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Chromosomal microarray: finding DNA that is missing or extra | CION Cancer Clinics
A chromosomal microarray scans the whole genome for pieces of DNA that are missing or present in extra copies. It sits between a karyotype and gene sequencing: it sees far smaller changes than a microscope can, but it does not read individual letters within a gene. This page explains when it is used in cancer genetics, how the test works, and what it cannot tell you. 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 a chromosomal microarray?
- When would a chromosomal microarray be recommended?
- How does a microarray actually find missing or extra DNA?
- The words this report uses, in plain language
- Microarray, karyotype, or gene sequencing: what does each find?
- What this page cannot tell you
- Four things people assume about chromosomal microarrays
- Common questions about chromosomal microarrays
The short answer
What is a chromosomal microarray?
A chromosomal microarray scans the whole genome for pieces of DNA that are missing or present in extra copies. It sits between a karyotype and a gene sequencing panel: it sees far smaller changes than a microscope ever could, but it does not read individual letters the way sequencing does. It is looking for gaps and extra copies, not spelling mistakes.
Why this scale of change matters
Some inherited conditions are not caused by one faulty letter in one gene. They are caused by a small piece of a chromosome being deleted or duplicated, sometimes so small it would never show up under a microscope but large enough to remove or double several genes at once.
Where it fits in cancer care
In cancer genetics, a microarray is used less often than a gene panel, but it is the right tool when a family pattern suggests a chromosome segment might be missing rather than a single gene fault. It is also widely used outside cancer, for developmental differences in children, which is where many families first meet the term.
A microarray finds gaps and extra copies. It does not read the DNA within a segment letter by letter.Where it is used
When would a chromosomal microarray be recommended?
It answers a particular kind of question that neither a karyotype nor a gene panel is built to answer alone.
A suspected missing or duplicated segment
When family history or an earlier result suggests a small stretch of a chromosome may be missing or doubled, a microarray scans the whole genome at once for exactly that kind of change.
Alongside developmental assessment
Microarrays are widely used when a child has unexplained developmental differences, since a chunk of missing or extra genetic material is a common and testable cause.
Often requested when
- A karyotype has come back normal but suspicion remains
- A named microdeletion or microduplication runs in the family
- Several related genes may be affected together
Following an inconclusive gene panel
If a gene panel looked normal but a larger structural cause is still suspected, a microarray checks for the kind of change that a letter-by-letter panel is not designed to see.
Why it is not a routine first test
Most inherited cancer risk comes from a single-letter change in one gene, which a microarray will not detect. It is chosen for a specific structural question, not offered as a general starting point.
Not sure whether this applies to you?
Ask an oncologistBehind the scenes
How does a microarray actually find missing or extra DNA?
Preparing your DNA
DNA from your blood sample is extracted, marked with a fluorescent tag, and applied to a small chip covered in thousands of tiny probes.
Comparing to a reference sample
A reference DNA sample, marked with a different colour tag, is applied at the same time so the two can be directly compared spot by spot.
Reading the signal at each spot
Where your DNA matches the reference amount, the colours balance evenly. Where a segment is missing or duplicated in you, the balance shifts, and the chip's scanner records exactly where.
Mapping the result
Software converts the pattern of shifted spots into a map showing which chromosome segments, if any, are missing or present in extra copies, for a geneticist to review.
On your report
The words this report uses, in plain language
- Copy number variant
- A segment of DNA present in more or fewer copies than expected. This is exactly what a microarray is built to find.
- Microdeletion
- A small missing piece of a chromosome, too small to see under a microscope but large enough to affect several genes.
- Microduplication
- A small extra copy of a piece of a chromosome.
- Probe
- A short, known piece of DNA fixed to the chip that your sample is compared against at each tested spot.
- Resolution
- How small a change the array can reliably detect. Higher resolution finds smaller changes.
- Variant of uncertain significance
- A copy number change whose effect is not yet clear, which needs specialist interpretation rather than assumption.
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Side by side
Microarray, karyotype, or gene sequencing: what does each find?
