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A unique and universal molecular barcode array

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Abstract

Molecular barcode arrays allow the analysis of thousands of biological samples in parallel through the use of unique 20-base-pair (bp) DNA tags. Here we present a new barcode array, which is unique among microarrays in that it includes at least five replicates of every tag feature. The use of smaller dispersed replicate features dramatically improves performance versus a single larger feature and allows the correction of previously undetectable hybridization defects.

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Figure 1: Description of the competitive growth assay.
Figure 2: Ability to resolve known TAG ratios.
Figure 3: Utilization of feature replicates to detect and mask array defects.

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Acknowledgements

This work was supported by a grant from the US National Human Genome Research Institute. We thank B. St. Onge, M. Hillenmeyer and S. Brachat for suggestions.

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Authors and Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, 94305, California, USA

    Sarah E Pierce

  2. Stanford Genome Technology Center, 855 S. California Avenue, Palo Alto, 94304, California, USA

    Eula L Fung, Daniel F Jaramillo, Ronald W Davis, Corey Nislow & Guri Giaever

  3. Department of Biochemistry, Stanford University School of Medicine, Stanford, 94305, California, USA

    Angela M Chu & Ronald W Davis

  4. Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, M5S3E1, ON, Canada

    Corey Nislow

  5. Faculty of Pharmacy, Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, M5S3E1, ON, Canada

    Guri Giaever

Authors
  1. Sarah E Pierce
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  2. Eula L Fung
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  3. Daniel F Jaramillo
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  4. Angela M Chu
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  5. Ronald W Davis
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  6. Corey Nislow
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  7. Guri Giaever
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Corresponding author

Correspondence to Guri Giaever.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Use of unassigned tag probes to estimate background hybridization. (PDF 136 kb)

Supplementary Figure 2

Effect of repairs on tag performance. (PDF 237 kb)

Supplementary Table 1

Detailed information on the repaired tags. (PDF 160 kb)

Supplementary Methods (PDF 152 kb)

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Pierce, S., Fung, E., Jaramillo, D. et al. A unique and universal molecular barcode array. Nat Methods 3, 601–603 (2006). https://doi.org/10.1038/nmeth905

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  • DOI: https://doi.org/10.1038/nmeth905

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