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CION Cancer Clinics
Whole exome sequencing: when a wider look makes sense | CION Cancer Clinics
Whole exome sequencing reads the working parts of almost every gene in one test. For inherited cancer risk it is rarely the first choice. It is usually considered when a focused panel found nothing but the family pattern is still striking, or when cancer comes with other unusual features. This page explains what an exome can find, what it can miss, and the decisions it asks of 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 whole exome sequencing, and is it used for cancer risk?
- When might a genetic counsellor suggest an exome?
- What happens when an exome is sequenced?
- What do the words on an exome report mean?
- How does an exome compare with a cancer gene panel?
- What this page cannot tell you
- Four things people believe about exome sequencing
- Common questions about whole exome sequencing
The short answer
What is whole exome sequencing, and is it used for cancer risk?
Whole exome sequencing reads the working parts of almost every gene you have, all in one test. For inherited cancer risk it is rarely the first test. It is usually kept for families where a focused panel found nothing but the pattern is still striking, or where cancer comes with other unusual features.
What the exome actually is
Most of your genetic code does not directly spell out instructions. The parts that do are called exons, and together they make up the exome. It is a small fraction of the whole code, but it is where most known disease-causing faults sit. That is why reading it is a sensible middle step between a panel and the full genome.
Why it is not the usual first test
Reading so many genes turns up many changes nobody can yet explain, and some findings unrelated to cancer at all. It also reads some cancer genes less thoroughly than a dedicated panel would. For most families, a panel chosen for their cancers gives a clearer answer, faster.
Exome testing of a tumour, used to guide treatment, is a different test. It looks for faults in the cancer, not in the family.When it is considered
When might a genetic counsellor suggest an exome?
An exome is usually a second or third step, chosen for a specific reason.
A panel found nothing, but the pattern is striking
Several young diagnoses, or rare cancers across relatives, with a negative panel. An exome can look at genes the panel did not include, including some only recently linked to cancer.
Cancer plus other unusual features
A child or young adult with cancer and, for example, developmental delay, unusual growth or birth differences. A syndrome affecting several body systems may involve genes no cancer panel covers.
A research study
Much of what is known about newer cancer genes came from exome studies. Some families are offered an exome as part of research, with clear rules about which results will be returned to them.
When it is not the right test
A family pattern that already fits a known syndrome, or a relative with a known fault. In both cases a narrower test answers the question more clearly.
Also not suited to
- Well people with no family history
- Anyone hoping for a general health check
Not sure whether this applies to you?
Ask an oncologistFrom sample to report
What happens when an exome is sequenced?
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Counselling comes first, and matters more here
You decide in advance whether you want to be told about findings unrelated to cancer, such as a fault linked to a heart condition. This choice is made before the test, not after.
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A sample, sometimes from both parents too
A blood sample is taken. Sometimes the parents give samples as well, which helps the laboratory tell a new change from one that runs in the family.
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The exome is read
A machine reads millions of short stretches of code and a computer pieces them together against a standard reference.
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The results are filtered
Specialists sift a very large number of differences down to the few that might explain the family's cancers. This step takes the most time.
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The data can be looked at again later
As more genes are linked to cancer, the stored data can sometimes be re-examined without another sample. Ask whether and how that will happen.
On your report
What do the words on an exome report mean?
- Exome
- The parts of all your genes that spell out instructions for the body, read together.
- Secondary finding
- A fault found in a gene unrelated to why you were tested, reported only if you agreed beforehand.
- Virtual panel
- Exome data looked at through a filter of chosen genes, so only those genes are reported.
- Coverage
- How thoroughly each part of a gene was read. Gaps in coverage mean a fault could be missed.
- Trio testing
- Testing a person and both parents together, to see which changes are new and which were inherited.
- Variant of uncertain significance
- A change nobody can yet call harmful or harmless. It should not change your care on its own.
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Side by side
How does an exome compare with a cancer gene panel?
