New technology now enables researchers to rapidly sequence megabases of both nuclear DNA and cDNAs generated from small RNA. This "deep sequencing," in turn, has given researchers the power to investigate a new set of biological problems.

Strictly speaking, "deep sequencing" implies highly redundant coverage of the target DNA, but researchers sometimes use "deep" as shorthand for the new, high-throughput equipment. In 2005, 454 Life Sciences, since acquired by Roche, introduced this expensive but powerful technology. In 2007, Illumina introduced an even more capable technology it acquired with Solexa.

At a March 10, 2008, symposium at the Academy, speakers showed results from both the 454 and Solexa systems. Michael Snyder of Yale University described three different uses of high-throughput sequencing of DNA. The other two speakers, Graham Ruby, of the Whitehead Institute for Biomedical Research at MIT and Katsutomo Okamura, of the Memorial Sloan-Kettering Cancer Center, use high-throughput sequencing to classify short RNAs.