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Deletion and duplication analysis: finding the faults sequencing can miss | CION Cancer Clinics
Deletion and duplication analysis looks for missing or extra chunks of a gene, which ordinary sequencing can miss. In some inherited cancer genes these larger changes make up a real share of harmful faults. This page explains what the analysis finds, how the laboratory does it, how to tell whether your report included it and when an older negative result deserves a second look. 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 deletion and duplication analysis?
- What kinds of change does it pick up?
- How does the laboratory actually count gene copies?
- The words you will meet, in plain language
- Sequencing alone, or sequencing plus copy counting?
- Four things people assume, and what is actually true
- What this page cannot tell you
- Common questions about deletion and duplication testing
The short answer
What is deletion and duplication analysis?
It is the part of a genetic test that looks for missing or extra chunks of a gene, rather than single spelling mistakes. Ordinary sequencing reads the letters of a gene one by one. It can miss a whole paragraph that has been deleted, or copied twice. This analysis counts how many copies of each part of the gene you have.
Why it matters
In some genes linked to inherited cancer, a noticeable share of harmful faults are these larger changes. They are well known in genes such as BRCA1, MSH2, EPCAM, PMS2 and VHL. If a test reads the letters but does not count the pieces, a real fault in one of these genes can be missed, and a negative result can be falsely reassuring.
Is it usually included?
Most modern hereditary cancer panels include it as standard, often done from the same sequencing data. Not every test does, and many older tests did not. Look on your report for words such as deletion and duplication, copy number or CNV analysis. If you cannot find them, ask the counsellor.
A negative report only means the laboratory did not find what it looked for. It is worth knowing what it looked for.What it can and cannot see
What kinds of change does it pick up?
Think of a gene as a chapter made of paragraphs, called exons. These are the changes this analysis is built to catch, and the ones it can miss.
A deleted piece
One or more exons are missing from one copy of the gene. This is the most common finding, and it usually breaks the gene's instruction in the same way a spelling mistake would.
A whole missing gene
The entire gene, and sometimes its neighbours, is missing from one copy. In VHL, for example, whole-gene deletions are a recognised cause of the condition.
A duplicated piece
One or more exons appear twice. Whether that breaks the gene depends on where the extra copy sits, so duplications are often harder to interpret than deletions.
What it can miss
- A piece flipped around in place
- A piece moved to another chromosome
- Changes in genes with a look-alike copy elsewhere
- Very small changes near the limit of detection
Not sure whether this applies to you?
Ask an oncologistIn the laboratory
How does the laboratory actually count gene copies?
The same sample
Your usual blood or saliva sample is used. Nothing extra is taken from you, and there is no separate appointment. For families in the districts, the sample can often be sent from a local collection centre.
Counting the reads
Sequencing machines read each part of the gene many times. If one exon shows about half the expected number of reads, one copy may be missing. If it shows more, it may be duplicated.
Checking a second way
Because counting can be fooled, a possible change is usually confirmed with another method, most often MLPA. This step is what makes the result reliable enough to act on.
The report
A confirmed change is classified like any other variant, from benign to pathogenic, and written up for the doctor who ordered the test. It names the gene, which exons are affected and whether pieces are missing or extra.
On your report
The words you will meet, in plain language
- Exon
- One of the pieces of a gene that carries the actual instruction. Reports name deleted or duplicated exons by number.
- Copy number
- How many copies of a piece of DNA you have. Normally it is two, one from each parent.
- Copy number variant, or CNV
- A difference in that number, meaning a deletion or a duplication. Like any variant, it can be harmless or harmful.
- MLPA
- A laboratory method designed to count exons in a gene. It is widely used to confirm deletions and duplications.
- Heterozygous deletion
- A piece missing from one of your two copies. This is the usual finding in inherited cancer genes.
- Pathogenic
- Known to cause disease. A pathogenic deletion is treated exactly like any other harmful fault in that gene.
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Side by side
Sequencing alone, or sequencing plus copy counting?
Sequencing alone
Sequencing with deletion and duplication analysis
Finds single-letter and small changes
Also finds missing or extra exons and whole genes
Can miss large changes completely
Covers the main types of harmful change
A negative may need a second look
A negative is far more complete
Relatives may be falsely reassured
Relatives can be tested for the exact change
Common in older tests
Standard in most current panels
Commonly believed
Four things people assume, and what is actually true
"My test was negative years ago, so there is no fault."
