Whole Exome Sequencing

Focus on coding regions of the genome

Whole exome sequencing (WES) provides coverage of more than 95% of the exons, (the expressed or the protein-coding regions of the genome), which harbor the majority of the large genetic variants and single nucleotide polymorphisms (SNPs) associated with human disease phenotypes.1 Of the ~3 X 109 bases that comprise the human genome, only about 1% is represented by coding sequences.1 By focusing on this most relevant portion of the genome, WES offers researchers the ability to use sequencing and analysis resources more efficiently. WES strategy starts by narrowing down the details of variants to be studied by filtering against databases such as HapMap, from the approximately 3.5 million SNPs identified in the human genome project. This focus enables a simpler way for discovery and validation of causative genes and common and rare variants. Exome sequencing has been proven useful in the identification of mutations involved in rare Mendelian diseases.2

 

Whole genome sequencing (WGS) vs whole exome sequencing

Both WGS and WES have their own advantages. Understanding the major differences between them could help in determining which method would work best for a particular research purpose.

  • WES covers only the expressed regions of the genome while WGS provides coverage for both exons (the expressed sequences) and introns (the intervening sequences)
  • WES uses enrichment strategies with probes against specific regions of interest while WGS uses a reference genome for alignment of all sequences of the genome
  • Due to the fact that the whole genome needs to be sequenced, WES is more cost efficient than WGS

 

Why whole exome sequencing?

  • Enables comprehensive coverage of exons to target medically relevant genomic regions, including known disease-associated sites and untranslated regions (UTRs)
  • Increases variant discovery potential, including rare and low-frequency mutations using next generation sequencing (NGS) technology
  • Eliminates the need to sequence the entire genome, offering a cost-effective alternative to WGS  

 

WES can be useful in multiple scenarios:

  • Where the causative gene is known for a particular disease (monogenic) and it needs to be investigated for finding the specific variants
  • In cases where the causative gene is unknown and it needs to be investigated
  • In cases where multiple genes are suspected to be involved in a particular disease (polygenic)

 

How does WES work?

During library preparation, genomic DNA is fragmented, and targeted regions are captured by hybridization using biotinylated oligonucleotide probes in solution. The captured target sequences are isolated using streptavidin beads, and after washing and elution steps, are used for subsequent amplification and sequencing.

Roche Sequencing Solutions offers an entire suite of products for NGS sample preparation, ranging from sample QC, target enrichment to library quantification that enable the preparation of high-quality DNA libraries, critical for obtaining high-quality whole exome sequencing data.

  1. Rabbani et al. The promise of whole-exome sequencing in medical genetics. 2014, J of human genetics, 59, 5-15.
  2. Yang et al. Clinical whole-exome sequencing for the diagnosis of Mendelian disorders. 2013. N Engl J Med. 369:1502-1511.