Counting absolute numbers of molecules using unique molecular identifiers

Nature Methods volume 9, pages72–74(2012)Cite this article

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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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Figure 1: UMIs can be generated by adding oligonucleotide labels, fragmenting, taking a small enough aliquot or a combination thereof.
Figure 2: Digital karyotyping by counting the absolute number of molecules.
Figure 3: Accuracy of mRNA-seq can be improved by the UMI method.

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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.

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Author notes

  1. Teemu Kivioja and 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. Department of Biosciences and Nutrition, Science for Life Laboratory, 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

Authors
  1. Teemu Kivioja
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  2. Anna Vähärautio
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  3. Kasper Karlsson
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  4. Martin Bonke
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  5. Martin Enge
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  6. Sten Linnarsson
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  7. Jussi Taipale
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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.

Corresponding authors

Correspondence to Sten Linnarsson or Jussi Taipale.

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Competing interests

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

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Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Table 1, Supplementary Note (PDF 1812 kb)

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Kivioja, T., Vähärautio, A., Karlsson, K. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 9, 72–74 (2012). https://doi.org/10.1038/nmeth.1778

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