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Cancer whole-genome sequencing: present and future

Oncogene volume 34, pages 59435950 (03 December 2015) | Download Citation

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Abstract

Recent explosive advances in next-generation sequencing technology and computational approaches to massive data enable us to analyze a number of cancer genome profiles by whole-genome sequencing (WGS). To explore cancer genomic alterations and their diversity comprehensively, global and local cancer genome-sequencing projects, including ICGC and TCGA, have been analyzing many types of cancer genomes mainly by exome sequencing. However, there is limited information on somatic mutations in non-coding regions including untranslated regions, introns, regulatory elements and non-coding RNAs, and rearrangements, sometimes producing fusion genes, and pathogen detection in cancer genomes remain widely unexplored. WGS approaches can detect these unexplored mutations, as well as coding mutations and somatic copy number alterations, and help us to better understand the whole landscape of cancer genomes and elucidate functions of these unexplored genomic regions. Analysis of cancer genomes using the present WGS platforms is still primitive and there are substantial improvements to be made in sequencing technologies, informatics and computer resources. Taking account of the extreme diversity of cancer genomes and phenotype, it is also required to analyze much more WGS data and integrate these with multi-omics data, functional data and clinical-pathological data in a large number of sample sets to interpret them more fully and efficiently.

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Acknowledgements

We thank researchers and technical staffs in RIKEN-IMS and Professor Miyano and his fellows in Human Genome Center, Institute of Medical Science, The University of Tokyo for their great efforts to cancer genome sequencing in ICGC project. The super-computing resource ‘SHIROKANE’ was provided by Human Genome Center, The University of Tokyo (http://sc.hgc.jp/shirokane.html). This work was supported partially by RIKEN President’s Fund 2011, the Princess Takamatsu Cancer Research Fund, and Takeda Science Foundation.

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  1. Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan

    • H Nakagawa
    • , C P Wardell
    • , M Furuta
    • , H Taniguchi
    •  & A Fujimoto

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The authors declare no conflict of interest.

Corresponding author

Correspondence to H Nakagawa.

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DOI

https://doi.org/10.1038/onc.2015.90

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