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The International Cancer Genome Consortium Data Portal

Nature Biotechnology volume 37, pages 367–369 (2019)Cite this article

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To the Editor — The International Cancer Genome Consortium (ICGC) is a global initiative to build a comprehensive catalog of mutational abnormalities in the major tumor types. Here we present the ICGC’s Data Portal, a user-friendly platform for efficient visualization, analysis and interpretation of large, diverse cancer datasets. The portal currently contains data from 84 worldwide cancer projects, collectively representing about 77 million somatic mutations and molecular data from over 20,000 contributors. We use scalable big-data technologies to overcome the challenges of storing, annotating and exploring large and complex datasets1, thereby facilitating powerful integrative analyses that may shed new light on cancer biology. For example, the integration of large numbers of tumor genomes in the ICGC portal will enable the identification of rare molecular subtypes that have distinctive clinical behavior. Ultimately, this may lead to the development of new and better diagnostic tools, as well as more targeted therapies and drugs.

Advances in sequencing and molecular profiling technologies have rapidly accelerated the generation of cancer-related genetic, molecular and clinical data. Although the original ICGC portal system, based on a traditional SQL database2, supported contributions to the ICGC project for the first three years, it was unable to support the growing data demands. To overcome these challenges, the ICGC Data Portal was developed, with not only highly efficient search algorithms for interactive querying and browsing but also intuitive and powerful user interfaces to help users interpret complex molecular and associated clinical data.

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Fig. 1: The ICGC Data Portal Facet Search interface.
Fig. 2: Using the ICGC Data Portal.

Code availability

Software code of the ICGC infrastructure, including the ICGC Data Portal, is available at https://github.com/icgc-dcc under the GNU General Public License Version 3.

Data availability

The ICGC dataset is available at https://dcc.icgc.org/. Data access is governed by the ICGC Data Access Office for non-US projects and by the dbGaP Authorized Access program for US-based projects.

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Acknowledgements

The authors received support for this work from the Ontario Institute for Cancer Research (OICR) through funding provided by the government of Ontario.

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Author notes

  1. These authors contributed equally: Junjun Zhang, Rosita Bajari, Dusan Andric.

Authors and Affiliations

  1. Ontario Institute for Cancer Research, Toronto, Ontario, Canada

    Junjun Zhang, Rosita Bajari, Dusan Andric, Francois Gerthoffert, Alexandru Lepsa, Hardeep Nahal-Bose, Lincoln D. Stein & Vincent Ferretti

  2. CHU Sainte-Justine Research Center, Montreal, Quebec, Canada

    Vincent Ferretti

Authors
  1. Junjun Zhang
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  2. Rosita Bajari
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  3. Dusan Andric
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  6. Hardeep Nahal-Bose
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  7. Lincoln D. Stein
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  8. Vincent Ferretti
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Contributions

V.F. and J.Z. led the system design and implementation with contributions from L.D.S., D.A. and R.B.; D.A. and A.L. contributed to the software architecture design and coding; J.Z., R.B. and H.N.-B. contributed to system quality control; F.G. managed the software developer team. The manuscript was prepared by R.B. and V.F. with contributions from L.D.S., J.Z. and D.A. All authors reviewed the manuscript.

Corresponding author

Correspondence to Vincent Ferretti.

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The authors declare no competing interests.

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Editor’s Note: This article has been peer-reviewed.

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Supplementary Information

Supplementary Figures 1–3, Supplementary Tables 1–2, and Supplementary Notes 1–4

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Zhang, J., Bajari, R., Andric, D. et al. The International Cancer Genome Consortium Data Portal. Nat Biotechnol 37, 367–369 (2019). https://doi.org/10.1038/s41587-019-0055-9

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