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Comparison of algorithms for the detection of cancer drivers at subgene resolution

Nature Methods volume 14, pages 782–788 (2017)Cite this article

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Abstract

Understanding genetic events that lead to cancer initiation and progression remains one of the biggest challenges in cancer biology. Traditionally, most algorithms for cancer-driver identification look for genes that have more mutations than expected from the average background mutation rate. However, there is now a wide variety of methods that look for nonrandom distribution of mutations within proteins as a signal for the driving role of mutations in cancer. Here we classify and review such subgene-resolution algorithms, compare their findings on four distinct cancer data sets from The Cancer Genome Atlas and discuss how predictions from these algorithms can be interpreted in the emerging paradigms that challenge the simple dichotomy between driver and passenger genes.

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Figure 1: Finding mutation drivers across biological scales.
Figure 2: Comparison of the overall predictions of each method.
Figure 3: Evaluating the predictions of each method and type of algorithm based on CGC data.
Figure 4: Using mutation clusters to improve the definition of cancer drivers.

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Acknowledgements

We would like to thank the people working at The Cancer Genome Atlas for their efforts and for making all the data publicly available. E.P.-P. and A.G. acknowledge the support from the Cancer Center grants P30 CA030199 (to our institute) and R35 GM118187 (A.G.). A.K. was supported by startup funds of G.G. and by a collaboration with Bayer AG. D.T. is supported by project SAF2015-74072-JIN, which is funded by the Agencia Estatal de Investigacion (AEI) and Fondo Europeo de Desarrollo Regional (FEDER). N.L.-B. acknowledges funding from the European Research Council (consolidator grant 682398). A.V. and T.P. acknowledge funding by the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 305444 (RD-Connect).

Author information

Author notes

  1. Eduard Porta-Pardo

    Present address: Barcelona Supercomputing Centre (BSC), Barcelona, Spain

  2. Tirso Pons

    Present address: Stem cells and Immunity Laboratory, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain

Authors and Affiliations

  1. Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA

    Eduard Porta-Pardo, Daniela Grases & Adam Godzik

  2. Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA

    Atanas Kamburov & Gad Getz

  3. Harvard Medical School, Boston, Massachusetts, USA

    Atanas Kamburov & Gad Getz

  4. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

    Atanas Kamburov & Gad Getz

  5. Department of Experimental and Health Sciences, University Pompeu Fabra (UPF), Barcelona, Spain

    David Tamborero & Nuria Lopez-Bigas

  6. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain

    David Tamborero & Nuria Lopez-Bigas

  7. Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

    Tirso Pons

  8. Barcelona Supercomputing Centre (BSC), Barcelona, Spain

    Alfonso Valencia

  9. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain

    Alfonso Valencia & Nuria Lopez-Bigas

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Contributions

E.P.-P. and A.G. conceived the project. E.P.-P., D.T. and T.P. researched the data for the article. E.P.-P., A.K. and D.T. analyzed the data. All authors were involved in writing the article and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Adam Godzik.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Coverage of the human proteome by different types of biological features.

Fraction of the proteome that is covered by linear regions (left), structures with over 95% sequence identity between the protein and the template (middle) or structures with a BLAST e-value between the protein and the template below 1e-9. The fraction is calculated for both, the absolute number of proteins (left columns) as well as the total number of residues (right columns). The distinction between the two is important because it is usually the case that we only know the structure for a fraction of the protein.

Supplementary Figure 2 Results of the different algorithms in the BLCA dataset.

Visualization is limited to genes detected by at least 4 methods or known drivers in BLCA detected by at least one algorithm.

Supplementary Figure 3 Results of the different algorithms in the BRCA dataset.

Visualization is limited to genes detected by at least 4 methods or known drivers in BRCA detected by at least one algorithm.

Supplementary Figure 4 Results of the different algorithms in the LUAD dataset.

Visualization is limited to genes detected by at least 4 methods or known drivers in LUAD detected by at least one algorithm.

Supplementary Figure 5 Sub-gene resolution algorithms detect more oncogenes than tumor-suppressors.

(a) Barplot showing the fraction of genes detected by each method that are oncogenes, tumor-suppressors, have a dual-role or whose mode of action is not yet known. (b) Fold-enrichment of each method in detected oncogenes or genes with dual-role when aggregating all four datasets.

Supplementary Figure 6 Description of the datasets.

(a) Mutation types in each patient of the different dataset. The majority of mutations are missense. (b) Number of patients (top) and violin plot showing the distribution of number of mutations (bottom) in each dataset. Each dot represents a sample.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 1200 kb)

Supplementary Table 1

Availability and statistical tests used by each method. (XLSX 13 kb)

Supplementary Table 2

Performance of the different methods in the BLCA dataset. (XLSX 10 kb)

Supplementary Table 3

Performance of the different methods on the BRCA dataset. (XLSX 10 kb)

Supplementary Table 4

Performance of the different methods on the GBM dataset. (XLSX 10 kb)

Supplementary Table 5

Performance of the different methods on the LUAD dataset. (XLSX 11 kb)

Supplementary Table 6

Driver genes not detected by whole-gene methods. (XLSX 26 kb)

Supplementary Table 7

Candidate novel driver genes detected only by sub-gene resolution algorithms. (XLSX 17 kb)

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Porta-Pardo, E., Kamburov, A., Tamborero, D. et al. Comparison of algorithms for the detection of cancer drivers at subgene resolution. Nat Methods 14, 782–788 (2017). https://doi.org/10.1038/nmeth.4364

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