Extended kinship analysis of historical remains using SNP capture
Extended kinship analysis of historical remains using SNP capture
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DOI：
10.1016/j.fsigen.2021.102636
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发表时间：
2022-03-01
影响因子：
3.1
通讯作者：
Marshall, Charla
中科院分区：
文献类型：
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作者：
Gorden, Erin M.;Greytak, Ellen M.;Marshall, Charla
DNA辅助鉴定历史遗迹需要对高度降解的DNA进行遗传分析，并与已知亲属的DNA进行比较。这可以通过使用适用于降解的骨骼样本的杂交捕获和下一代测序方法来针对单核苷酸多态(SNPs)来实现。在本研究中，设计了两个SNP捕获面板，分别针对类似于25000(25K)和类似于95000(95K)核SNP，以实现远亲关系估计(最高可达四级亲属)。使用Illumina MiSeq台式测序仪，在死后75年成功地从14个骨骼元素中恢复了低覆盖率的SNP数据。所有样本都含有降解的DNA，但质量不同，14个样本的平均片段长度从32bp到170bp不等。在Parabon FX法医分析平台上进行SNP与已知家系参考DNA的比较，该平台使用一种针对胞嘧啶脱氨基的低覆盖率测序数据进行优化的似然方法进行亲属关系预测。25K小组平均产生了15,000个SNP，这使得在21个配对比较中的16个中，有16个能够进行准确的亲属关系预测，并获得了强大的统计支持。95K小组将平均SNP增加到42,000个，并在强大的统计支持下获得了额外的准确的亲属关系预测(21个配对比较中的17个)。这项研究表明，SNP捕获与台式平台上的大规模并行测序相结合，可以从受损样本中产生足够的SNP恢复，从而实现准确的、扩展的亲属关系预测。
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 similar to 25,000 (25 K) and similar to 95,000 (95 K) nuclear 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 using an Illumina MiSeq benchtop sequencer. All samples contained degraded DNA but were of varying quality with mean fragment lengths ranging from 32 bp to 170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fx Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with cytosine deamination. The 25 K panel produced 15,000 SNPs on average, which allowed for accurate kinship prediction with strong statistical support in 16 of the 21 pairwise comparisons. The 95 K panel increased the average SNPs to 42,000 and resulted in an additional accurate kinship prediction with strong statistical support (17 of 21 pairwise comparisons). This study demonstrates that SNP capture combined with massively parallel sequencing on a benchtop platform can yield sufficient SNP recovery from compromised samples, enabling accurate, extended kinship predictions.