Brief Communication | Published:

Counting absolute numbers of molecules using unique molecular identifiers

Nature Methods volume 9, pages 7274 (2012) | Download Citation

Abstract

Counting individual RNA or DNA molecules is difficult because they are hard to copy quantitatively for detection. To overcome this limitation, we applied unique molecular identifiers (UMIs), which make each molecule in a population distinct, to genome-scale human karyotyping and mRNA sequencing in Drosophila melanogaster. Use of this method can improve accuracy of almost any next-generation sequencing method, including chromatin immunoprecipitation–sequencing, genome assembly, diagnostics and manufacturing-process control and monitoring.

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Acknowledgements

We thank M. Taipale, H. Secher Lindroos, E. Ukkonen and T. Whitington for critical review of the manuscript, and E. Iwarsson (Karolinska University Hospital) for the trisomy-21 DNA. This work was supported by European Research Council project Growth Control, Academy of Finland postdoctoral researcher's projects 122197 and 134073, and the Swedish Foundation for Strategic Research grant MDB09-0052.

Author information

Author notes

    • Teemu Kivioja
    •  & Anna Vähärautio

    These authors contributed equally to this work.

Affiliations

  1. Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Helsinki, Finland.

    • Teemu Kivioja
    • , Anna Vähärautio
    •  & Martin Bonke
  2. Department of Computer Science, University of Helsinki, Helsinki, Finland.

    • Teemu Kivioja
  3. Science for Life Laboratory, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.

    • Teemu Kivioja
    • , Anna Vähärautio
    • , Martin Enge
    •  & Jussi Taipale
  4. Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

    • Kasper Karlsson
    •  & Sten Linnarsson

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Contributions

S.L., J.T., A.V., T.K. and M.E. conceived and designed experiments. A.V., K.K. and M.B. performed biological experiments. S.L., J.T., A.V. and T.K. analyzed data. J.T., A.V., T.K., M.E. and S.L. wrote the paper.

Competing interests

S.L. and J.T. have submitted a patent application on the absolute molecule counting method (UK patent application 1016608.0).

Corresponding authors

Correspondence to Sten Linnarsson or Jussi Taipale.

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    Supplementary Text and Figures

    Supplementary Figures 1–7, Supplementary Table 1, Supplementary Note

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DOI

https://doi.org/10.1038/nmeth.1778

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