Published online 8 September 2004
Nucleic Acids Research, Vol. 32 No. 16 © Oxford University Press 2004; all rights reserved
Whole-genome expression profiling through fragment display and combinatorial gene identification
Global Genomics AB, Tomtebodavägen 21B, SE-171 77 Stockholm, Sweden and 1 Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 1, SE-171 77 Stockholm, Sweden
* To whom correspondence should be addressed. Tel: +46 850 884 718; Fax: +46 830 1750; Email: slinnarsson{at}globalgenomics.com
Received February 25, 2004; Revised June 15, 2004; Accepted August 20, 2004
There is a growing demand for highly parallel gene expression analysis with whole genome coverage, high sensitivity and high accuracy. Open systems such as differential display are capable of analyzing most of the expressed genome but are not quantitative and generally require manual identification of differentially expressed genes by sequencing. Closed systems such as microarrays use gene-specific probes and are, therefore, limited to studying specific genes in well-characterized species. Here, we describe Tangerine, a PCR-based system that combines the scope and generality of open systems with a robust and immediate identification algorithm using publicly available sequence information. By combinatorial analysis of three independent and complete DNA indexing profiles, each displaying the complete set of expressed transcripts on capillary electrophoresis, the method allows transcripts to be simultaneously quantified and identified. The method is sensitive, accurate and reproducible, and is amenable to high-throughput automated operation.