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Direct multiplexed measurement of gene expression with color-coded probe pairs

Nature Biotechnology volume 26, pages 317–325 (2008)Cite this article

A Corrigendum to this article was published on 01 June 2008

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Abstract

We describe a technology, the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 fM and 0.5 fM, and a linear dynamic range of over 500-fold. Comparison of the NanoString nCounter gene expression system with microarrays and TaqMan PCR demonstrated that the nCounter system is more sensitive than microarrays and similar in sensitivity to real-time PCR. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels.

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Figure 1: Overview of NanoString nCounter gene expression system.
Figure 2: The linearity and reproducibility of the NanoString spike-in controls.
Figure 3: Reproducibility and differential gene expression plots for 509 genes on the NanoString nCounter platform.
Figure 4: Comparison of detected/undetected calls for the NanoString and Affymetrix assays.
Figure 5: Comparison plots of NanoString nCounter to Affymetrix GeneChip and Applied BioSystems TaqMan platforms.

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Change history

  • 16 May 2008

    The list of authors for this paper omitted the final author, Krassen Dimitrov, and should have read as follows: Gary K Geiss1, Roger E Bumgarner2, Brian Birditt1, Timothy Dahl1, Naeem Dowidar1, Dwayne L Dunaway1, H Perry Fell1, Sean Ferree1, Renee D George1,5, Tammy Grogan1, Jeffrey J James1, Malini Maysuria1, Jeffrey D Mitton1, Paola Oliveri3,5, Jennifer L Osborn1,5, Tao Peng2, Amber L Ratcliffe1, Philippa J Webster1, Eric H Davidson3, Leroy Hood4 & Krassen Dimitrov4,5 Affiliation number five should have included his present address and thus read: 5Present addresses: Department of Genome Sciences, Box 355065, University of Washington, Seattle, Washington 98195, USA (R.D.G.), Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK (P.O.), Department of Bioengineering, Box 355061, University of Washington, Seattle, Washington 98195, USA (J.L.O.) and Australian Institute for Bioengineering and Nanotechnology, Building 75—Cnr of College and Cooper Road, The University of Queensland, Brisbane QLD 4072 Australia (K.D.).

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Acknowledgements

We would like to acknowledge Edward Kelly, at the Center for DNA Sequencing and Gene Analysis, UW School of Pharmacy, Department of Pharmaceutics for TaqMan analysis and the University of Washington's Center for Array Technologies for processing of Affymetrix arrays. Poliovirus (PV) stocks were the kind gift of Kurt Gustin's laboratory (University of Idaho).

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Author notes

  1. Renee D George, Paola Oliveri, Jennifer L Osborn, Leroy Hood & Krassen Dimitrov

    Present address: Present addresses: Department of Genome Sciences, Box 355065, University of Washington, Seattle, Washington 98195, USA (R.D.G.), Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK (P.O.), Department of Bioengineering, Box 355061, University of Washington, Seattle, Washington 98195, USA (J.L.O.) and Australian Institute for Bioengineering and Nanotechnology, Building 75—Cnr of College and Cooper Road, The University of Queensland, Brisbane QLD 4072 Australia (K.D.),

Authors and Affiliations

  1. NanoString Technologies Inc., 201 Elliott Ave West, Suite 300, Seattle, 98119, Washington, USA

    Gary K Geiss, Brian Birditt, Timothy Dahl, Naeem Dowidar, Dwayne L Dunaway, H Perry Fell, Sean Ferree, Renee D George, Tammy Grogan, Jeffrey J James, Malini Maysuria, Jeffrey D Mitton, Jennifer L Osborn, Amber L Ratcliffe & Philippa J Webster

  2. The Department of Microbiology, Box 358070, University of Washington, Seattle, 98195, Washington, USA

    Roger E Bumgarner & Tao Peng

  3. Division of Biology 156-29, California Institute of Technology, Pasadena, 91125, California, USA

    Paola Oliveri & Eric H Davidson

  4. The Institute of Systems Biology, 1441 N. 34th St., Seattle, 98103, Washington, USA

    Krassen Dimitrov

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Contributions

G.K.G. designed the experiments, analyzed data and prepared the manuscript. D.L.D., S.F., P.J.W. and G.K.G. designed and developed the NanoString system described. T.D. and J.D.M. developed probe selection and image analysis software, respectively. N.D. performed all nCounter assays described. B.B., R.D.G., T.G., J.J.J., M.M., J.L.O. and A.L.R. provided ideas and technical support. T.P. and P.O. provided microarray and real-time PCR data and samples. R.E.B. contributed to experimental design, scientific direction and manuscript preparation. H.P.F., E.H.D. and L.H. provided scientific direction and experimental concepts. K.D. provided the ideas and design of this technology and participated in the initial research.

Corresponding author

Correspondence to Gary K Geiss.

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Competing interests

The following authors are current or past employees of and/or have an equity stake in NanoString technologies: G.K.G., B.B., T.D., N.D., D.L.D., H.P.F., S.F., R.D.G., T.G., J.J.J., M.M., J.D.M., J.L.O., A.L.R., P.J.W., E.H.D., L.H. and K.D.

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Geiss, G., Bumgarner, R., Birditt, B. et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26, 317–325 (2008). https://doi.org/10.1038/nbt1385

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