Medical Oncologist
CION Cancer Clinics
Sanger sequencing: the original DNA test, still used today | CION Cancer Clinics
Sanger sequencing was the first method used to read genetic information letter by letter, and clinics still use it today. It is no longer how most cancer genetic testing starts, but it remains the way a single gene fault already found by another test gets confirmed, and the way a known family fault is checked in a relative. This page explains what it does well, and where it has been overtaken. At CION Cancer Clinics in Hyderabad, our oncologists review your family history with you and guide you to the right genetic counselling and testing.
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Medically reviewed by Dr. Naresh GunduConsultant Medical Oncologist · MBBS, DNB (Internal Medicine), DM (Medical Oncology, AIIMS) · last reviewed September 2026, next review due September 2027
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On this page
- What is Sanger sequencing, in plain terms?
- When would a laboratory choose Sanger sequencing today?
- How does a Sanger read actually work?
- The words this report uses, in plain language
- Sanger sequencing or a bigger panel: what is the difference?
- What this page cannot tell you
- Four things people assume about Sanger sequencing
- Common questions about Sanger sequencing
The short answer
What is Sanger sequencing, in plain terms?
Sanger sequencing reads the exact order of letters in a short stretch of DNA, one letter at a time. It was the method that first sequenced human genes, and for a single change in a single gene it is still one of the most accurate tests there is. What has changed is its place in the pathway. It used to be the whole test. Now it is usually the last step.
Why it is still around
Newer methods read many genes together, and are excellent at finding a change. They are not always the best at proving one beyond doubt in a single tricky spot. Sanger sequencing does one job very well: it reads one small stretch of one gene and states plainly what is there. That is exactly what a laboratory needs before something goes on your report as a confirmed finding rather than a possible one.
Where it fits in your test
Most people having genetic testing today start with a panel that reads several genes together. If that panel flags something, the laboratory usually checks that one spot again with Sanger sequencing before your doctor ever sees the result. When a relative is later tested for that same known family fault, Sanger sequencing is often the only test used, because there is no need to search anywhere else in the gene.
Sanger sequencing does not replace a panel. It confirms, and it targets. It does not search broadly on its own anymore.Where it still does the job
When would a laboratory choose Sanger sequencing today?
It is not the first test most people have anymore, but it has not disappeared. These are the situations where it is still the right tool.
Confirming a bigger test's finding
When a multigene panel or a broader scan flags a possible fault, most laboratories will not report it until an independent Sanger read of that exact spot agrees. It is the checking step behind results you never see happen.
Testing one relative for one known fault
Once a family's exact fault is known, relatives do not need the whole gene searched again. A single, targeted Sanger read of that precise spot is faster to arrange and cheaper than repeating a full panel.
Usually looks like
- A parent, sibling or child of someone already diagnosed
- A named variant already sitting on a family report
- A quick yes-or-no answer, not a fresh search
A handful of awkward genes
A small number of genes have stretches that broader tests still read unevenly, often because the sequence nearby is repetitive or unusually rich in certain letters. Sanger sequencing checks those stretches directly, one letter at a time, and does not get confused by them.
Why the choice matters to you
None of this changes what sample you give. It changes how long the confirming step takes and how confident the laboratory is before your doctor calls you. Ask your counsellor which parts of your result were confirmed this way if you want to know.
Not sure whether this applies to you?
Ask an oncologistBehind the scenes
How does a Sanger read actually work?
Copying the target stretch
The laboratory copies just the small stretch of the gene it needs to read, over and over, until there is enough material to work with. Nothing outside that stretch is touched.
The reading reaction
A chemical reaction builds new copies of that stretch and marks each letter with a different colour as it is added, one position at a time, in order.
The read-out
A machine records the colours in order and turns them into a chart, called a chromatogram, that a trained analyst can read directly as a sequence of letters.
Comparing to the reference
That sequence is lined up against the normal version of the gene. Anywhere the two differ is the finding, and it is checked again before being written into a report.
On your report
The words this report uses, in plain language
- Targeted testing
- Looking at one specific, already-known spot in a gene, rather than searching the whole gene.
- Confirmatory testing
- A second, independent test used to check a finding before it is reported as certain.
- Chromatogram
- The coloured chart a Sanger machine produces. Each colour is one letter of the sequence.
- Reference sequence
- The standard, expected version of a gene that your result is compared against.
- Cascade testing
- Testing relatives, one by one, for a fault already found in someone in the family.
- Variant
- A spelling difference from the reference sequence. Most are harmless; some are not.
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Side by side
Sanger sequencing or a bigger panel: what is the difference?
