P121 – Pushing the Boundaries of Kinship Inference: High-Density SNP Profiling of 400-Year-Old Skeletal Remains.

16:19

Wednesday August 19^th

Station 07

Duration: 12 minutes

03. Human identification

Isabel Navarro Vera

Introduction

The generation of DNA profiles from historical skeletal remains is a core challenge in forensic genetics due to diagenesis and severe fragmentation. Traditional STR analysis often fails as it requires relatively long DNA fragments. This study demonstrates how Massively Parallel Sequencing (MPS) with short-amplicon SNP panels can overcome these limitations to resolve complex genealogical structures in archaeological contexts where commingled remains are present.

Materials and Methods

Skeletal remains from the 16th to 18th centuries were recovered from a family crypt in Gelves, Spain. Anthropological analysis determined the Minimum Number of Individuals (MNI) at 12. DNA from selected bone samples was extracted and sequenced using the ForenSeq® Kintelligence HT kit (10,230 kinship-informative SNPs), specifically optimized for degraded material with 97.8% of amplicons below 150 bp. The present work focuses on four of the 12 individuals (I4, I13, I21, and I22) with a post-mortem interval range of ~200 years.

Results

Sequencing performance showed a direct correlation between DNA quality and read depth. Samples with better DNA yield exhibited the highest coverage, with >80% of alleles exceeding 50x read depth. Although lower concentrated samples showed lower metrics, over 70% of SNPs maintained >20x coverage. Overall, an average of 88% of markers achieved a coverage >20x, ensuring high genotype call confidence. These profiles successfully resolved a four generation pedigree, with kinships ranging from a Mother/Son relationship between I21 and I22 with an log10LR= 452.63; to a Great-grandfather/Great-grandson dyad between I13 and I4 (log10LR 42.63). Y-chromosome SNPs confirmed a shared patrilineage for the male individuals, while X-chromosome analysis validated maternal links, effectively mitigating kinship overestimation derived from sister allele dropout, typically found in degraded samples.

Conclusion

This research confirms that forensic SNP-based workflows can achieve a level of confidence in archaeological material comparable to contemporary casework. By reconstructing a four-generation pedigree from 400-year-old remains, this study represents a qualitative leap in historical bioarchaeology, demonstrating the power of FIGG to resolve identities in complex historical burials.

Beyond archaeology, this study provides a powerful proof-of-concept for the forensic identification of severely compromised remains in modern cold cases and missing persons investigations.

Authors

Isabel Navarro-Vera (Citogen, Spain)
Alba Hernández-Maza (Citogen, Spain)
Carmen García (Indepenent researcher, Spain)

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P121 – Pushing the Boundaries of Kinship Inference: High-Density SNP Profiling of 400-Year-Old Skeletal Remains.

Introduction

Materials and Methods

Results

Conclusion

Authors

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