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Home / Cancer Genomics / Whole Exome Sequencing (WES)

Whole Exome Sequencing (WES)

Whole exome sequencing analyses the protein-coding regions of approximately 20,000 genes. Although the exome makes up only about 1 to 2% of the genome, it contains the majority of known disease-causing variants.

WES is a powerful test for patients with suspected genetic disorders that are clinically complex or have not been diagnosed by earlier tests.

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Whole Exome Sequencing (WES)
Sample Peripheral blood 3 to 5 mL in EDTA from the patient, and each parent for trio testing
Turnaround 4 to 6 weeks from receipt of all samples
Method Exome capture and NGS, HPO-guided prioritisation
Clinical Area Rare and Inherited Disorders; Reproductive and Prenatal Genetics
Clinical Indications Method and Coverage Sample & Preparation Documents & Timing Limitations Results & Counselling Charges & Downloads
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Clinical Indications

  • Developmental delay or intellectual disability with a normal microarray
  • Multiple congenital anomalies
  • Suspected genetic syndrome without a clear single-gene diagnosis
  • Early-onset or complex epilepsy
  • Neuromuscular, metabolic or neurodegenerative disorders
  • Conditions with high genetic heterogeneity
  • Fetal anomalies with a normal karyotype and microarray

Method & Coverage

Method

DNA is extracted from blood, and the coding regions and adjacent intronic splice regions are captured and sequenced by next-generation sequencing. Variants are filtered and prioritised according to the patient's clinical features, using standardised Human Phenotype Ontology (HPO) terms, and inheritance pattern. Variants are classified according to the ACMG/AMP guidelines and reported using HGVS nomenclature.

Trio testing

Testing the affected individual together with both biological parents is called trio testing. It allows rapid identification of de novo variants, confirms the phase of variants in recessive conditions and reduces the number of variants of uncertain significance. Trio WES gives a higher diagnostic yield than testing the affected individual alone.

Diagnostic yield

Published studies report a diagnostic yield of approximately 25 to 40% for WES in children with suspected genetic disorders, depending on the clinical presentation and whether trio testing is performed.

Secondary findings

WES may identify pathogenic variants in genes unrelated to the reason for testing that are medically actionable, such as genes associated with hereditary cancer or cardiac conditions. These secondary findings are reported only when the patient has consented, in line with ACMG recommendations.

Sample & Preparation

  • Peripheral blood: 3 to 5 mL in an EDTA tube from the patient, and from each parent for trio testing.
  • Extracted DNA: at least 1 µg of high-quality DNA.
  • Detailed clinical information, family history and previous test results.
  • Signed consent, including the choice regarding secondary findings.
  • Transport: room temperature, reaching the laboratory within 72 hours.
See also general sample requirements and reasons samples may be rejected

Documents & Timing

Documents

  • Label every sample with at least two patient identifiers, matching the requisition form.
  • Include the completed requisition form, clinical information and signed consent.

Turnaround Time

4 to 6 weeks from receipt of all samples.

Limitations

  • Deep intronic and regulatory variants are not covered.
  • Copy number variants, repeat expansions (such as Fragile X syndrome) and structural rearrangements are not reliably detected.
  • Some regions of the exome have low coverage or high similarity to other regions and may not be analysed fully.
  • Mitochondrial DNA variants and low-level mosaicism may not be detected.
  • A negative result does not exclude a genetic diagnosis. Data can be reanalysed later as knowledge improves.

Results & Counselling

How results are reported

Each report is prepared by a qualified scientist, reviewed independently and signed out by an authorised specialist. Reports state the test performed, the regions analysed, the result and its interpretation, recommendations for follow-up and the limitations of the test.

Report: A signed report is sent to the referring doctor.

Genetic Counselling

A genetic counsellor can explain what this test can and cannot show before it is done, and what the result means once it is available.

Charges & Downloads

Prices depend on the test and clinical situation. Ask our team for current price information.

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