Whole exome sequencing

In 2018, whole exome sequencing (WES) was first scheduled for assessment in conjunction with genomic micro-array testing.
  • After initial research, the scope of the 2018 assessment was narrowed to include only genomic micro-array testing.
  • In 2019, WES was selected by the HCA director for it's own assessment which was completed in 2020.

Status: Decision completed

Policy context

Whole exome sequencing was selected as a topic for health technology assessment based on high concerns regarding safety and medium concerns for efficacy and cost.

Primary criteria ranking

  • Safety = High
  • Efficacy = Medium
  • Cost = Medium

Assessment timeline

  • Draft key questions published: March 19, 2019
  • Public comment period: May 15 to 28, 2019
  • Final key questions published: June 24, 2019
  • Draft report published: September 4, 2019
  • Public comment period: September 5 to October 4, 2019
  • Final report published: October 22, 2019
  • HTCC public meeting: November 22, 2019


Whole exome sequencing (WES) may be applicable to testing for a wide range of genetic disease. It is most commonly used when a disorder is suspected to be genetic but is not recognizable clinically or when the patient's symptoms are consistent with a wide range of genetic disorders. The National Institutes of Health recommend a family physician consider that a condition may be genetic when a patient has any of the following: dysmorphic features, multiple anomalies, unexplained neurocognitive impairment, or a family history suggestive of a genetic disease. Other signs of a potential genetic disorder include a much earlier onset of symptoms than is common,  a multifocal presentation (i.e., bilateral cataracts, many colon polyps, etc.; or an unusual combination of symptoms). Some conditions with pediatric onset may not be diagnosed in childhood, leading to adult patients who may present with a confusing mix of symptoms.

WES identifies the DNA base pair sequence of the protein coding regions of the genome, including proximal regulatory segments and the splicing junctions. WES is primarily used to identify small changes in base pair sequences that disrupt protein function and cause disease, but new bioinformatics software has increased the ability to identify chromosomal copy number variants (i.e., larger deletions or duplications involving larger stretches of DNA) from sequenced data. WES may be done for clinical or research purposes. Diagnostic WES testing is ordered by a physician or other health care professional and is conducted in a clinical diagnostic laboratory to aid in the diagnosis of a patient. The proband's parents or siblings may be sequenced to help interpret identified variants. Research WES testing is used to identify and characterize a common disease gene or genes among multiple families or patients with a similar phenotype.

WES uses next generation sequencing (NGS) technologies, which makes many copies of the target genome, cuts them into random sequences, and then simultaneously sequences the resulting fragments. WES requires multiple layers of bioinformatics analysis, often referred to as the analysis pipeline. This pipeline includes identifying variants in the sequenced genome against a reference genome, identifying the gene in which the variant occurs and its function, classifying variants as pathogenic (or not) in relationship to the patient's clinical phenotype, and reporting all variants identified that are associated with the clinical phenotype along with other American College of Medical Genetics and Genomics (ACMG)-defined medically actionable findings in genes not associated with the patient's clinical phenotype.