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What are whole exome sequencing and whole genome sequencing?
Reviewed by Medicinsk Expert•Last updated: 2026-10-22•Testing

What are whole exome sequencing and whole genome sequencing?

Whole exome and whole genome sequencing are advanced next-generation sequencing methods used to identify genetic variations by determining the order of DNA building blocks.

Overview of DNA Sequencing

Determining the order of DNA building blocks (nucleotides) in an individual's genetic code is known as DNA sequencing. This technique is used to test for genetic disorders. Modern healthcare and research increasingly rely on next-generation sequencing (or next-gen sequencing), which utilizes new technologies to rapidly sequence large amounts of DNA.

The original technology, Sanger sequencing, was a breakthrough that helped scientists determine the human genetic code. While it remains in use today for sequencing short pieces of DNA, it is time-consuming and expensive. Next-generation sequencing has significantly accelerated this process—reducing the time required to sequence a human genome from years to days or weeks—while simultaneously lowering costs.

Whole Exome Sequencing

Whole exome sequencing focuses on the exome, which consists of all the exons in a genome. Exons are the pieces of an individual's DNA that provide instructions for making proteins and are thought to make up approximately 1 percent of a person's genome.

  • This method allows for the identification of variations in the protein-coding region of any gene.
  • Because most known disease-causing mutations occur in exons, this is considered an efficient method for identifying potential genetic disorders.

Whole Genome Sequencing

While whole exome sequencing is effective, researchers have found that DNA variations outside of the exons can also affect gene activity and protein production, leading to genetic disorders. Whole genome sequencing addresses this by determining the order of all the nucleotides in an individual's DNA, allowing for the identification of variations in any part of the genome.

Limitations and Future Outlook

Although these methods identify significantly more genetic changes than select gene sequencing, the clinical significance of much of this information remains unknown. Not all genetic changes affect health, making it difficult to determine if an identified variant is involved in a specific condition. Furthermore, testing may reveal incidental or secondary findings, which are variants associated with a different, undiagnosed genetic disorder.

Beyond clinical use, these sequencing methods are vital for research. Continued study of exome and genome sequences helps determine whether new genetic variations are associated with health conditions, which will improve disease diagnosis in the future.

Frequently Asked Questions

Testing both biological parents and an affected child simultaneously—a process called trio sequencing—allows geneticists to filter through tens of thousands of harmless background variations. By comparing the child's genetic data to the parents', clinicians can quickly determine whether a suspicious mutation was inherited from an unaffected parent or arose spontaneously in the child as a new (de novo) mutation, substantially increasing diagnostic accuracy.
Whole exome sequencing focuses strictly on protein-coding regions (exons), which harbor roughly 85 percent of known disease-causing mutations and offer a cost-effective diagnostic route. Clinicians typically escalate to whole genome sequencing when exome sequencing is inconclusive, or when they suspect structural variants, non-coding regulatory mutations, deep intronic changes, or repeat expansion disorders that standard exome sequencing cannot reliably detect.
Incidental or secondary findings are unexpected genetic variants discovered during sequencing that are medically actionable but unrelated to the primary condition being evaluated. For example, testing performed for an unexplained neurological disorder might unexpectedly reveal a hereditary cancer mutation (such as BRCA1) or a cardiovascular risk gene (such as familial hypercholesterolemia). Patients generally have the right to opt in or opt out of receiving these secondary findings before testing begins.
Genomic databases and medical knowledge expand continuously, with new gene-disease links discovered every week. A variant of unknown significance or an unflagged gene change identified today might be proven to cause a specific disorder a year or two from now. Reanalyzing stored sequencing data every one to two years can provide a definitive diagnosis without requiring a new blood draw or the cost of repeating the entire test.
Source: MedlinePlus, National Library of Medicine

MedlinePlus brings together authoritative health information from the National Library of Medicine (NLM), the National Institutes of Health (NIH), and other government agencies and health-related organizations.

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