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DNA sequencing refers to the process of determining the base sequence (i.e. the order of adenine, guanine, cytosine and thymine nucleotides) of the DNA double helix. While normal DNA sequence variation exists between individuals, pathogenic variation of genes regulating key cellular processes can initiate tumorigenesis and lead to cancer.

Next-generation sequencing (NGS) technology represents a variety of modern sequencing approaches that are based on sequencing of millions of small DNA fragments in parallel. Sequence information obtained from the individual fragments are aligned together bioinformatically allowing fast and cost-effective approach for genomic sequencing.

Identification of tumor-specific genomic features provides valuable information that can be used to molecularly classify cancers, explore molecular mechanisms underlying tumorigenesis and identify key actionable targets for therapeutic intervention. Furthermore, analysis of longitudinal samples during the disease course can be used to gain insights on the overall tumor dynamics and mechanisms leading to therapy resistance.

Typical NGS-based DNA sequencing approaches include:

  1. Use of targeted gene panels for sequencing. For many clinical applications, targeted sequencing of predefined gene sets is preferred. Using this approach, only the known clinically relevant genes are sequenced, keeping the costs and produced sequencing information reasonable. Using this method, high sequencing depth of the target regions can be achieved, allowing the identification of low frequency gene variants within a heterogeneous tissue sample.
  2. Whole exome sequencing (WES). Next-generation sequencing of all the exons (i.e. exome) provides sequence information of ~1 % of the human genome. With this targeted sequencing approach, variations in the protein-coding region of the genome can be identified. As most known disease-causing mutations occur in the protein-coding regions of the genome, WES is considered to be an efficient approach for the identification of pathogenic mutations and a cost-effective alternative for whole genome sequencing.
  3. Whole genome sequencing (WGS). Next-generation sequencing of the whole genome provides sequence information of all the 3.2 billion bases in the genome. Therefore, WGS can be used to identify variants residing at any genomic loci, typically at a low coverage. In addition to sequence variations, WGS can be used to reveal DNA copy number variations, such as gene amplifications and deletions.

While the use of targeted gene panels is often the choice of method in clinical setting due to cost-effectiveness and fast clinical interpretation, WES and WGS provide valuable tools for scientific research for the discovery of new disease-causing variants. Overall, the use of NGS-based methods in cancer diagnostics and during disease follow-up facilitate the development and application of individualized cancer care.

References:

Rick Kamps R, Brandão RD, van den Bosch BJ, Paulussen ADC, Xanthoulea S, Blok MJ, and Romano A. Next-generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int J Mol Sci, 18(2):308, 2017.

Horak P, Fröhling S and Glimm H. Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls. ESMO Open, 1(5): e000094, 2016.

Gagan J and Van Allen EM. Next-generation sequencing to guide cancer therapy. Genome Med, 7(1):80, 2015.

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