Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE 19902, USA.
SNA International, LLC (Contractor Supporting the AFMES-AFDIL), Alexandria, VA 22314, USA.
Genes (Basel). 2023 Apr 27;14(5):994. doi: 10.3390/genes14050994.
This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.
本研究评估了 DNA 定量在分析 SNPs、mtDNA 和 STR 靶标时预测历史样本成功的有用性。使用了六个历史背景下的 30 个埋葬样本，其死后年龄从 80 年到 800 年不等。样本经过文库制备和两个诱饵面板（FORCE 和线粒体基因组）的杂交捕获，以及 STR 分型（常染色体 STR 和 Y-STR）。尽管平均可映射片段范围从 55-125bp，但所有 30 个样本均产生了较小的（约 80bp）常染色体 DNA 靶标 qPCR 结果。qPCR 结果与 DNA 谱分析成功呈正相关。在 10X 覆盖度下，即使人类 DNA 输入低至 100pg，也有样本产生了 ≥80%的 FORCE SNPs。所有 30 个样本的线粒体基因组覆盖率均≥100X，尽管人类 DNA 输入较低（低至 1pg）。使用 PowerPlex Fusion，在人类 DNA 输入≥30pg 时，auSTR 基因座的检出率超过 40%。基于 Y-STR 靶标 qPCR 的输入≥24pg 时，至少可以恢复 59%的 Y-STR 基因座。结果还表明，人类 DNA 数量是预测成功的更好指标，而不是人类与外源性 DNA 的比例。qPCR 进行准确的定量是可行的，可用于历史骨骼样本，从而筛选提取物以预测 DNA 谱分析的成功。
