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Hybridization capture and low-coverage SNP profiling for extended kinship analysis and forensic identification of historical remains

Erin M. Gorden, Ellen M. Greytak, View ORCID ProfileKimberly Sturk-Andreaggi, Janet Cady, Timothy P. McMahon, Steven Armentrout, View ORCID ProfileCharla Marshall
doi: https://doi.org/10.1101/2020.09.17.300715
Erin M. Gorden
1Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA
2SNA International LLC, Alexandria, Virginia, USA
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Ellen M. Greytak
3Parabon NanoLabs, Inc., Reston, Virginia, USA
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Kimberly Sturk-Andreaggi
1Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA
2SNA International LLC, Alexandria, Virginia, USA
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  • ORCID record for Kimberly Sturk-Andreaggi
Janet Cady
3Parabon NanoLabs, Inc., Reston, Virginia, USA
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Timothy P. McMahon
1Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA
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Steven Armentrout
3Parabon NanoLabs, Inc., Reston, Virginia, USA
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Charla Marshall
1Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA
2SNA International LLC, Alexandria, Virginia, USA
4Forensic Science Program, The Pennsylvania State University, State College, Pennsylvania, USA
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  • ORCID record for Charla Marshall
  • For correspondence: charla.k.marshall.ctr@mail.mil
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Abstract

DNA-assisted identification of historical remains requires the genetic analysis of highly degraded DNA, along with a comparison to DNA from known relatives. This can be achieved by targeting single nucleotide polymorphisms (SNPs) using a hybridization capture and next-generation sequencing approach suitable for degraded skeletal samples. In the present study, two SNP capture panels were designed to target ∼25,000 (25K) and ∼95,000 (95K) autosomal SNPs, respectively, to enable distant kinship estimation (up to 4th degree relatives). Low-coverage SNP data were successfully recovered from 14 skeletal elements 75 years postmortem, with captured DNA having mean insert sizes ranging from 32-170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fχ Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with DNA damage. The 25K and 95K panels produced 15,000 and 42,000 SNPs on average, respectively allowing for accurate kinship prediction in 17 and 19 of the 21 pairwise comparisons. Whole genome sequencing was not able to produce sufficient SNP data for accurate kinship prediction, demonstrating that hybridization capture is necessary for historical samples. This study provides the groundwork for the expansion of research involving compromised samples to include SNP hybridization capture.

Author Summary Our study evaluates ancient DNA techniques involving SNP capture and Next-Generation Sequencing for use in forensic identification. We utilized bone samples from 14 sets of previously identified historical remains aged 70 years postmortem for low-coverage SNP genotyping and extended kinship analysis. We performed whole genome sequencing and hybridization capture with two SNP panels, one targeting ∼25,000 SNPs and the other targeting ∼95,000 SNPs, to assess SNP recovery and accuracy in kinship estimation. A genotype likelihood approach was utilized for SNP profiling of degraded DNA characterized by cytosine deamination typical of ancient and historical specimens. Family reference samples from known relatives up to 4th degree were genotyped using a SNP microarray. We then utilized the Parabon Fχ Forensic Analysis Platform to perform pairwise comparisons of all bone and reference samples for kinship prediction. The results showed that both capture panels facilitated accurate kinship prediction in more than 80% of the tested relationships without producing false positive matches (or adventitious hits), which were commonly observed in the whole genome sequencing comparisons. We demonstrate that SNP capture can be an effective method for genotyping of historical remains for distant kinship analysis with known relatives, which will support humanitarian efforts and forensic identification.

Competing Interest Statement

Steven Armentrout, Ellen McRae Greytak, and Janet Cady are employees of Parabon NanoLabs, Inc., the developer and commercial vendor of the Parabon Fχ Forensic Analysis Platform.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Posted September 18, 2020.
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Hybridization capture and low-coverage SNP profiling for extended kinship analysis and forensic identification of historical remains
Erin M. Gorden, Ellen M. Greytak, Kimberly Sturk-Andreaggi, Janet Cady, Timothy P. McMahon, Steven Armentrout, Charla Marshall
bioRxiv 2020.09.17.300715; doi: https://doi.org/10.1101/2020.09.17.300715
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Hybridization capture and low-coverage SNP profiling for extended kinship analysis and forensic identification of historical remains
Erin M. Gorden, Ellen M. Greytak, Kimberly Sturk-Andreaggi, Janet Cady, Timothy P. McMahon, Steven Armentrout, Charla Marshall
bioRxiv 2020.09.17.300715; doi: https://doi.org/10.1101/2020.09.17.300715

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