Chromosomal microarray
Karyotype and gene sequencing
Finds missing or extra DNA segments
A karyotype sees only large changes; sequencing reads single letters
Scans the whole genome at similar resolution throughout
A karyotype is limited by what a microscope can resolve
Cannot detect a balanced rearrangement, since nothing is missing
A karyotype can see a balanced rearrangement directly
Cannot read single-letter spelling changes within a gene
Sequencing is built specifically to read those letters
Being straight with you
What this page cannot tell you
It cannot tell you whether a microarray is the right test for your family. That depends on the specific pattern in your history, and whether a structural cause or a single-gene cause is more likely. A genetic counsellor makes that call, not a general description of the technology.
It cannot rule out a single-gene fault
A clean microarray result says nothing about the letters inside your genes. If your family history strongly suggests a single-gene inherited cancer syndrome, gene sequencing is still needed alongside or instead of a microarray.
Who this does not apply to
Most people being tested for inherited cancer risk will not be offered a microarray, because most inherited cancer risk comes from a single-letter gene change rather than a missing or duplicated segment. It is reserved for situations where a structural cause is specifically suspected.
If you are unsure whether your situation calls for a microarray, a gene panel, or both, ask your counsellor to explain the reasoning directly.Commonly believed
Four things people assume about chromosomal microarrays
"A microarray reads my genes letter by
letter."
It scans for whole segments that are missing or duplicated. Reading the letters within a gene is a separate test, called sequencing.
"If the microarray is clear, my genes are
fine."
A clear microarray only rules out missing or extra segments. A single-letter fault within an otherwise normal-sized gene would not be picked up by this test at all.
"A microarray is just a more detailed
karyotype."
It finds far smaller changes than a karyotype can, but it cannot see a balanced rearrangement, where nothing is actually missing. The two tests overlap in purpose but are not interchangeable.
"Every unusual finding on a microarray is
serious."
Some copy number changes are common, harmless variations between people. Others are genuinely significant. Telling the two apart needs specialist review, not a reading of the raw report.
Questions we are asked
Common questions about chromosomal microarrays
Is a chromosomal microarray the same as a gene
panel?
No. A gene panel reads the letters within chosen genes. A microarray looks for whole segments of DNA that are missing or present in extra copies, which is a different kind of change entirely.
Can a microarray diagnose an inherited cancer
syndrome?
Only if that syndrome is caused by a missing or duplicated segment. Most inherited cancer syndromes are caused by a single-letter gene change instead, which needs sequencing rather than a microarray to find.
What sample does a microarray need?
Usually a blood sample, in the same way most genetic tests are collected. There is nothing different about giving the sample; the difference is in what the laboratory looks for afterwards.
My child's microarray found a copy number variant.
What does that mean?
It means a segment of DNA is present in more or fewer copies than usual. Some of these are harmless variation and some are significant. A clinical geneticist reviews the specific segment involved to tell you which.
Does a microarray replace the need for a karyotype?
Not entirely. A microarray finds smaller missing or extra segments than a karyotype can, but it cannot see a balanced rearrangement, where nothing is actually lost. Some situations still need both.
Why would a microarray be suggested if my gene panel
was normal?
Because a normal panel only means no single-letter fault was found in the genes tested. If a structural cause, such as a missing segment, is still suspected, a microarray looks for that separately.
Is this test only used for children with developmental
differences?
That is its most common use, but it is also used in cancer genetics when a family pattern points to a possible missing or duplicated chromosome segment rather than a single gene fault.
Where do I start if a microarray has been mentioned for
my family?
Ask the doctor or counsellor who raised it what structural question it is meant to answer. Call the CION helpline if you would like the reasoning explained again in simpler terms.
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 is a chromosomal microarray analysis?
- National Cancer Institute — NCI Dictionary of Genetics Terms: Copy Number Variant
- GeneReviews (NCBI) — Genetic Testing: Overview
- ACMG — Technical Standards for Chromosomal Microarray Analysis
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
Karyotyping and chromosome analysisThe older, microscope-based way of seeing chromosomesLarge genomic rearrangements and why panels can miss themWhy a normal gene panel does not rule out a structural changeDeletion and duplication analysisA closer look at the specific changes a microarray findsWhich test would your situation need?Matching the right test to the right family question
Talk to us
Been offered a microarray and not sure it is the right test?
Describe your family history to us and we will help you understand whether a microarray, a gene panel, or both make sense. One helpline serves every CION centre.