The entire field of ancient DNA research is built around the challenge of demonstrating that the sequences recovered represent the ancient individual and not the modern researchers who handled the material.

In the mid-1990s, the methods for managing this contamination challenge were still being developed.

Researchers used several approaches: working in dedicated cleanrooms where modern DNA was minimized through air filtration and surface decontamination; amplifying the same region of the ancient genome multiple times from independent extractions to confirm that the results were consistent; analyzing known modern DNA sequences as controls; and examining the results for the specific chemical damage patterns that authentic ancient DNA shows but modern contamination does not.

The Stone and Stoneking analysis applied these precautions to the Hourglass Cave material.