Joachim Messing, who tends to get pointed out at conferences by admiring colleagues as “the M13 guy” thanks to his early work with the DNA phage for cloning and sequencing applications, is back in the genomics fray with a new, highly accurate approach to fingerprinting.
In particular for genomes where someone might not have resources to sequence the whole thing, Messing, director of the Waksman Institute at Rutgers University, recommends fingerprinting as a good way to get plenty of information. And with work he and his lab have done recently, the method is getting even faster and more accurate: Messing has converted much of his own fingerprinting work to capillary machines — the ABI 3700, for starters, though he’s hoping to move to the 3730 to take advantage of the longer reads — to avoid the distortions common in gels.
“The precision in the capillary is much, much higher,” Messing says, “and doesn’t need human interference.” His team has been working on the maize genome with this approach, made possible with a custom reagent kit from ABI.
Capillary fingerprinting makes the process faster and cleaner, but it can also save money. “It’s much more expensive to get genetic markers,” Messing says, pointing out that for his genetic map of maize, he got by with just a few thousand markers and wound up with 25X to 30X coverage in about eight months. The project finished up early this year, and Messing says that the data look promising, although he hasn’t gone through all the results exhaustively yet. Using the 3700 allowed Messing’s team to “pull in … more of the singletons,” he adds.
Messing is already looking for a new reagent kit from ABI so he can upgrade his fingerprinting work to the 3730. That would offer a better spread of band sizes, he says.
The technique can be used by anybody, but Messing says it makes the most sense for people who already have access to the instruments. “It’s probably not efficient if you don’t have the equipment,” he says. And, he adds, it’s not worthwhile for all genomes — using whole-genome shotgun is still a good alternative, he says, for cases where the fingerprint map isn’t critical.
— Meredith Salisbury