Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Data quality in genomics and microarrays

Nature Biotechnology volume 24, pages 1112–1113 (2006)Cite this article

Objective quality control indices are needed to facilitate clinical implementation of DNA microarrays used in transcriptional profiling as well as other types of genomic analysis.

DNA microarrays are increasingly used for investigating gene expression in human diseases with the hope of identifying signatures that correlate with specific clinical outcomes. The discovery of these signatures offers the tantalizing possibility that they could be translated into fully fledged clinical diagnostic tests. Significant hurdles exist, however, in transitioning microarray technology and gene expression analysis into the complicated realm of the clinic. Namely, gene expression genomic data quality, a measure of its general reproducibility and ultimately, its true biological relevance, requires significant improvement1. For example, comparing gene expression studies using different microarray formats is fraught with difficulty, even under circumstances in which the same type of tissue is analyzed2. A recent prominent example illustrates a case where different clinical conclusions were derived from the same gene expression data set3.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

Buy

All prices are NET prices.

Figure 1: DNA microarray analysis of human tissues involves multiple steps and protocols.

References

  1. Steinmetz, L.M. & Davis, R.W. Nat. Rev. Genet. 5, 190–201 (2004).

    Article  CAS  Google Scholar 

  2. Tan, P.K. et al. Nucleic Acids Res. 31, 5676–5684 (2003).

    Article  CAS  Google Scholar 

  3. Tibshirani, R. N. Engl. J. Med. 352, 1496–1497 (2005).

    Article  CAS  Google Scholar 

  4. Jarvinen, A.K. et al. Genomics 83, 1164–1168 (2004).

    Article  CAS  Google Scholar 

  5. Bammler, T. et al. Nat. Methods 2, 351–356 (2005).

    Article  Google Scholar 

  6. Irizarry, R.A. et al. Nat. Methods 2, 345–350 (2005).

    Article  CAS  Google Scholar 

  7. Larkin, J.E., Frank, B.C., Gavras, H., Sultana, R. & Quackenbush, J. Nat. Methods 2, 337–344 (2005).

    Article  CAS  Google Scholar 

  8. Shi, L. et al. BMC Bioinformatics 6 Suppl 2, S12 (2005).

    Article  Google Scholar 

  9. MACQ Consortium. Nat. Biotechnol. 24, 1151–1161 (2006).

  10. Baker, S.C. et al. Nat. Methods 2, 731–734 (2005).

    Article  CAS  Google Scholar 

  11. Cobb, J.P. et al. Proc. Natl. Acad. Sci. USA 102, 4801–4806 (2005).

    Article  CAS  Google Scholar 

  12. van Bakel, H. & Holstege, F.C. EMBO Rep. 5, 964–969 (2004).

    Article  CAS  Google Scholar 

  13. Eason, R.G. et al. Proc. Natl. Acad. Sci. USA 101, 11046–11051 (2004).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medicine, Division of Oncology,

    Hanlee Ji & Ronald W Davis

  2. Department of Biochemistry and Department of Genetics at Stanford University School of Medicine, 269 Campus Drive, CCSR 1115, Stanford, 94305-5151, California, USA

    Hanlee Ji & Ronald W Davis

Authors
  1. Hanlee Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ronald W Davis
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ji, H., Davis, R. Data quality in genomics and microarrays. Nat Biotechnol 24, 1112–1113 (2006). https://doi.org/10.1038/nbt0906-1112

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0906-1112

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing