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Highly efficient somatic-mutation identification using Escherichia coli mismatch-repair detection

Nature Methods volume 4, pages 713–715 (2007)Cite this article

Abstract

The discovery of somatic mutations in cancer tissue is extremely laborious, time-consuming and costly. In an evaluation comparing mismatch repair detection (MRD) against Sanger sequencing for somatic-mutation detection, we found that MRD had a specificity of 96% and a sensitivity of 92%. Our results showed that MRD is a robust and cost-effective alternative to Sanger sequencing for identifying somatic mutations in human tumors.

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Figure 1: Conceptual overview of the experimental design.
Figure 2: Schematic of the analysis done to compare the performance of MRD and Sanger sequencing.
Figure 3: Low-abundance-mutation detection.

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Acknowledgements

We thank J. Peña for graphical help with Figure 1, the DNA sequencing lab for thoughtful discussions, D. Kenski and M. Eby for careful review of the manuscript and G. Cavet, J. Kaminker, S. Guerrero, J. Yuan and S. Lohr for help with informatics analysis and database management.

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Author notes

  1. Brock A Peters and Zhengyan Kan: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, 94080, California, USA

    Brock A Peters, Zhengyan Kan, Dragan Sebisanovic, Kanan Pujara, Peter Hong, Bernard Chow, Jeremy Stinson, Frederic de Sauvage & Somasekar Seshagiri

  2. Department of Pathology, Genentech, 1 DNA Way, South San Francisco, 94080, California, USA

    Thinh Q Pham, Howard Stern, Paul Waring, Kenneth J Hillan & David A Eberhard

  3. Affymetrix Inc., 7300 Shoreline Ct., South San Francisco, 94080, California, USA

    Zhiyong Wang, Victoria E H Carlton, Jianbiao Zheng & Malek Faham

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  1. Brock A Peters
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Corresponding author

Correspondence to Somasekar Seshagiri.

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Competing interests

All authors are employed by either Genentech or Affymetrix, and own stock in their respective companies.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3, Supplementary Tables 1, 2, 4–6, Supplementary Methods. (PDF 608 kb)

Supplementary Table 3

Amplicon call rates by sample. (XLS 846 kb)

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Peters, B., Kan, Z., Sebisanovic, D. et al. Highly efficient somatic-mutation identification using Escherichia coli mismatch-repair detection. Nat Methods 4, 713–715 (2007). https://doi.org/10.1038/nmeth1081

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