Characterising Somatic Mutations in Cancer Genome by Means of Next‐generation Sequencing

Abstract

Cancer genome sequencing studies have identified tens of thousands of somatic mutations in various human cancers to date. This data has started to generate new insights into mutation patterns and their differences between various cancers. Further, the mutation patterns have also helped to elucidate mechanism involved in generating mutations in cancer genome such as deoxyribonucleic acid (DNA)‐repair processes and mutagen exposures. With the introduction of next‐generation sequencing technologies, cancer genome sequencing has evolved from a targeted sequencing approach to whole‐exome sequencing and whole‐genome sequencing (WGS) approaches. However, each sequencing approach has its strengths and limitations. It is widely anticipated that WGS would eventually replace targeted and exome sequencing. WGS offers a unique advantage to study structural variants or rearrangements and fusion genes in a single experiment, in addition to point mutations. However, currently the WGS is still prohibitively expensive for a large number of samples. Despite these technological advances, several challenges still remain, such as discerning driver mutations from benign mutations and collection of high‐quality primary tumour tissues to minimise tissue heterogeneity. Ultimately, a comprehensive delineation of the somatic mutations in the cancer genome would require WGS of a large number of samples from various cancer types and subtypes. Congruent to this goal, the International Cancer Genome Consortium was initiated and upon completion of the project, its data is expected to further enhance our knowledge and understanding of the biological mechanisms underlying cancer development.

Key Concepts:

  • Several sequencing approaches are available to decipher the somatic mutation profile of cancer genome, including targeted sequencing, whole‐exome sequencing (WES) and whole‐genome sequencing (WGS).

  • Targeted sequencing is a hypothesis‐driven approach where candidate genes were often selected based on knowledge of previously reported mutated genes or their related functions in cancer development, such as the kinome or phosphatome.

  • The ability to study different cancers and their subtypes in a comparatively higher throughput to exome and WGS is an important advantage of the targeted sequencing approach.

  • The introduction of multiple commercial exome enrichment kits has circumvented the technical challenges in isolating the entire exome for sequencing.

  • Although WES interrogates only approximately 1–2% of the entire human genome, the several hundred somatic mutations identified in WES studies have already prohibited all of them to be examined by follow‐up studies in larger sample series.

  • The advances of NGS technologies and rapidly declining sequencing cost have enabled the completion of a number of WGS studies for various cancers.

  • The patterns of somatic mutations provided by WGS are useful in elucidating the mechanisms of generating the mutations in cancer genome such as DNA‐repair processes and differences in mutagen exposure.

  • A further advantage over the other two sequencing approaches of WGS is its ability to identify structural rearrangements.

  • Although WES and WGS approaches have now been shown to be technically feasible, several challenges still remain.

  • Delineating patterns of somatic mutations in the cancer genome require a comprehensive interrogation of cancer genomes (entire genome, exome or a large number of candidate genes) in series of up to hundreds of samples.

Keywords: somatic mutation; targeted sequencing; whole‐exome sequencing; whole‐genome sequencing; next‐generation sequencing; cancer genome; single nucleotide variation; copy number variation; structural rearrangement; fusion gene

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Chin L, Andersen JN and Futreal PA (2011) Cancer genomics: from discovery science to personalized medicine. Nature Medicine 17: 297–303.

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Chong, Mei Ling, Ku, Chee Seng, Wu, Mengchu, and Soong, Richie(Feb 2012) Characterising Somatic Mutations in Cancer Genome by Means of Next‐generation Sequencing. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023379]