By John S. MacNeil
Sharing sequence and annotation data nowadays is fairly simple: Go to an online database and download it. But sharing reagents, such as the cDNA clones researchers need for microarray and other functional genomics experiments, is another matter. With the explosion of interest in popular mammalian genomes such as the human and mouse, how does one research group — or even a highly organized consortium — devise a process for sharing the reagents that other scientists need to advance genomic science?
Yoshihide Hayashizaki at the RIKEN Genomic Sciences Center in Yokohama, Japan, thinks he’s found one solution. As director of the institute’s mouse genomics initiative, he’s led the effort to catalog and annotate every mouse cDNA, and his hope is that researchers around the world can take RIKEN’s contributions to genomics — both the data and the clones — and run with them. So Hayashizaki came up with an idea: If researchers can download sequence data, why not print out a hard copy of all the clones onto sheets of paper, and distribute the clones in a book?
The idea makes sense for several reasons, Hayashizaki says. Typically, academic journals require that authors who publish their work also make their starting reagents available to other researchers for experiments to reproduce the published results or as a starting point for future investigations. The standard protocol for transporting reagents such as cDNAs, however, requires researchers to ship either transformed E. coli or clones in tubes or microtiter plates, a process both expensive and laborious. Hayashizaki’s innovation, which he dreamed up in 1995 upon taking the reins of RIKEN’s mouse genome encyclopedia initiative, was to immobilize cDNAs onto water-soluble paper, and print a book containing RIKEN’s entire collection of mouse cDNAs, which now number more than 60,000.
Thus far Hayashizaki’s group has printed just one book containing all the 60,000 clones — but the process wasn’t easy. First his group experimented with different types of water-soluble paper to find one thin enough to bind into a book of reasonable size, and of sufficient quality to ensure the integrity of the clones over the long term. Then, in order to complete the first DNA Book in time to coincide with the April 14 announcement that the Human Genome Project was complete, Hayashizaki had several members of his group spend two months manually “stamping” clones into spots on the pages of the book with a 96-pin tool, he says.
“Actual printing and DNA printing are totally different,” he says. “Usually, you have four colors of inks, but in this case, we had to print 60,000 DNA inks. People used multiple needles like stamps,” he adds. “Stamp, stamp, stamp!” The result, he says, was a bound, two-centimeter-thick book containing 120,000 spots — each of 60,000 clones printed in duplicate.
Although Hayashizaki applied for a patent on the technique in 1995 — he was awarded a US patent in 2001 — only in the past year has his group attempted to conduct a large-scale trial of how effective the DNA Book could be at safely distributing research-quality clones. In April, Hayashizaki published a paper in Genome Research describing the DNA Book, and every copy of the journal included a sheet printed with 12 cDNA plasmids of genes involved in the Krebs cycle. In the paper, Hayashizaki encouraged researchers to try amplifying the clones using PCR, and report back via a customized website whether the clones survived their journey intact.
So far, feedback has been positive, Hayashizaki says. While he plans to wait another two months to give researchers additional time to test out his printed clones, his own group has received two copies of the journal, and is checking to see if they can amplify those clones without a hitch. “Because we haven’t received reprints, we couldn’t do multiple trials,” he adds. His group has shown that the clones remain stable at least six months after printing, and Hayashizaki says in theory the printed clones should last for a year.
Over the next few months, Hayashizaki’s group plans to finish developing an automated printer capable of churning out 200 DNA books by early next year — not to mention saving his group members from stamping out cDNAs all day. At that point, he plans to hand over responsibility for producing and distributing the books to Dnaform, a RIKEN spin-off that will sell the books at cost to interested researchers.
One more problem remains, at least for US researchers, Hayashizaki hastens to add. Invitrogen has laid claim to the cDNA clones Dnaform hopes to distribute in DNA books, based on a US patent covering the reverse transcriptase that RIKEN used to convert the mouse mRNAs into their complementary cDNAs. Dnaform and Invitrogen failed to agree on the terms of a commercial license, and pending the final result of a court battle between Invitrogen and BD Biosciences Clontech, Dnaform may have difficulty legally distributing the DNA books in the US.
“RIKEN hopes everyone uses [the DNA books],” Hayashizaki says, “but we don’t know what will happen, and Dnaform is very cautious about distributing to the USA.”