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Whole exome sequencing


Whole exome sequencing (WES) is a targeted next-generation sequencing method that identifies all protein-coding genes (exons) in the genome. These regions contain most large genetic variants and single nucleotide polymorphisms (SNPs) associated with human disease. By enriching for exons, you can focus on genomic regions relevant to your specific area of research.

What is whole exome sequencing?

Whole exome sequencing (WES) is the approach used to sequence only the protein-coding regions of the human genome. Because protein-coding exons only comprise about 1% of the genome, targeting exons—while conversely excluding other regions―can lower both the cost and time of sequencing. Surprisingly, and in contrast to their small size contribution to the genome, exons contain 85% of disease-associated variants, making this level of sequencing compelling for disease research studies.

Primarily, WES is performed using hybridization capture, a technique that uses 5′ biotin-modified oligonucleotide probes to “capture” the regions of interest for sequencing.

Probes can also be positioned to overcome challenging motifs, such as repetitive sequences. Using probes in this manner maximizes the number of protein-coding regions that can be effectively captured.

Whole exome sequencing workflow

WES is a type of targeted next-generation sequencing (NGS). As with all NGS protocols, sequencing libraries must be prepared with genetic material from the sample of interest. Then, target enrichment captures the exomes of interest before sequencing.

Whole genome sequencing (WGS) vs. Whole exome sequencing (WES)

Whole genome sequencing (WGS) is used to determine the order of every single nucleotide in an individual’s genome. This is a powerful way to uncover genomic variation, including disease-associated mutations. However, sequencing entire genomes remains expensive.

Of the roughly 3 billion base pairs in the human genome, just 1–2% are translated into functional proteins. The areas of the genome that encode functional proteins are called exons. Sequencing only exons (whole exome sequencing; WES) is cheaper and faster than sequencing the entire genome.

Whether you choose to perform WGS or WES will depend on a number of factors. Key differences between the two workflows include:

  • Search depth. Whole genome sequencing captures variation in any area of the genome, including non-coding regions. If there is a chance the disease you are studying is associated with such variation, WGS is the better option or alternatively, a customized exome panel can be utilized.
  • Sequencing depth. Since such a smaller percentage of the genome is sequenced through WES, a deeper sequencing coverage of regions of interest (ROIs) can be achieved. This is important for researchers requiring comprehensive coverage of single-nucleotide variants (SNVs) and indels―common in population genetics, with genetic diseases, and cancer genetics research.
  • Reagents. WGS requires more sequencing reagents than WES, but WES requires additional preparation reagents (probes) and extra protocol steps (hybridization).
  • Cost. WES is cheaper and faster than WGS.
  • Data analysis. WGS produces large datasets that are more complex to analyze in comparison to WES datasets. Such datasets often need sophisticated bioinformatics expertise.


Applications of whole exome sequencing

WES is a practical method for mapping rare variants to elucidate complex disorders [1]. It is also a feasible option for population genetics and discovery science, or data mining, when searching for associations or linking genes to phenotypes [2]. WES is particularly useful in oncology research.

Benefits of whole exome sequencing

Using NGS technology gives researchers more comprehensive data and more discovery power than can be achieved through PCR. Since WES is targeted sequencing, it results in a more manageable data output (~5 Gb) for genotyping applications than whole genome sequencing (~90 Gb). WES provides a lower cost with faster analysis time than WGS.


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xGen Exome Research Panel v2 white paper

Learn how our large-scale production platform, using PCR-free synthesis, provides a unique advantage over array-based platforms by delivering consistent exome panel performance over time.

The IDT advantage

The xGen™ Exome Hyb Panel v2 consists of 5′ biotin–modified oligonucleotide probes that are individually synthesized and individually analyzed by electrospray ionization mass spectrometry (ESI-MS) and optical density (OD) measurement. Individual probes are made in large lots, then aliquoted. The probes are also normalized before pooling to ensure that each probe is represented in the panel at the correct concentration. Probes that fail quality control are resynthesized.

This rigorous manufacturing process gives the xGen Exome Hyb Panel v2 a unique advantage over array-derived pools where missing or truncated probes cannot be identified before sequencing. With our proprietary synthesis methods, even probes with high GC and AT content are appropriately represented in the panel.

Get started with whole exome sequencing

Are you working in an area that would benefit from whole exome sequencing? See how we can help you easily improve your workflows and results.



  1. Williams HJ, Hurst JR, et al. (2016) The use of whole-exome sequencing to disentangle complex phenotypes Eur J Hum Genet 24(2):298–301.
  2. Bamshad MJ, Ng SB, et al. (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12(11):745–755.