Sanger sequencing
Multigene panel
Reads one small, chosen stretch of one gene
Reads many genes together in one run
Best for confirming or targeting a known spot
Best for searching broadly when the fault is unknown
Cannot tell you about genes it was not aimed at
Can surface findings in genes nobody suspected
Usually the last, confirming step
Usually the first, searching step
The right tool for testing a known family fault
The right tool for the first person tested in a family
Being straight with you
What this page cannot tell you
It cannot tell you which test your situation needs. That depends on whether anyone in your family has already been tested, and if so, what was found. A genetic counsellor works that out from your family tree, not from a page like this one.
It cannot read a chromatogram for you
If you have been handed a printed chart with coloured peaks, it is written for a laboratory scientist, not for you. Bring it to the counsellor or doctor who ordered the test rather than trying to interpret it yourself.
Who this does not apply to
If nobody in your family has a known gene fault yet, Sanger sequencing on its own is unlikely to be your starting test. Most people in that position begin with a broader panel, and only move to a targeted Sanger test once something specific has been found.
If you are unsure which stage you are at, call the helpline and describe what testing, if any, has already been done in your family.Commonly believed
Four things people assume about Sanger sequencing
"It is old technology, so it must be less
accurate."
For reading one small, chosen stretch of DNA, Sanger sequencing is extremely accurate, which is exactly why it is still used to confirm findings from newer, broader methods rather than the other way round.
"If my panel already used newer technology, why
would they use an older method too?"
The two methods do different jobs. The panel searches broadly; Sanger sequencing checks one spot with extra certainty before it is written on your report as confirmed.
"A relative needs the same full panel I had."
Once your exact fault is known, a relative usually needs only a targeted Sanger test of that one spot, not the whole panel repeated from scratch.
"Sanger sequencing can search a whole gene for
anything unusual."
It reads only the stretch it is aimed at. Searching an entire gene, or many genes, for an unknown fault is a job for a broader panel, not for Sanger sequencing alone.
Questions we are asked
Common questions about Sanger sequencing
Is Sanger sequencing still used, or has it been replaced?
It is still used, just for a narrower job. Broader panels have taken over the first, searching step, but laboratories still rely on Sanger sequencing to confirm a finding and to test relatives for one known fault.
Why did my laboratory report mention two different tests?
Most likely a panel found something first, and a Sanger read then confirmed that exact spot independently before it was written up. Seeing both named on your paperwork usually means the finding was checked twice, not that something went wrong.
Can Sanger sequencing find a fault a panel missed?
Only in the small number of awkward stretches that broader tests read unevenly. It is not a general safety net for the rest of the gene, because it only reads where it is specifically aimed.
My family already knows our fault. Do I need the full panel?
Usually not. A targeted Sanger test of that exact, already-known spot is normally enough, is quicker to arrange, and costs less than repeating a full search.
How is a sample collected for Sanger sequencing?
The same way as most genetic tests: a blood draw, or sometimes saliva. There is nothing different about giving the sample itself; the difference is entirely in how the laboratory reads it afterwards.
What does it mean if my report says a variant was
"confirmed by Sanger sequencing"?
It means the finding was checked a second time with an independent, highly accurate method before being reported to your doctor. It is a marker of care taken, not a separate diagnosis.
Can Sanger sequencing be used on a stored tissue sample?
Sometimes, if the sample is well preserved and the stretch of interest is intact. Whether an older stored sample can be used is a question for the laboratory doing the testing, not something to assume either way.
Where do I start if I am not sure which test I need?
Speak to a genetic counsellor before choosing anything. They will ask what testing, if any, has happened elsewhere in your family and recommend the right test for your exact situation, not a generic one.
Your Specialists
Meet CION's oncologists. Bring your family history or genetic report to them.
Our medical oncologists see people with a strong family history of cancer, arrange genetic counselling and testing where it fits, and plan the checks that follow.
Medical Oncologist
Dr. C. Raghavendra Reddy
MBBS(Gold Medal), DNB(General Medicine), DM(Medical Oncology)(Gold Medal)
Medical Oncologist
Dr. Bharati Devi Gorantla
MBBS, MD(General Medicine), DM(Medical Oncology)(Adyar,Chennai), ECMO, MRCP SCE(UK)
Medical Oncologist
Dr. Owais Mohammed
MBBS, MD (General Medicine), DrNB (Medical Oncology), ECMO, MRCP SCE (Medical Oncology) (UK)
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Sources
- MedlinePlus Genetics — What are the types of genetic tests?
- National Cancer Institute — Genetic Testing for Inherited Cancer Susceptibility Syndromes
- GeneReviews (NCBI) — Genetic Testing: Overview
- NHS — Genetic and genomic testing
This page is general information, not a prescription. Do not change or stop any treatment based on what you read here. If anything is worrying you, contact your own treating team — or call our helpline and we will help you reach the right specialist.
Keep reading
Related pages
Next-generation sequencing: how it actually worksThe broader test Sanger sequencing usually followsMultigene panel testing explainedThe searching step that comes before a confirming Sanger readWhich test would your situation need?A plain guide to matching the test to your family historyHow to read a germline genetic test reportWhat the rest of your report is telling you
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