Ancient DNA laboratories address this problem through specific design features and protocols. Physical isolation from the main laboratory building, with positive-pressure air systems to prevent outside air from entering. Dedicated staff who do not work in other DNA laboratories. Full-body protective equipment — gloves, masks, coveralls — worn by everyone entering the facility. Bleach decontamination of all surfaces and equipment. Blank controls processed alongside specimens to detect any contamination that makes it through the other safeguards.
The specific analytical approaches used for ancient DNA also differ from those used in standard forensic contexts. Because ancient DNA is typically present in very short fragments — sequences of perhaps 50 to 100 base pairs rather than the thousands or tens of thousands present in fresh samples — the standard amplification and sequencing methods used in forensic DNA analysis need to be adapted or replaced. Next-generation sequencing technologies, which can sequence millions of short DNA fragments simultaneously, have transformed ancient DNA research in the twenty-first century, allowing researchers to work with DNA quality that would have been unusable with earlier methods.
For the Fitzjames identification, the specific analytical target was the Y chromosome. Y-chromosome profiling from ancient specimens requires recovering sufficient Y-chromosome-specific sequences to characterize the Y-chromosome lineage — the specific set of Y-chromosome variants that identify the paternal line from which the specimen came. This can be done through targeted sequencing approaches that specifically amplify Y-chromosome sequences, or through broad sequencing approaches that capture all DNA present and then identify the Y-chromosome-specific portions computationally.
The comparison against Nigel Gambier’s Y-chromosome profile used the same kind of Y-chromosome markers to establish whether the two profiles were consistent with shared paternal-line ancestry. Finding that the profiles matched — that the specimen and the living man shared the same Y-chromosome variants — was the central finding that supported the identification.