If that test did not include deletion and duplication analysis, a large change could have been missed. When the family history is strong, it is worth asking whether an older negative should be revisited.
"A duplication means double the risk."
Extra copies do not add risk the way numbers add up. A duplication matters only if it breaks the gene's instruction, and many are classified as uncertain until more is known.
"This needs a new sample or a biopsy."
It uses the same blood or saliva as the rest of the test. If your original laboratory still holds the sample, extra analysis can sometimes be added without drawing blood again.
"Any deletion in a cancer gene is dangerous."
Most harmful deletions do break the gene, but not every copy number change is harmful. Each one is classified on the evidence, exactly like a spelling change, and some are reported as uncertain.
Being straight with you
What this page cannot tell you
It cannot tell you whether your own test included this analysis, or what a deletion or duplication on your report means. Reports vary between laboratories, and the same finding can mean different things in different genes. What your specific variant means is a question for the counsellor who ordered the test.
It covers inherited testing only
This page is about testing your blood or saliva for changes you were born with. Tumour samples also show deletions, but those arose in the cancer itself and answer a treatment question, which our targeted therapy pages cover. A deletion found in a tumour does not tell you whether it is inherited.
Who this does not apply to
Most people do not need a genetic test at all, and so do not need to think about this. If your family has no pattern that suggests inherited cancer, the finer points of test method will not change anything for you. It matters most for families with a strong history and a negative or older result, where a missed large change is a real possibility.
Questions we are asked
Common questions about deletion and duplication testing
How do I know if my test included it?
Look in the methods section of your report, often in small print near the end. It may say deletion and duplication analysis, copy number analysis, CNV detection or MLPA. If none of these appear, ask the laboratory or your counsellor directly. They can usually answer within a day or two.
Should an older negative test be repeated?
Sometimes. If the old test did not count gene copies, and the family history strongly suggests an inherited cause, repeating or extending the test may be worthwhile. A counsellor weighs the family pattern, the genes involved and what the first test covered before recommending it.
Does it cost extra?
Many current panels include it in the listed price, because it is done from the same sequencing data. Separate confirmation by MLPA, or a stand-alone MLPA test for one gene, may be charged separately. Ask for a written quote that states what is covered before the sample is sent.
Will it delay my result?
Usually not when it is part of the panel. If a possible deletion needs confirming with a second method, the report can take a little longer. That wait is worth it, because an unconfirmed copy number change should not be acted on by you or your relatives.
Can my relatives be tested for my deletion?
Yes. Once a harmful deletion or duplication is confirmed, relatives can be tested for that exact change, usually by MLPA. This is a targeted test and is simpler than a full panel. The counsellor will explain who should be offered it first, and in what order.
Is a deletion worse than a spelling change?
Not usually. A pathogenic deletion and a pathogenic spelling change in the same gene are generally managed the same way, with the same screening and the same options. What matters is the gene and the classification. The type of change rarely alters the plan.
What is MLPA and when is it used alone?
MLPA is a laboratory method that counts the exons of a chosen gene. It is used alone when a family's deletion is already known, or when one gene is strongly suspected and sequencing was negative. For most first tests, a panel with built-in copy counting is used instead.
My report says a CNV of uncertain significance. What now?
Treat it like any variant of uncertain significance. It should not change your screening or lead to surgery on its own. Your care is planned on your family history. Ask how you will be told if the laboratory ever reclassifies it, since that can happen as evidence grows.
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 — Genetic Testing for Inherited Cancer Susceptibility Syndromes
- National Cancer Institute — Genetics of Breast and Gynecologic Cancers (PDQ)
- ACMG and ClinGen (Genetics in Medicine) — Technical standards for the interpretation and reporting of constitutional copy-number variants
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
Large genomic rearrangements and why panels can miss themThe bigger changes, and the tests that find themMLPA testing explainedThe method most labs use to confirm a deletionWhen an older negative test should be repeatedIf your test predates copy countingMultigene panel testing explainedWhat a modern panel reads, and what it reports
Talk to us
Not sure what your genetic report actually covered?
Bring your report, including the methods section. We will help you see whether deletion and duplication analysis was done and whether a counsellor should review it. One helpline serves every CION centre.