The core technique was autosomal SNP analysis: examining hundreds of thousands of positions across the full genome where individual people carry different genetic variants. When an unknown person’s autosomal profile is compared against the profiles in a large database of voluntarily submitted profiles, the comparison can identify people who share significant amounts of genetic material — biological relatives who share a common ancestor.
The relationships revealed by autosomal SNP matching follow predictable patterns. A parent and child share approximately fifty percent of their DNA. First cousins share approximately twelve percent. Second cousins share approximately three percent. Third cousins share less than one percent, but the sharing is still detectable and distinguishable from background noise in a well-characterized analysis. Even more distant relatives can sometimes be identified if the database is large enough and the profile quality is high enough.
The challenge with the Chandler sample was that the quality was not high. Fourteen years of paraffin storage had degraded the DNA to the point where only approximately seven percent of the genome remained readable. Entire chromosomes were absent from the recoverable data. The standard implementation of autosomal SNP analysis for forensic genealogy purposes — which had been developed on cases with much better-preserved samples — could not simply be applied.
The DNA Doe Project adapted. They conducted multiple rounds of sequencing on the available material, extracting as much genetic information as possible from each run and then combining the results mathematically to produce the best possible composite profile. They worked with the degraded data carefully, applying statistical methods to distinguish genuine genetic variants from sequencing artifacts that the damaged material might produce.