Whole exome
Cancer gene panel
Reads almost every gene
Reads a chosen group of cancer genes
Some cancer genes read less thoroughly
Each chosen gene read in depth
Many more uncertain changes to explain
Fewer uncertain changes
May reveal findings unrelated to cancer
Stays within cancer genes
Usually costs more and takes longer
Usually quicker and less costly
Being straight with you
What this page cannot tell you
It cannot tell you whether an exome is right for your family. That depends on what has already been tested, what the family pattern looks like, and whether other features point beyond cancer. A genetic counsellor or clinical geneticist weighs those together with you.
It cannot interpret an exome result
What your specific variant means is a question for the counsellor who ordered the test. Exome reports are complex, and a single report can hold a clear finding, several uncertain ones and a secondary finding side by side. Please do not try to read one alone.
Who this does not apply to
Most people do not need an exome. If you have not yet had a focused panel, or a fault is already known in your family, a narrower test is the right next step. Studies on how often an exome helps after a negative cancer panel are still limited, so it is offered case by case.
If you have had a negative panel and still have questions, call the helpline and describe your family. Someone will tell you honestly whether further testing is worth discussing.Commonly believed
Four things people believe about exome sequencing
"An exome reads everything, so a negative rules everything out."
It reads most genes but not all of each one equally well, and it can miss faults where whole sections of a gene are missing. A negative exome is not a complete all-clear.
"More genes always means a better answer."
More genes also means more uncertain changes and more findings to explain. For most families, a panel matched to their cancers gives a cleaner answer.
"I will be told everything the test finds."
You are told what relates to why you were tested, and secondary findings only if you agreed to them. Changes of unknown meaning in unrelated genes are not usually reported.
"An exome is the same as whole genome sequencing."
The genome is almost all of your code. The exome is the small part that spells out instructions. They find different things and cost different amounts.
Questions we are asked
Common questions about whole exome sequencing
Is an exome better than a cancer gene panel?
Not for most families. A panel reads the relevant cancer genes in more depth and returns fewer uncertain results. An exome is useful mainly when a panel has already been negative and the family pattern is still striking, or when cancer comes with other unusual features.
What is a secondary finding?
A fault in a gene unrelated to why you were tested, such as one linked to a heart condition, which may still matter for your health. Laboratories report these only if you agreed before the test. Decide calmly, with your counsellor, whether you want to know.
Why would my parents need to give samples?
Comparing your exome with your parents' helps the laboratory see which changes are new in you and which you inherited. That can make an uncertain result easier to understand. It is not always needed, and your counsellor will say when it helps.
How long does an exome take?
Usually longer than a panel, because the filtering and review steps take specialist time. Ask the centre for the laboratory's usual turnaround before the sample is sent. Results should be given in an appointment, not by message.
Does an exome cost much more than a panel in India?
It usually costs more, though prices vary between laboratories. Ask for the cost of both options in writing. Check with the centre before assuming insurance, Aarogyasri or Ayushman Bharat will pay for any genetic test.
Can my exome be looked at again in future?
Often, yes. The stored data can sometimes be re-examined as new genes are linked to cancer, without a new sample. Ask whether the laboratory offers this, whether there is a charge, and who is responsible for asking.
My exome was negative. Does that mean nothing is inherited?
Not entirely. An exome can miss faults in parts of genes it read less thoroughly, and some missing gene sections. Some families have more cancer than expected with no single gene behind it, and screening is still planned on the family history.
Where do I start if I think I need one?
Bring any earlier genetic reports and a written list of every cancer in the family, with rough ages, on both sides. A genetic counsellor will tell you whether an exome makes sense. Call the CION helpline if you are unsure who to see.
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 whole exome sequencing and whole genome sequencing?
- National Human Genome Research Institute — Exome
- National Cancer Institute — Genetic Testing for Inherited Cancer Susceptibility Syndromes
- Cancer Research UK — Inherited cancer genes and increased cancer risk
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
Whole Genome Sequencing ExplainedThe next step wider, and how it differsExome vs Genome vs Panel: Which Does WhatAll three wide tests compared side by sideMultigene Panel Testing ExplainedThe test most families should have firstWhy a Bigger Panel Is Not Always BetterThe real cost of reading more genes
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