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MLPA testing: how laboratories find missing sections of a gene | CION Cancer Clinics
MLPA is a laboratory test that counts how many copies of each section of a gene you carry. It finds inherited faults where a whole section is missing or doubled, which ordinary sequencing can miss. It is usually run alongside sequencing, not instead of it. This page explains how it works, when it is used, and what it still cannot see. 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
The short answer
What is MLPA, and what does it look for?
MLPA is a laboratory test that counts how many copies of each section of a gene you have. It is used to find inherited faults where a whole section of a gene is missing or doubled. Ordinary sequencing reads the letters of a gene very well, but it can read straight past a section that is not there at all.
What the letters stand for
MLPA is short for multiplex ligation-dependent probe amplification. In plain terms, many small probes are sent into your DNA at once, each designed to find one section of a gene. The laboratory then measures how many of each probe found a match. Fewer matches than expected points to a missing section.
Why it is still used alongside modern panels
Many panels now try to count gene sections from their own sequencing data. That works well in most places, but some results are borderline and some genes are tricky to read. MLPA gives laboratories a second, independent way to check a suspected deletion before it goes on a report. It also remains the main test in some laboratories for certain genes.
MLPA is almost never the only test. It is usually paired with sequencing, and each covers what the other cannot.When it is ordered
In which situations is MLPA used?
You may never hear the word MLPA until it appears on a report. These are the usual reasons it was run.
Checking a known cancer gene thoroughly
For genes such as BRCA1, BRCA2 and the genes behind Lynch syndrome, a complete test reads the letters and also counts the sections. MLPA is one way of doing the counting part.
Confirming a finding from a panel
If a panel's software suggests a section may be missing, MLPA is often used to confirm it before it is reported. A deletion should never be reported on a borderline signal alone.
Testing relatives for a known deletion
Once a deletion is confirmed in one person, relatives can be tested for that same missing section. MLPA is a quick and practical way to do this.
Usually tested first
- Brothers and sisters
- Adult children
- Parents, where alive
Looking at gene switches
A special version can check whether a gene has been switched off by chemical tags rather than broken. This is explained on our methylation testing page.
Not sure whether this applies to you?
Ask an oncologistIn the laboratory
How does MLPA work, step by step?
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DNA is taken from your sample
A blood sample is the usual source, the same as for any inherited test. Stored DNA from an earlier test can sometimes be used.
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Probes are added, one pair per section
Each probe is made in two halves that only join together when both land side by side on the exact section they were designed for.
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Joined probes are copied many times
Only probes that found their target and joined up get copied. Each probe is a slightly different length, so they can be told apart later.
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The copies are sorted and measured
A machine sorts the copies by length and measures how much of each there is. Each section of the gene now has its own signal.
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Your signals are compared with normal samples
A signal at about half the normal level suggests one copy of that section is missing. A higher signal suggests an extra copy. A normal signal means both copies are there.
On your report
The words you will meet, in plain language
- Exon
- One section of a gene that carries instructions. MLPA results are given exon by exon.
- Deletion
- A section present in only one copy instead of two. The other copy, from your other parent, is usually normal.
- Duplication
- A section present in an extra copy. Duplications can also break a gene, depending on where they sit.
- Copy number
- How many copies of a section you carry. Normally two, one from each parent.
- Probe
- A short, man-made piece of DNA designed to stick to one exact section of a gene.
- Single-exon result
- A change in just one section. These are checked again, because a tiny spelling change under a probe can mimic a deletion.
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Side by side
MLPA and sequencing: what each one sees
MLPA
Sequencing
Counts copies of each gene section
Reads the letters of each gene section
Finds missing or extra sections
Finds spelling changes of one or a few letters
Looks at a small number of chosen genes
Can read many genes at once
Misses most spelling changes
Can miss missing sections without a counting check
Being straight with you
What MLPA and this page cannot tell you
MLPA only looks at the sections its probes were built for. It cannot see a section that was flipped the wrong way round, because nothing is missing and nothing is added. It does not map exactly where a deletion starts and stops, and it depends on good-quality DNA to give a clean signal.
