TO THE TRANSCRIPTOME

"Getting the entire genome expression assay on a single chip has been a significant advancement," says Greg Yap, senior marketing director for DNA analysis at Affymetrix. Yet he notes that many scientists don't want to limit their studies to protein-coding genes, which account for just 2% of transcription; they want to view transcription genome-wide. "Everyone has heaved a sigh of relief that the whole human-genome expression arrays were available, but those are really gene-expression arrays, and what we have to look at is genome expression, the transcriptome," says Yap. "It turns out that much more of the genome is transcribed than was originally predicted through the standard bioinformatic methods," he adds.

Affymetrix researchers are currently using a specialized GeneChip microarray to "tile" millions of DNA probes representative of the complete human genome. The company recently published data that identifies transcription factor-binding sites across human chromosomes 21 and 22.

Advances have also been made in SNP analysis. SNPs represent the most common source of genetic variation, and the human genome is thought to contain over 10 million of them, about one every 300 bases. Working through that many markers is practically impossible without a shortcut.

In April, Affymetrix announced the early-access availability of its GeneChip Mapping 100K Array Set, a two-chip product slated for summer release. "This assay, for the first time, is enabling customers to try studies that they have always wanted to do but have never had the technologies to be able to do before," says Yap. "It was just not economical to look at hundreds of thousands of SNPs with existing technologies. Our 100K product will help get these experiments going," he adds. Illumina is also planning to release a 100,000-SNP chip for beta testing by year's end.