A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices

  1. Jian-Bing Fan1,3,
  2. Joanne M. Yeakley1,
  3. Marina Bibikova1,
  4. Eugene Chudin1,
  5. Eliza Wickham1,
  6. Jing Chen1,
  7. Dennis Doucet1,
  8. Philippe Rigault1,
  9. Baohong Zhang1,
  10. Richard Shen1,
  11. Celeste McBride1,
  12. Hai-Ri Li2,
  13. Xiang-Dong Fu2,
  14. Arnold Oliphant1,
  15. David L. Barker1, and
  16. Mark S. Chee1
  1. 1 Illumina, Inc., San Diego, California 92121, USA
  2. 2 Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA

Abstract

We report a flexible, sensitive, and quantitative gene-expression profiling system for assaying more than 400 genes, with three probes per gene, for 96 samples in parallel. The cDNA-mediated annealing, selection, extension and ligation (DASL) assay targets specific transcripts, using oligonucleotides containing unique address sequences that can hybridize to universal arrays. Cell-specific gene expression profiles were obtained using this assay for hormone-treated cell lines and laser-capture microdissected cancer tissues. Gene expression profiles derived from this assay were consistent with those determined by qRT-PCR. The DASL assay has been automated for use with a bead-based 96-array matrix system. The combined high-throughput assay and readout system is accurate and efficient, and can cost-effectively profile the expression of hundreds of genes in thousands of samples.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2167504.

  • ↵3 Corresponding author. E-MAIL jfan{at}illumina.com; FAX (858) 202-4680.

    • Accepted February 11, 2004.
    • Received November 13, 2003.
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This Article

  1. doi: 10.1101/gr.2167504 Genome Res. 14: 878-885 Cold Spring Harbor Laboratory Press

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