Staying clean

Left: José-Manuel Benito / wikimedia.org

User:
Noreen Tuross, Harvard University, Cambridge, Mass.

Project:
Using genetic techniques to establish relationships among ancient hominids.

Problem:
Almost all the DNA in archeological samples is rife with contamination — bacterial, fungal, or just plain unidentified. Avoiding amplification of human DNA, either from other samples or from lab personnel, can be a challenge.

Solution:
Tuross uses a combination of precautions and double-checks to minimize incidences of artifactual DNA becoming data. "Because of the way we have to do PCR in ancient samples — which is low annealing temperatures, high cycle numbers, and sometimes a lot of Taq — that's sort of a recipe for brewing up a contaminant," notes Tuross.

Using a HEPA-filtered clean room, Tuross' lab extracts DNA from ancient artifacts such as bones. From there, the DNA samples are brought to a separate building for amplification and sequencing. "And the amplicand never, ever comes back into the lab," she explains, noting that this is standard procedure in "more serious" laboratories.

Beyond such physical preventives, analysis is also a key safeguard: Sequences should be compared to databases to be sure they're of the anticipated taxonomic group. Morever, and perhaps counter-intuitively, you shouldn't be able to amplify long pieces because the DNA is usually too damaged. If you get sequences of more than 50—200 bases, "it's probably not real," Tuross says.

Cost:
The PCR itself uses standard off-the-shelf reagents, but building and maintaining the clean room bumps up the costs.