be ligated to create a cDNA concatemer with each ditag being separated by the AE recognition site. These concatemers are then transformed into bacteria for amplification through bacterial replication. The cDNA concatemers can then be isolated and sequenced using modern high-throughput DNA sequencers, and these sequences can be analysed with computer programs which quantify the recurrence of individual tags. Analysis The output of SAGE is a list of short sequence tags and the number of times it is observed. Using sequence databases a researcher can usually determine, with some confidence, from which original mRNA (and therefore which gene) the tag was extracted. Statistical methods can be applied to tag and count lists from different samples in order to determine which genes are more highly expressed. For example, a normal tissue sample can be compared against a corresponding tumor to determine which genes tend to be more (or less) active. History In 1979 teams at Harvard and Caltech extended the basic idea of making DNA copies of mRNAs in vitro to amplifying a library of such in bacterial plasmids. In 1982–1983, the idea of selecting random or semi-random clones from such a cDNA library for sequencing was explored by Greg Sutcliffe and coworkers. and Putney et al. who sequenced 178 clones from a rabbit muscle cDNA library. In 1991 Adams and co-workers coined the term expressed sequence tag (EST) and initiated more systematic sequencing of cDNAs as a project (starting with 600 brain cDNAs). The identification of ESTs proceeded rapidly, millions of ESTs now available in public databases (e.g. GenBank). In 1995, the idea of reducing the tag length from 100 to 800 bp down to tag length of 10 to 22 bp helped reduce the cost of mRNA surveys. In this year, the original SAGE protocol was published by Victor Velculescu at the Oncology Center of Johns Hopkins University. Although SAGE was originally conceived for use in cancer studies, it has been successfully used to describe the transcriptome of other diseases and in a wide variety of organisms. Comparison to DNA microarrays The general goal of the technique is similar to the DNA microarray. However, SAGE sampling is based on sequencing mRNA output, not on hybridization of mRNA output to probes, so transcription levels are measured more quantitatively than by microarray. In addition, the mRNA sequences do not need to be known a priori, so genes or gene variants which