Next-generation sequencing (NGS) is now used across Indian oncology services, from choosing targeted therapy to clarifying resistance. The challenge is not ordering the test, but reading the report correctly and acting on it safely. This guide explains what to ask for upfront, how to assess report quality, and how to interpret findings without getting buried in technical detail.
Why NGS matters in routine oncology care
NGS evaluates multiple genes in one run, which can be valuable when tissue is scarce. Many Hospitals & Health Systems are standardising pathways so results reach tumour boards faster. This also aids documentation.
Common reasons to order include:
- Metastatic or relapsed solid tumours where targeted options or trials are being considered
- Suspected hereditary syndromes where genetic testing for cancer changes surveillance and family screening
- Treatment resistance, where a new biopsy or plasma test can reveal emerging drivers
Choosing the right test: tumour, germline, or paired
Start with the clinical question: “What therapy now?” versus “Who else is at risk?” Tumour testing looks for acquired (somatic) changes; germline testing looks for inherited variants and needs counselling safeguards. Tumour-only testing can hint at a germline finding, but it cannot confirm it.
Test type | Sample | Best use | What you should see in the report |
Somatic tumour panel | FFPE tumour or plasma | Therapy and trials | Tumour % or ctDNA comment, coverage, LoD |
Germline panel | Blood or saliva | cancer predisposition test | Classification method and referral note |
Paired tumour-normal | Tumour plus blood | Cleaner somatic calls | How suspected germline findings are handled |
For breast and ovarian cancer care, plan early when genetic testing for breast cancer can influence surgery, systemic therapy, and cascade testing.
Request form and sample basics that change accuracy
The quality of an NGS result begins before sequencing. A “good” sample with a “thin” form still creates uncertainty for the clinician reading the report.
Include, wherever possible:
- Diagnosis, stage, tumour site, and key pathology notes
- Current treatment question and prior lines of therapy
- Block ID, fixation details, and whether the specimen was decalcified
- Tumour percentage estimate, and whether macrodissection was done
If you are sending plasma, note recent surgery or systemic therapy, because low circulating tumour DNA can produce false negatives.
How to read the report: QC first, then findings
Start with technical performance. If the assay could not “see” well, the interpretation cannot be confident. Validation guidance stresses reporting assay limits and region-level coverage for clinically used panels.
Report term | What it means | Why it matters clinically |
Tumour purity or tumour % | How much tumour DNA is present | Low purity can mask true variants |
Depth of coverage | Reads per region | Higher depth supports low VAF detection |
VAF | Proportion of reads with the variant | Helps judge clonality and confidence |
LoD | Lowest VAF reliably detected | “Not detected” below LoD is not reassuring |
Failed or low-coverage regions | Parts not adequately sequenced | Key genes may need repeat or alternate testing |
Once QC is acceptable, review the summary, then check supporting details such as transcript, reference build, and caveats for borderline calls.
Actionability, evidence tiers, and uncertainty
A clinician-ready report should separate “what is known” from “what is possible”. Many laboratories use a tiered framework that links variants to levels of clinical evidence and actionability.
When interpreting, check for:
- Whether a drug suggestion is approved for that tumour type or supported only by trials
- Notes on resistance markers and whether they match treatment history
- Careful handling of uncertain variants, which should not drive therapy
If a report suggests an inherited finding from tumour profiling, it should recommend confirmation on a normal sample with counselling.
People and process: getting from report to decision
NGS is easiest to use when you treat it as a workflow, not a PDF. Reporting recommendations also stress readable clinical summaries backed by traceable technical detail.
Useful supports include:
- A molecular tumour board for complex or rare variants
- A clinical genomic scientist or molecular pathologist to clarify curation and assay limits
- Genetic counselling pathways for suspected germline findings
Common pitfalls and safeguards in Indian practice
These issues come up often and can be reduced with a few habits:
- “No actionable variants” without QC and coverage notes
- Under-calling due to low tumor content, necrosis, or decalcified samples
- Misreading tumor-only results as inherited, or missing the need for confirmation
- Treating a DNA test for cancer markers as a substitute for staging and histology
If a result looks borderline, ask whether orthogonal confirmation (for example, IHC or FISH) is recommended for that alteration class.
Closing thoughts
Read NGS reports in a set order: sample and QC, alteration classes covered, clinically relevant calls, then evidence level. Done consistently, this approach reduces delays, avoids over-interpretation, and supports clearer patient discussions in busy clinics.
FAQs
1) How quickly should I order NGS in a new metastatic solid tumour case?
If targeted decisions are likely, early testing can reduce delays. Coordinate with pathology so tissue is planned for both diagnosis and molecular workup.
2) Can I rely on a negative NGS report to rule out a target?
Not always. Check tumour purity, LoD, and whether key regions failed coverage. If a critical gene is under-covered, consider repeat testing or another method.
3) What does “variant of uncertain significance” mean for treatment?
It means the evidence is insufficient to link that change to the response. It is usually for future re-interpretation, not immediate therapy selection.
4) When should I send a patient for germline testing after tumour profiling?
Send when family history, age, tumour type, or a tumour finding suggests inherited risk, and confirm on a normal sample before family testing.
5) How should I use DNA markers for cancer like MSI or TMB?
Use them alongside tumour type, stage, and clinical status. Ensure the report states the method and thresholds used, because cut-offs can vary across assays.
