The CHOP PediSeq Project

The Pediatric Clinical Sequencing Project

Whole Exome Sequencing Results

Whole genome and whole exome sequencing will find many variants or mutations in your genome. There are two main categories of results. Click on the category of results to learn more.

1) Results related to the condition that prompted sequencing (“Primary Findings”)

2) Results unrelated to the condition that prompted sequencing (“Incidental Findings”)



Whole Exome Sequencing Results: Primary Findings


There are three main types of results related to the condition that prompted sequencing (“primary findings”): Negative, Positive and Variants of Uncertain Significance. They are shown and described below.


1. “Negative for a disease-associated mutation” means that no mutation was found in any gene known to be involved or suspected to be involved with the condition. This result does not exclude a possible genetic cause because not all genetic changes are found by current testing.

2. “Positive for a disease-associated mutation” means that a mutation was found in a gene that is known to be associated OR suspected to be associated with the condition.

  • Disease-Associated Mutation (Known Disease Gene): A disease-causing mutation was found in a gene known to be associated with the condition. Such a result may lead to changes in recommendations for medical management and treatment. Testing other family members as well as prenatal testing may be available to determine if other individuals are affected.
  • Suspected Disease-Associated Mutation (Uncertain Disease Gene): A mutation was identified in a gene that does NOT have a well known association with the condition. The gene may be suspected to be associated with the condition based on the gene’s function in the body or how it interacts with other genes. In such cases, it is not certain if the mutation found is the cause of the person’s condition. Additional information may become available in the future to clarify what this result means.

3. “Variant of uncertain significance” means that a variant was found in a gene associated or possibly associated with the condition, but is it not clear if the variant causes the condition. Testing parents and relatives might help determine whether the variant is the underlying cause of the patient’s condition. In the future, new information may allow the variant to be reclassified as a negative or positive result.



Whole Exome Sequencing Results: Incidental Findings

Incidental findings are genetic variants or results unrelated to the condition that prompted sequencing. Incidental findings could tell us about other symptoms or diseases that a person may have or might develop, how a person might respond to certain medications, or the potential risks of having a child with a specific genetic disease. One example of an incidental finding would be finding a variant related to diabetes in someone who had exome sequencing to identify the cause of her hearing loss. The variant related to diabetes is an incidental finding because it is unrelated to the patient’s evaluation for genes causing her hearing loss.

When a person undergoes exome or genome sequencing, they may or may not receive results of incidental findings. The test results that a person receives depend on various factors including the laboratory that performs the testing, the clinician who orders the testing, and the patient’s or family’s preferences. Some laboratories may not release certain types of incidental findings or may not analyze genetic variants that are thought to be unrelated to the condition that prompted sequencing.

We can divide incidental findings into different categories. These categories are based on several factors: 1) the impact the genetic variant will have on a person’s health and 2) whether a person could improve his or her health based on this finding. Some genetic variants or results may have a very serious impact on a person’s health, while others may have very little effect. Health problems caused by some variants may be treatable or preventable, while others may not. A disease or genetic variant that has options for maintaining or improving your health through changes in treatment or management of the condition is called medically actionable. Categories of incidental findings are outlined in the diagram below.









Below is a table that compares different types of incidental findings and their potential usefulness and frequency.


Visit our Benefits, Limitations, and Risks of WES page to learn more about whole exome sequencing and what exome sequencing results might mean for your family.




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