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Whole exome sequencing


Whole exome sequencing (WES) is a targeted next generation sequencing method that identifies all the protein-coding genes (exons) in the genome. Regions of interest are hybridized to target-specific, biotinylated oligos and separated from rest of the DNA. By enriching for exons, you can focus on genomic regions relevant to your study.

What is whole exome sequencing?

Exome sequencing is invaluable for sequencing only the protein-coding regions of the human genome. It is primarily performed using hybridization capture, a technique that uses 5′ biotin-modified oligonucleotide probes to “capture” the region of interest for sequencing. Probes can be arranged in different ways to sequence regions of interest. For example:

  • Tiling probes allows regions that are sequenced to align end to end.
  • Overlapping probes permits extra sequencing to occur at the ends of probes to ensure that no part of the sequence is missed.

Probes can also be positioned to overcome challenging motifs such as repetitive sequences. This ensures that all protein-coding regions captured can be accurately identified.

Focusing on protein-coding exons (and excluding other regions of the genome) can lower the cost and time of sequencing, as exons make up approximately 1% of the genome. In contrast to their small size contribution to the genome, exons contain 85% of the variants that are associated with disease, so this level of sequencing is preferred for diagnostic applications [1].

    Applications of whole exome sequencing

    Whole exome sequencing is a practical method for mapping variants that are rare in the population to elucidate complex disorders [2]. It is also a feasible option for population genetics and discovery science, or data mining, when searching for associations or linking genes to phenotypes [3]. Whole exome sequencing is particularly useful in oncology research and is currently used for cancer diagnostics [4]. Information gained from WES can provide insight into prognoses and personalized treatment options [5].

    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 is provided at a lower cost with a faster analysis time than WGS. Whole exome sequencing using NGS also has a faster turnaround time than other types of sequencing like Sanger, or shotgun, sequencing.

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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.

    Whole exome sequencing workflow

    Exome sequencing is a type of targeted next generation sequencing. After genomic material is extracted from the sample, libraries must be prepared. Library prep includes the addition of adapters to identify the samples or molecules in the sample and to help the DNA or RNA adhere to the sequencing apparatus. Exome sequencing specifically enriches or captures the exome before the sequencing step.


    • Illumina
    • Pacific Biosciences
    • Oxford Nanopore Technologies

    The IDT advantage

    The xGen Exome Research Panel 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 and then aliquoted to maintain reproducibility. The probes are then 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 Research Panel a unique advantage over array-derived pools, in which missing or truncated probes cannot be identified before sequencing. Using IDT proprietary synthesis methods, even probes with high GC and AT content are appropriately represented in the panel.

    To provide increased depth of coverage and enable high multiplexing of samples, the xGen Exome Research Panel targets only the coding sequences (CDS) of human coding genes in the RefSeq database.

    Get started with whole exome sequencing

    Working in an area that would benefit from exome sequencing? Just starting? See how you can easily improve your workflows and results.

    xGen Exome Research Panel v2

    The xGen Exome Research Panel v2 consists of 415,115 individually synthesized and quality controlled xGen Lockdown Probes. The Exome Research Panel spans a 34 Mb target region (19,433 genes) of the human genome and covers 39 Mb of end-to-end tiled probe space.

    Learn more

    Lotus DNA Library Prep Kit

    The Lotus DNA Library Prep Kit enables streamlined preparation of high-quality next generation sequencing (NGS) libraries from double-stranded DNA (dsDNA)—generate libraries suitable for PCR-free, PCR-amplified, and targeted sequencing applications on Illumina platforms.

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    xGen Stubby Adapter and Unique Dual Index Primer Pairs

    Ensure maximum accuracy in your NGS reads with xGen Stubby Adapter and Unique Dual Indexing (UDI) Primer Pairs. A convenient indexing option for a variety of applications from whole-genome to targeted sequencing, the kit provides adapters and unique i5 and i7 primer pairs that can be used with TruSeq™-compatible library prep for sequencing on Illumina instruments.

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    NGS Discovery Pools

    NGS Discovery Pools allow you to build custom panels quickly at a fraction of the cost of conventional custom panels.

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    Explore exome sequencing uses


    1. Choi M, Scholl UI, et al. (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 106(45):19096–19101.
    2. 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.
    3. Bamshad MJ, Ng SB, et al. (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12(11):745–755.
    4. Kamps R, Brandao RD, et al. (2017) Next-generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int J Mol Sci 18(2):308.
    5. Rabbani B, Nakaoka H, et al. (2016) Next generation sequencing: implications in personalized medicine and pharmacogenomics. Mol Biosyst 12(6):1818–1830.