driven by a VUS alone. Reclassification may occur as data accumulates and can be requested when additional evidence becomes available.

No actionable variant / negative

— No pathogenic variant detected in genes covered by the panel

No clinically actionable somatic variants were detected within the panel's scope. This does not mean the tumor lacks genetic drivers — variants outside the panel's gene coverage or below the assay's detection threshold are not excluded. Pre-analytic factors (low tumor content, FFPE quality, RNA integrity) may affect test sensitivity.

MSI / TMB / HRD status

— Biomarker status relevant to immunotherapy or PARP inhibitor eligibility

Microsatellite instability (MSI), tumor mutational burden (TMB), and homologous recombination deficiency (HRD) are reported where included in the panel. MSI-high and high TMB may indicate eligibility for immune checkpoint inhibitor therapy. HRD-positive status is relevant to PARP inhibitor candidacy. Thresholds and clinical implications vary by tumor type and guideline — review with the treating oncologist.

Oncology · clinical detail

Acceptance, limitations & reporting

General guidance to support ordering decisions. Specific thresholds, specimen requirements, and assay availability are confirmed per case with the reference laboratory before testing.

Sample acceptance criteria

Solid tumor: FFPE block or unstained slides with adequate, macrodissectable tumor content; specimens below 30% tumour cellularity may be canceled or yield indeterminate results.
Liquid biopsy: peripheral blood collected into 2 × 10 mL Streck BCT tubes, shipped within 7 days at room temperature.
Hematologic panels: fresh bone marrow or peripheral blood in the specified anticoagulant, kept within the required temperature range.
Specimen labeling must match the requisition; tumor type and relevant clinical history support interpretation.

Assay limitations

NGS panels detect variant classes within their design; some gene fusions, large structural variants, and low-frequency subclonal variants may not be reliably detected.
Sensitivity depends on tumor content, nucleic-acid quality, and sequencing coverage; degraded or low-input specimens reduce detection.
A negative result does not exclude variants outside panel coverage or below the assay's limit of detection.
Liquid biopsy detection depends on circulating tumor DNA shed, which varies by tumor type and burden; a negative cfDNA result may warrant tissue testing.
Somatic tumor testing does not establish germline status; suspected hereditary findings require dedicated germline testing and consent.

What's reportable

Pathogenic and likely pathogenic somatic variants relevant to the tumor type, with therapeutic, trial, or prognostic context where established.
Biomarker status (MSI, TMB, HRD) where included in the selected assay.
Variants of uncertain significance per the laboratory's reporting policy.
Quality and coverage metrics and any limitations affecting interpretation.

Therapy and trial associations depend on tumor type and current guidelines and are interpreted by the treating oncologist.

Oncology · common questions

Oncology testing — questions physicians ask

When should I order a liquid biopsy instead of tissue NGS?

Tissue NGS remains the first choice for initial profiling when adequate, representative tumour tissue is available. Liquid biopsy (cfDNA) is appropriate when tissue is unavailable or inaccessible, when repeat biopsy carries unacceptable risk, or when monitoring for acquired resistance on targeted therapy. In advanced disease the two can be complementary — tissue for the baseline profile, cfDNA to track resistance evolution.

How much tumour content is needed for solid-tumour NGS?

For FFPE solid-tumour profiling we generally require a macrodissectable specimen with adequate tumour cellularity; samples below roughly 30% tumour content may be cancelled or yield indeterminate results. Sensitivity also depends on nucleic-acid quality and sequencing coverage, so degraded or low-input specimens reduce detection.

How long does oncology molecular profiling take?

Typical turnaround is approximately 17 days for solid-tumour NGS and around 12 days for liquid biopsy from specimen receipt at the reference laboratory, and about 14 days for hematologic panels. Times vary with assay complexity, specimen quality, and whether reflex or add-on testing is required.

Does a negative NGS result rule out targetable mutations?

No. A negative result does not exclude variants outside the panel's gene coverage or below the assay's limit of detection. Pre-analytic factors such as low tumour content or FFPE quality can also affect sensitivity. Where clinical suspicion is high, consider tissue testing, an alternative assay, or repeat sampling.

Is somatic tumour testing the same as germline testing?

No. Somatic tumour testing characterises variants in the tumour and does not establish germline (inherited) status. A suspected hereditary finding requires dedicated germline testing with appropriate consent and, where indicated, genetic counselling.

Oncology testing

Start with the clinical question

Share the tumor type, available specimen, and clinical decision point. AC can help identify the appropriate assay and pathway before ordering.

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