WES Clinical Applications

Researchers who once relied on WGS for reliable variant information are now turning to WES for its faster turnaround time and cost-effectiveness. Considerable evidence is emerging that applying WES in clinical research settings will lead to improved diagnosis and, in some cases, treatment of genetic disease. WES may improve patient health outcomes and facilitate the more efficient use of healthcare resources.

Mendelian Disorders

Exome sequencing has revolutionized Mendelian disorder research. The first report of selectively sequencing a whole exome was published in 2009 by Sarah Ng and her colleagues at the University of Washington.1 The research group reported the targeted capture and massively parallel sequencing of the exomes from 12 people, four of which were affected by a rare, dominantly-inherited disorder called Freeman Sheldon syndrome (FSS), which is caused by mutations in the MYH3 gene. FSS is characterized by multiple contractures at birth, head and face abnormalities, hand and foot defects, and skeletal malformations. Although the genetic defect behind the disease was already known, the research defined the MYH3 gene as disease-causing in FSS patients from more than 300 million bases of DNA noise, and demonstrated proof-of-concept for WES as a tool for studying Mendelian disorders using a small number of unrelated, affected individuals.1

Depending on the exome panel used, WES can provide coverage of more than 95% of exons and contain 85% of the known mutations resulting in Mendelian disorders and many of the disease-predisposing SNPs that occur throughout the genome.2 Variants detected cumulatively from WES studies are used widely in clinical services, leading to more accurate genotype-phenotype correlations and new insights into the role of rare genomic variation in disease. Online Mendelian Inheritance in Man®, an online catalog of human genes and genetic disorders (OMIM.org), has recorded a steady increase in both the number of phenotypes with an identified genetic etiology, and the number of genes associated with a clinical phenotype. This research, along with other worldwide efforts, has elucidated the molecular and genomic architecture of Mendelian conditions. The broader availability of exome sequencing has supported these discoveries.3

Diagnostics

The first diagnosis established by WES was published by Murim Choi and his colleagues from the Yale University School of Medicine in 2009.4 The team used WES to study a patient referred for Bartter syndrome, a rare inherited disorder characterized by a defect in the thick ascending limb of the loop of Henle. They showed that the patient carried a novel homozygous mutation in the SLC26A3 gene, which is associated with congenital chloride-losing diarrhea (CLD). In this case, WES established the correct diagnosis as CLD.

Since then, WES has become common in diagnosing rare diseases. For example, a study by a research team led by Alexander Hoischen at Radboud University Medical Center showed that exome sequencing could be used as a genetic test to diagnose primary immunodeficiencies. The researchers tested 254 patients with primary immunodeficiencies and showed that the techniques granted a diagnosis for 28% of patients. They concluded that exome sequencing harbored an advantage over gene panels as a truly generic test for all genetic diseases, including in silico extension of existing gene lists and re-analysis of existing data.5

Other diseases diagnosed using WES include a new ocular variant associated with Leber congenital amaurosis (PEX1 gene mutation),6 oculocutaneous albinism (SLC45A2 gene mutation),7 and neutropenia (G9PC3 gene mutation).7

Cancer Research

WES has potential to provide insight into cancer mechanisms because exome sequence variation may influence the predisposition for cancer development. Although smaller targeted panels are valuable for cancer research and diagnostics because of the depth of sequencing that they enable, WES is more suitable for discovering specific regions to further investigate.

WES is ideal for analyzing formalin-fixed paraffin-embedded (FFPE) samples, which are frequently used for storing tumor biopsies, where limited DNA yields are common.8

For example, a team led by Edward Generozov at the Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency used WES to sequence DNA extracted from FFPE tumor samples to better understand the mechanisms of prostate cancer pathogenesis, which could serve as a basis for developing new therapeutic approaches.9

Although exome sequencing cannot identify structural and noncoding variants across the entire genome as WGS can, it allows at least 20 times as many samples to be sequenced over the same time frame. In studies focused on identifying rare variants or somatic mutations with medical relevance, sample size and the interpretability of functional impact are critical to success.

References:

  1. S.B. Ng et al., “Targeted capture and massively parallel sequencing of 12 human exomes,” Nature, 461(7261):272-6, 2009. 
  2. B. Rabbani et al., “The promise of whole-exome sequencing in medical genetics,” J Hum Genet, 59:5–15, 2014. 
  3. Y.A. Barbitoff et al., "Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage," Sci Rep, 10:2057, 2020. 
  4. M. Choi et al., “Genetic diagnosis by whole exome capture and massively parallel DNA sequencing,” Proc Natl Acad Sci USA, 106(45):19096-101, 2009. 
  5. P. Arts et al., "Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies," Genome Med, 11:38, 2019. 
  6. J. Majewski et al., “A new ocular phenotype associated with an unexpected but known systemic disorder and mutation: novel use of genomic diagnostics and exome sequencing,” J Med Genet, 48:593–96, 2011. 
  7. B. Meder et al., “Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies,” Circ Cardiovasc Genet, 4:110–22, 2011. 
  8. S.J. McDonough et al., "Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods," PLoS ONE,14(4): e0211400, 2019. 
  9. A.S. Nikitina et al., "Data on somatic mutations obtained by whole exome sequencing of FFPE tissue samples from Russian patients with prostate cancer," Data Brief, 25:104022, 2019.