Two types of whole-exome sequencing (WES) are proband and trio.

We’re going to be taking a look at what each consists of, as well as their differences.

Next, case studies which utilized either methodology, and what the results were.

Then, we go over who should take which test. Is proband or trio right for you?

Finally, we take a look at what the future holds for WES as a whole.


Proband WES

  • Individual who serves as the beginning of a genetic study of a family is called a proband[1]
  • Applicable for rare causative recessive variant detection[2]
  • Diagnosis within cited case would have been end result, even without trio-WES[2]
  • Less costly than trio-WES, but less coverage
  • This may be deemed a pitfall, depending on patient condition

Trio WES

  • Due to requiring a sample from proband and both parents, trio is designated as the methodology label[3]
  • Due to this, trio-WES inherently provides a wider scope of coverage
  • Highest diagnostic yield for family trios (proband, mother, father)[4]
  • Elected methodology by physicians if there is a strong inference of genetic etiology, and the parent samples are needed[5]
Diagnostic Rate
Diagnostic rates of singleton proband testing (proband-WES) compared to Trio (trio-WES) across various clinical indications, photo courtesy of Nature

Patients of Proband or Trio WES

Proband WES

In 2019, proband-WES was applied to a case study of 33 patients to detect deleterious variants associated with a rare type of hearing loss[6]

  • Autosomal recessive non-syndromic hearing loss (ARNSHL) is highly heterogeneous, accounting for 80% of NSHL cases
  • Determined to be a very cost-effective and precise way of identifying causative variants within this case study
  • Case study pertaining to a rare genetic hearing loss condition resulted in a diagnostic rate of 48.5%[6]
  • Although trio-WES diagnostic rates were unspecified, it is noted that proband-WES diagnostic rates were higher in this specific case study

In 2019, a case study of 108 patients suffering from rare neurodevelopmental diseases concluded with a diagnostic rate of 38%[4]

  • After four additional sequence variants were determined to be pathogenic, trio-WES was applied
  • Adjusted diagnostic rate of due to trio-WES being applied 41.8%
  • Proband-WES is praised as being a cost-effective tool in this case study, opposed to the more costly trio-WES

Trio WES

In 2020, trio-WES diagnosed a 4-month-old female infant with schizencephaly, a rare genetic disease which results in cortical malformation, coupled with global developmental delay[7]

  • Image shown above is of the case’s Sanger sequencing, and thereafter, sequence alignment of the EFNB1 protein
  • The detected heterozygous alteration, via trio-WES, is a direct result of phenotypic and genotypic wild type in both parents

In 2017, a then seven-year-old was initially referred for clinical evaluation 4 years prior[8]

  • He was ultimately diagnosed via trio-based WES with Shaaf-Yang syndrome
  • It is the first case of a MAGEL2 gene mutation inherited from a mosaic father
  • Tangentially related to circadian rhythm pathway genes, MAGEL2 is a mutation which has very common relations to both Prader-Willi syndrome and Shaaf-Yang syndrome[9]
  • Mosaic signifies two or more genetically different sets of cells present within a person or tissue
Swab
Lab technician employs a swab test, photo courtesy of Unsplash

Which WES test is right for me?

Below are some key points to consider when opening a dialogue with your physician about which test may be best suited for your situation.

Trio-based WES testing will always, objectively, have a wider scope of coverage.

The reason being is, it tests the proband (initial patient) as well as both parents, and often times a higher diagnostic rate results from the additional range.

Proband

  • Elected methodology by physicians if there is strong inference of genetic etiology where parent samples are not needed[1]
  • Also used when parents are deceased or absent
  • Less coverage than trio-WES for diagnosing genetic rare diseases

Trio

  • Highly applicable for detecting de novo variants[6]
  • Elected methodology by physicians if there is strong inference of genetic etiology where parent samples are needed[1]
  • Higher diagnostic rates than proband-WES
  • Wider scope is implied, given that it tests both parents
  • Applicable for rare causative heterozygous dominant variant detection[2]
  • Applicable when wanting to determine pathogenicity of variants[6]

The Future of WES

Standardized coupling of copy number variation sequencing (CNVseq) with trio-WES (Tri-CNVseq), specifically

  • When coupled with modern techniques like CNVseq, trio-WES diagnostic rates were significantly higher[10]
  • Tri-CNVseq diagnostic yield: 57.4% vs. trio-WES diagnostic yield: 44.4%[10]
  • Further former related studies of trio-WES diagnostic yield with no coupling: 42%[11], 38.7%[12]

Increased diagnostic rates, as technology advances, for undiagnosed rare genetic diseases utilizing proband or trio methodology

  • More affordability, especially for proband methodology
  • WES has been stated as having a large impact on health care at large for diagnosing rare genetic diseases (both proband and trio methodologies)[13]
  • Further applications such as exome capture transferability, nonhuman species, discovering health traits, and more[14]

Sources
  1. Baylor Genetics - Proband Whole Exome Sequencing
  2. Utility of trio-based exome sequencing
  3. Baylor Genetics - Trio Whole Exome Sequencing
  4. Proband-Only Clinical Exome Sequencing for Neurodevelopmental Disabilities
  5. Trio Exome Analysis
  6. Proband Whole-Exome Sequencing Identified Genes …
  7. Trio-Based Whole-Exome Sequencing Identifies a De novo EFNB1 Mutation
  8. Pitfalls of trio-based exome sequencing
  9. MAGEL2 mutation
  10. Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders
  11. Exome sequencing has higher diagnostic yield compared to simulated disease-specific panels …
  12. Whole-exome sequencing helps the diagnosis and treatment in children with neurodevelopmental delay
  13. Exome Sequencing in Today’s Lab
  14. Exome Sequencing: Current and Future Perspectives
  15. Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders
  16. Whole-exome sequencing in undiagnosed genetic diseases