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Whole exome sequencing for cancer research


Genetic mutations are more likely to impact health outcomes when they occur in protein-coding genes. Cancer is a disease that can progress quickly, so understanding what mutations effect protein-coding genes can establish effective treatment and improve prognosis. Exons that make up the protein-coding genes comprise 1% of the human genome, so focusing sequencing on this portion of the genome is more cost-effective than whole genome sequencing and will provide more comprehensive data than other sequencing methods.

What is whole exome sequencing?

Identifying the DNA sequence of all the protein-coding genes in a genome is called whole exome sequencing (WES). This is a targeted next generation sequencing method using hybridization capture. This next generation sequencing approach uses parallel sequencing, providing a faster turnaround time than Sanger sequencing or shotgun sequencing. Exome sequencing panels can be expanded to include noncoding genes and other genetic elements that are relevant to cancer.

What can whole exome sequencing do?

WES reveals mutations in disease-associated genes. Therefore, it could:

  • Inform patient risk of developing specific types of cancer
  • Provide a clearer picture of genetic abnormalities that effect tumor progression, like microsatellite instability, to aid prognosis
  • Help clinicians use precision medicine to decide how to treat a patient’s cancer

Benefits of whole exome sequencing for cancer research

Using NGS technology gives researchers more comprehensive data and more discovery power than can be achieved through PCR. In cancer research, comprehensive data is used for tumor profiling. Deeper sequencing enables more sensitive somatic mutation detection. WES also provides the opportunity for greater discovery power for revealing heritable mutations compared to PCR. WES is provided at a lower cost with a faster analysis time than WGS. WES using NGS also has a faster turnaround time than other types of sequencing like Sanger or shotgun sequencing.

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Next generation sequencing in the clinic

Munich Leukemia Laboratory in Munich, Germany, leads leukemia diagnostics and research in Europe. Read about how their team improved customer turnaround time and report quality using IDT customized xGen Lockdown Panels.

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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

IDT offers library preparation, adapters, and enrichment panels for cancer exome sequencing. Streamlined library prep workflows and flexible kit configurations accommodate multiple study designs. The enrichment panels are comprised of individually synthesized and quality controlled xGen Lockdown Probes, so custom content can be added to the exome panel to fit specific research needs, such as detecting important events like gene fusions. Discovery research and prototyping can be performed using NGS Discovery Pools, which are fast and cost-effective. Once you finalize your design, you can use xGen Lockdown Probe Pools to create a custom panel for long-term studies using a single manufacturing lot for superior consistency. These kits are compatible with Illumina sequencing systems.

Building an NGS-based platform for clinical cancer care

Foundation Medicine, Inc uses IDT's xGen Lockdown Probes to develop robust NGS-based assays for hundreds of cancer-related genes. These targeted panels deliver highly sensitive and specific detection of all classes of genomic alterations in routine clinical FFPE samples.

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.

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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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