Whole Exome Sequencing (WES) analyzes the exome, which is the approximately one to two percent of the human genome containing protein-coding genes. This region holds the majority of known disease-causing variations. A WES report translates raw genetic data into clinically meaningful information through a systematic process of classification and context. The goal of this analysis is to identify specific genetic changes that may explain a person’s symptoms or indicate a predisposition to future health conditions. Receiving a report containing tens of thousands of variations can be overwhelming without a clear framework.
Decoding Variant Classification
A WES report identifies every change in the DNA sequence compared to a standard reference genome. These changes are called “variants,” a neutral term describing a difference, unlike a “mutation,” which specifically refers to a disease-causing change. Clinical laboratories use a standardized, five-tiered system developed by the American College of Medical Genetics and Genomics (ACMG) to assess the clinical significance of each variant. This classification estimates the likelihood of a variant causing a specific condition.
The highest certainty is assigned to Pathogenic variants (greater than 99% certainty) or Likely Pathogenic variants (90% to 99% likelihood). Scientists reach this determination by combining multiple lines of evidence. This evidence includes population data showing the variant is rare in healthy people, computational models predicting a harmful effect, and functional studies demonstrating a loss of gene activity. These clear classifications often lead directly to a diagnosis and a personalized medical management plan.
The opposite end of the spectrum includes Likely Benign and Benign variants, which are common population differences not associated with disease. Variants are classified as Benign if they are found frequently in large public databases of healthy individuals, such as gnomAD. These variants are usually filtered out and are not included in the final report, as they do not contribute to the medical diagnosis.
The most common classification is the Variant of Uncertain Significance (VUS). A VUS is assigned when there is insufficient scientific evidence to classify a genetic change as clearly harmful or harmless. This uncertainty is common because WES identifies many unique variants that have never been studied before. Although a VUS is reported, it is not used for clinical decision-making or diagnosis until more evidence supports its reclassification.
Primary, Secondary, and Incidental Findings
WES findings are categorized by their potential harm and the context of their discovery. Primary Findings are the results directly related to the medical reason the test was ordered, such as a suspected neurological disorder. The laboratory focuses on analyzing variants within genes known to be associated with the patient’s symptoms to reach a diagnosis.
The report may also include Secondary Findings, which are unrelated to the original medical indication but are intentionally searched for because they are medically actionable. These are typically Pathogenic or Likely Pathogenic variants in genes associated with hereditary cancers or heart conditions. The ACMG maintains a list of genes for which these findings are reported because preventative measures or early treatment options are available. Patients are usually given the option to opt-in or opt-out of receiving these specific Secondary Findings before testing.
Incidental Findings, in contrast, are discovered purely by chance and were not specifically sought out by the laboratory. These findings often do not meet the criteria for being immediately medically actionable, such as finding a carrier status for a mild condition. The key difference is whether the finding is on the list of genes the lab proactively analyzes for actionable results.
Interpreting Negative and Inconclusive Results
It is common for WES to result in either a negative or an inconclusive report. A Negative Result means that no Pathogenic or Likely Pathogenic variants were found that could explain the patient’s symptoms. However, a negative report does not entirely rule out a genetic cause for the condition.
One reason for a negative result is the technical limitation of WES, which only sequences the protein-coding regions (about 1% to 2% of the genome). The disease-causing change may reside in non-coding regions, such as deep intronic areas or regulatory elements, which WES does not cover. Also, WES is not designed to reliably detect certain types of large genomic changes, including large deletions, duplications, or repeat expansions, which require alternative testing methods.
An Inconclusive Result is often dominated by a large number of Variants of Uncertain Significance (VUS). Although the test may have identified a candidate change, current scientific literature lacks enough evidence to make a clinical judgment. Genetic science is continuously evolving, and a VUS may be reclassified in the future as new research emerges. Laboratories often offer re-analysis, where the raw data is re-interpreted after one to two years to see if any VUS has been upgraded to a Pathogenic classification.
Next Steps: Counseling and Family Planning
The final interpretation of a WES report must be done with the guidance of a healthcare professional, most often a certified genetic counselor. The genetic counselor acts as a translator, helping the patient understand the technical details, the certainty of the findings, and the implications for their personal health. They integrate the genetic findings with the patient’s clinical history and provide personalized risk communication.
For a Pathogenic finding, the results translate into a specific Clinical Management plan. This plan may involve recommending increased medical surveillance, such as more frequent screening tests, or initiating preventative measures or specific treatment pathways. The counselor helps the patient navigate these decisions and provides educational resources to ensure the information is clearly understood.
The results of a WES test also have implications for the biological family members of the person tested. Genetic counselors facilitate Family Cascade Testing, which involves offering testing to parents, siblings, and children of the person who received the pathogenic finding. Confirmatory testing for a specific variant is important for family members to determine if they are at risk or are carriers. This process allows at-risk relatives to receive the benefits of early medical intervention or make informed decisions about reproductive planning.