It cannot read your report for you
If your report names a deletion or duplication, what that means for you and your relatives depends on the gene, the sections involved and how the laboratory classified it. What your specific variant means is a question for the counsellor who ordered the test.
Who this does not apply to
Most people will never need MLPA, because most people do not need inherited testing. It is not a test you choose on its own. If your family history does not suggest an inherited pattern, neither MLPA nor sequencing is likely to change anything for you. If your doctor is testing a tumour to choose a medicine, that is a separate question, covered on our targeted therapy pages.
Commonly believed
Four things people assume about MLPA
"MLPA is an old test, so modern panels have replaced it."
Panels now do much of the counting themselves. MLPA is still widely used to confirm what they find, and for genes where panel counting is unreliable.
"A normal MLPA result means I have no gene fault."
It means no missing or extra sections were found in the genes tested. Spelling changes need sequencing, and genes outside the test were not looked at.
"A deletion in one exon is less important than a big one."
A single missing section can switch a gene off just as completely. Once confirmed, its meaning depends on the gene and the section, which is for a counsellor to explain.
"MLPA needs a fresh tumour sample."
For inherited testing, MLPA is run on DNA from blood or saliva. Tumour samples answer a different question and are handled separately.
Questions we are asked
Common questions about MLPA testing
Do I need a separate sample for MLPA?
Usually not. MLPA can normally be run on DNA already taken from your blood sample for sequencing. If the laboratory has used up or discarded your earlier sample, a fresh blood sample is taken. Ask the laboratory whether it still holds your DNA.
Is MLPA done automatically with my panel?
Not always. Some laboratories run it on every panel for certain genes, some only to confirm a suspected finding, and some rely on panel software alone. The methods section of your report should say which approach was used.
What does a half signal on my report mean?
A signal at about half the normal level usually suggests one copy of that section is missing. Whether that is confirmed and what it means depends on the gene and the laboratory's checks. Your counsellor will explain what your own result shows.
Can MLPA give a false result?
It can. A tiny spelling change sitting right under a probe can make a section look missing when it is not. Poor quality DNA can also blur the signals. That is why single-section results are checked again before they are reported.
My old BRCA test did not include MLPA. Should I repeat it?
It may be worth asking, especially if your family history is strong and the old result was negative. Your counsellor will look at what the old test covered, what has happened in the family since, and whether a newer test would add anything.
Can relatives be tested with MLPA for my deletion?
Yes. Once your deletion is confirmed, relatives can be tested for that same missing section, often with MLPA. Testing is offered after counselling, and each adult decides for themselves whether and when to be tested.
Is MLPA expensive?
On its own it usually costs less than a full panel, but prices vary between laboratories and it is often bundled into a larger test. Ask what is included before paying, and whether Aarogyasri, Ayushman Bharat or your insurer covers any part of it.
Where do I start if my report mentions MLPA?
Take the full report to a genetic counsellor or your oncologist, along with a note of who in the family has had cancer. Call the CION helpline if you are not sure who to approach, and we will point you to the right clinic.
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 kinds of gene variants are possible?
- National Cancer Institute — NCI Dictionary of Genetics Terms: Copy Number Variant
- GeneReviews (NCBI) — BRCA1/2 Hereditary Breast and Ovarian Cancer
- GeneReviews (NCBI) — Lynch Syndrome
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
Deletion and duplication analysisThe wider family of tests MLPA belongs toLarge genomic rearrangements and why panels can miss themThe faults MLPA is built to findSanger sequencing and where it is still usedThe other older method laboratories still rely onMultigene panel testing explainedThe main test MLPA is usually paired with
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Does your report mention MLPA or a deletion?
Tell us what your report says and who in your family has had cancer, and we will help you find the right counsellor to explain it. One helpline serves every CION centre.