Illumina Whole Exome Sequencing

Due to the large size and cost of sequencing the entire human genome, a widely used alternative is the more affordable option of Whole Exome Sequencing. Exome sequencing primarily targets only the protein coding regions of the genome. Representing < 2% of the human genome, this approach focuses limited resources, sequencing reads, and bioinformatic compute time to the most well-characterized regions of the genome and the areas of greatest interest.

Exome sequencing is, by default, a panel-based sequencing test. Several exome capture kits are available, and each kit differs in many areas, such as enrichment strategies, target regions, and length of probes. As a result, kit selection impacts coverage uniformity and capture efficiency on a region-by-region basis and is imperative to obtaining informative results.

SeqCenter uses both the Twist Exome 2.0 and the Twist Mitochondrial panels to span a wide breadth of targets and provide deep coverage of all nuclear and mitochondrial genes linked to known clinically relevant phenotypes. The Twist 2.0 panel demonstrates superior completeness of coverage, capturing a total of 19,810 genes (36.5Kbp), and the additional Mitochondrial Panel covers all 37 mitochondrial genes (16.6 kbp). In addition, this panel combination includes some noncoding regions that are known to carry pathogenic or likely pathogenic variants. Additional details on the Twist Exome 2.0 and Mitochondrial panels, as well as an example of our WES methods, are available here.

Sample Requirements:

  • Total volume of 3 0µL or more
  • Eluted into water or dilute Tris/TE buffer
  • Sample concentration greater than:
    • 10 ng/µL measured by Qubit
    • 20 ng/µL measured by Nanodrop
  • Fragment length of at least 400bp

What You Will Receive:

  • Two fastq files (2 x 151bp) for each sample
  • Sequencing stats summary
  • Materials and methods summary
  • Data shared via Box folder within 2 weeks

Packages & Pricing

Sequencing Package
(Minimum Read Count Per Sample)
50x Exome Coverage
Minimum of 2Gbp exome data.
100x Exome Coverage
Minimum of 4Gbp of exome data.
200x Exome Coverage
Minimum of 10Gbp of exome data.
*Orders >48 Samples receive 5% discount

What is the difference between whole exome sequencing and whole genome sequencing?

Whole genome sequencing allows you to examine the complete genetic information within your sample. This sequencing effort requires an extremely high amount of sequencing data to generate the required coverage necessary to perform informative analyses. Whole Exome Sequencing (WES) primarily targets only the protein coding regions of the genome.

While WGS will always be considered the “gold standard,” WES can be an attractive alternative due to its focused range. The targeted WES approach provides extremely high coverage for a fraction of the cost of WGS at the same depth. By focusing on protein coding features, WES also inherently narrows the analysis to regions of the DNA that are better characterized and more likely to be causative in nature. This also reduces overall output sizes which are nontrivial for human data. As a high-impact, low-cost human sequencing approach, WES can be a cost-effective option for studies where very high depth of coverage is necessary, such as in rare variant detection in oncological studies.

An often-cited advantage is the reduced time required for WES. However, with the introduction of Illumina’s NovaSeq X Plus and PacBio’s Revio, in combination with SeqCenter’s guaranteed turnaround time of two weeks for both services, this “advantage” diminishes. With the release of these larger volume platforms, WGS, rather than WES, could be considered the more efficient form of sequencing from a long-term perspective, as well. After producing WGS data of the full genome once, the original sequencing data can be re-analyzed in the future as new targets are discovered.

Additional Resources

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