Extended kinship analysis of historical remains using SNP capture

Area of Science:

• Forensic Science
• Genetics
• Anthropology

Background:

• DNA analysis of historical remains is crucial for identification.
• Degraded DNA from skeletal samples presents significant analytical challenges.
• Existing methods may struggle with low-quality DNA and distant kinship estimation.

Purpose of the Study:

• To evaluate the efficacy of SNP capture and next-generation sequencing for kinship analysis in ancient DNA.
• To assess the performance of two SNP panels (25K and 95K) for distant relative identification.
• To determine the feasibility of using benchtop sequencing for forensic genetic applications.

Main Methods:

• Design and application of two SNP capture panels (~25,000 and ~95,000 SNPs).
• Targeted enrichment of nuclear SNPs using hybridization capture.
• Low-coverage, massively parallel sequencing on an Illumina MiSeq platform.
• Kinship analysis using the Parabon Fx Forensic Analysis Platform with a likelihood approach.

Main Results:

• Successful recovery of low-coverage SNP data from 14 skeletal elements up to 75 years postmortem.
• Degraded DNA samples with mean fragment lengths from 32 bp to 170 bp were analyzed.
• The 25K panel yielded ~15,000 SNPs, enabling accurate kinship prediction in 16/21 comparisons.
• The 95K panel yielded ~42,000 SNPs, improving accurate predictions to 17/21 comparisons.

Conclusions:

• SNP capture combined with benchtop sequencing effectively recovers genetic data from compromised skeletal samples.
• This approach enables accurate and statistically supported distant kinship predictions.
• The methodology is suitable for forensic applications involving historical remains and degraded DNA.