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Chromoscope: interactive multiscale visualization for structural variation in human genomes

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Fig. 1: The Chromoscope interface.

Data availability

The demonstration cancer genome data was obtained from the publicly available ICGC/TCGA PCAWG Consortium9 repository available at https://dcc.icgc.org/releases/. Demonstration data are limited to somatic mutation calls, which are publicly available, as opposed to germline mutation calls or raw sequencing reads. Additional data from cell lines were obtained from the SRA archive (project SRP162370), which is public, allowing us to showcase Chromoscope’s display of raw sequencing reads.

Code availability

The entire source code is publicly available at https://github.com/hms-dbmi/chromoscope under an MIT license (https://doi.org/10.5281/zenodo.7665959). The Chromoscope web application is available at https://chromoscope.bio.

References

  1. Cortés-Ciriano, I., Gulhan, D. C., Lee, J. J.-K., Melloni, G. E. M. & Park, P. J. Nat. Rev. Genet. 23, 298–314 (2022).

    Article  Google Scholar 

  2. Samsom, K. G. et al. J. Pathol. 258, 179–188 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Villani, A. et al. Nat. Cancer 4, 203–221 (2023).

    Article  CAS  PubMed  Google Scholar 

  4. Collins, R. L. et al. Nature 581, 444–451 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. 100,000 Genomes Project Pilot Investigators et al. N. Engl. J. Med. 385, 1868–1880 (2021).

  6. Robinson, J. T., Thorvaldsdottir, H., Turner, D. & Mesirov, J. P. Bioinformatics 39, btac830 (2023).

    Article  CAS  PubMed  Google Scholar 

  7. Diesh, C. et al. Genome Biol. 24, 74 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  8. L’Yi, S., Wang, Q., Lekschas, F. & Gehlenborg, N. IEEE Trans. Vis. Comput. Graph. 28, 140–150 (2022).

    Article  PubMed  Google Scholar 

  9. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature 578, 82–93 (2020).

    Article  Google Scholar 

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Acknowledgements

This work was supported by the US National Institutes of Health (R01HG011773, U01CA200059).

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Authors and Affiliations

  1. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

    Sehi L’Yi, Dominika Maziec, Victoria Stevens, Trevor Manz, Alexander Veit, Michele Berselli, Peter J. Park, Dominik Głodzik & Nils Gehlenborg

Authors
  1. Sehi L’Yi
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  2. Dominika Maziec
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  3. Victoria Stevens
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  4. Trevor Manz
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  5. Alexander Veit
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  6. Michele Berselli
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  7. Peter J. Park
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  8. Dominik Głodzik
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  9. Nils Gehlenborg
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Contributions

S.L. developed Chromoscope in close collaboration with D.G.; D.G., P.P. and N.G. conceived and supervised the project. D.M., V.S. and D.G. assisted with case studies. T.M. developed the Python package. D.M., M.B. and A.V. suggested critical improvements for the tool. The draft manuscript was written by S.L. and D.G. and all authors edited and gave feedback on the manuscript.

Corresponding authors

Correspondence to Peter J. Park, Dominik Głodzik or Nils Gehlenborg.

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Competing interests

N.G. is a co-founder and equity owner of Datavisyn. D.G. is a consultant for Repare Therapeutics. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks Tobias Rausch and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary information

Supplementary Information

Supplementary Notes, Supplementary Figure 1 and Supplementary Tables 1 and 2.

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L’Yi, S., Maziec, D., Stevens, V. et al. Chromoscope: interactive multiscale visualization for structural variation in human genomes. Nat Methods 20, 1834–1835 (2023). https://doi.org/10.1038/s41592-023-02056-x

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