WES (Whole Exome Sequencing)
Definition
The exome is the protein-coding part of the genome; it covers roughly 1-2% of the whole genome, yet the great majority of known disease-causing variants are located here. WES reads this entire region.
Genetiks technical specifications:
| Test | Coverage | Depth of analysis |
|---|---|---|
| WES (Index) | Analyzes the exons and exon-intron junction regions of ~22,000 gene regions | 100X coverage |
| WES + CNV | In addition to WES, exon-level copy number variations (CNV) of the genes | 200X coverage |
| WES Trio | Includes analysis of the mother, father and the affected individual | , |
Purpose
It examines gene-level changes of unknown cause. It is used in cases where a diagnosis could not be made with conventional tests (karyotype, targeted panel).
Why trio analysis is valuable: Analyzing the mother, father and patient together shows whether a variant has arisen newly (de novo) or was inherited from a parent. This distinction is critical both for the diagnosis and for determining the recurrence risk in a subsequent pregnancy.
Results
The result may be positive / negative / VUS. The VUS rate in WES is markedly higher than in targeted tests, because thousands of genes are read at the same time.
Diagnostic yield, multidisciplinary consensus and meta-analysis data:
| Condition | WES diagnostic yield |
|---|---|
| Overall | 36% |
| Isolated neurodevelopmental disorder | 31% |
| Neurodevelopmental disorder + associated conditions | 53% |
| (Comparison: microarray) | 15–20% |
Our review shows that exome sequencing consistently outperforms microarray in the evaluation of unexplained neurodevelopmental disorders. The consensus recommends placing WES at the start of the diagnostic algorithm for unexplained neurodevelopmental disorders.
Risks and Limitations
1. Exome ≠ genome. Variants in the non-coding (intronic) regions of a gene and in regulatory regions are missed. 2. Repeat regions and some structural changes cannot be read reliably by NGS. 3. The VUS burden is high, see the VUS entry. 4. Secondary findings: Variants unrelated to the disease being investigated but of clinical significance may be revealed (e.g. a cancer predisposition gene). Whether these findings will be reported should be discussed with the patient before testing.