EXOME ENRICHMENT

WHOLE-EXOME SEQUENCING

Overview – Introduction to exome sequencing

Exome sequencing is used to efficiently detect common single-nucleotide variants (SNVs) across a broad spectrum of applications. These applications include population, translational and cancer studies, as well as for identification of rare genetic variants that are presumably responsible for complex genetic diseases, such as Mendelian disorders.

Exome sequencing has swiftly gained acceptance and its use is currently expanding at a faster rate than that of any other targeted sequencing method. Sequencing the protein-coding part of the genome enables researchers to focus only on the genes where many disease-related variants have been localised. The method produces less data than whole-genome approaches do, making data management more feasible, while maximising the benefit in terms of the ratio of the amount of information versus resources, turnaround time and cost.

Our many years of experience and active involvement in a large number of acknowledged, publicly funded research projects have given GATC Biotech vast experience in exome sequencing. We have developed proprietary and fully automated GATC production standards for target enrichment libraries, optimising balanced target coverage. All of GATC Biotech’s next-generation sequencing services, including exome sequencing, are ISO 17025 accredited to make accurate sequencing data available for use in molecular diagnostics. 

Applications – Advantages of exome sequencing

Exome sequencing is ideal if you want to:

  • Target variants and mutations in protein-coding regions
  • Obtain in-depth coverage of exons
  • Focus on the genes most likely to be involved in phenotype-affecting mutations
  • Investigate rare variants  and determine the variations of all coding regions without bias 
  • Enhance interpretability and diagnostic value of sequencing results
  • Analyse numerous samples with fast turnaround times 
  • Reduce resources in data processing, management and analysis

Exome sequencing in oncology

Every tumour contains a mixture of germline or inherited mutations, as well as somatic alterations, which are tumour-specific genomic aberrations. Whereas some germline mutations can be used for evaluating the risk of cancer development in predisposed individuals, it is the somatic variants that are typically considered potential therapeutic targets.

Whole exome sequencing of DNA from tumour-only samples typically identifies both somatic and germline mutations. Germline mutations are clinically irrelevant due to their presence in both normal and cancer tissue. Importantly, germline mutations that are misidentified as somatic mutations could lead healthcare providers to select inappropriate treatment strategies that bring no health benefit to the patient and that uselessly increase healthcare costs. Alternatively, false characterisation of somatic mutations as germline mutations could lead physicians to disregard viable treatment options.

GATC Biotech attempts to avoid the consequences of misinterpreted genetic information by offering sequencing of DNA isolated from both tumour, as well as normal tissue of the same patient. Matched tumour-normal sequencing analysis enables accurate identification and subtraction of germline mutations from somatic aberrations. Filtering out non-cancer-related variants allows for precise identification and interpretation of genetic alterations, giving physicians more certainty as they determine the most appropriate treatment course for each patient’s cancer.

Workflow – Exome sequencing methods & technologies

Applying a streamlined library-preparation workflow that uses an optimised protocol in combination with the latest enrichment technologies produces a cost-efficient, reliable library structure and improves coverage of hard-to-capture regions during target enrichment. GATC Biotech uses post-capture indexing enrichment for sequencing based on Illumina technology. Multiplex options make it possible to process numerous samples in parallel—scalable in multiples of 30x depending on the sequencing coverage required. GATC Biotech’s exome sequencing is produced according to diagnostic standards (ISO 17025). 

In addition, GATC Biotech offers a complete, one-stop, exome-sequencing solution that maximises flexibility and convenience to our customers, offering everything from library preparation to data analysis and a comprehensive data report. Widespread pre-sequencing services complement our product portfolio. 

Description of capture process - Target enrichment
Fig. 1. Target capture workflow

Scientific expertise: exome sequencing

GATC Biotech cooperates with some of the most recognised institutions for cancer research and cancer diagnostics, including the German Cancer Research Center (DKFZ) and the NCT in Heidelberg. Since 2006, we have joined many collaborative exome-sequencing research projects in which we have sequenced a notable number of human exomes and were able to gain considerable experience in capturing, enriching, sequencing and analysing human exons. 

An extract of our involvement in publicly funded, collaborative research projects can be found here.

Publications

Find here, a list of selected research articles supported by GATC Biotech’s sequencing products, as well as the latest publications on exome sequencing.

 

Products related to exome sequencing

Eager to start your own whole exome sequencing project?  Then use our popular INVIEW EXOME solutions for exome profiling. From sample processing to sequencing to BioIT analysis, the complete service offers excellent coverage of the protein coding regions of the human genome. Easily and flexibly combine the latest Agilent SureSelect technologies for target enrichment with our expertise in DNA sequencing and with established QIAGEN Ingenuity Variant Analysis software for in-depth data analysis. Receive a final comprehensive data report as fast as two weeks following sample receipt and give your research an immediate boost.

Are you interested only in a few specific exons? Try our INVIEW AMPLICON for deepest next-generation sequencing of PCR products with Illumina or for generation of PCR fragments up to 3 kb in length with PacBio. 

Human exons make up only about 1% of the total genome. Despite the small number of exons, these protein coding regions harbour about 85% of the mutations associated with human disease. Focusing the sequencing power on the exome produces a high yield of relevant genetic variants that can help determine the molecular basis of complex disorders.

Have you thought about using next-generation sequencing for the genetic characterisation of a certain disease? Then consider INVIEW HUMAN EXOME, a sample-to-answer solution which includes DNA isolation, library preparation, sequencing and bioinformatics analysis with delivery times as fast as two weeks. Benefit from a robust approach with high sensitivity and specificity to find mutations in genes already known to cause human diseases or to capture novel causative genes by comparing individual exomes.  

Further reading on exome sequencing

Tetreault M., Bareke E., Nadaf J., Alirezaie N, Majewski J. Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities. Expert Rev Mol Diagn. 15 (6): 749-60 (2015).

Rabbani B., Tekin M., Mahdieh N. The promise of whole-exome sequencing in medical genetics. J Hum Genet 59(1): 5-15 (2014).