利用有腐烂迹象和无腐烂迹象个体的头骨样本进行分子年龄预测:结合翻译后蛋白质修饰和 DNA 甲基化分析的多元方法

IF 2.2 3区 医学 Q1 MEDICINE, LEGAL
J. Becker, V. Bühren, L. Schmelzer, A. Reckert, S. B. Eickhoff, S. Ritz, J. Naue
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引用次数: 0

摘要

对于身份不明的尸体,预测死者死亡时的年龄可以提供重要信息。在这种情况下,方法的可能性取决于组织的可用性,因为在正常环境条件下,骨骼会因矿化而保存很长时间。DNA 甲基化(DNAm)随年龄的变化以及喷托苷(Pen)和 D-天冬氨酸(D-Asp)的积累可能是预测年龄的有用分子标记。将这些分子钟结合到一个年龄预测模型中似乎有利于最大限度地减少个体间和个体内的差异。因此,我们开发了(I)基于这三种分子钟的年龄预测模型,(II)研究了通过组合来提高年龄预测的效果,(III)研究了是否也可以使用这三种分子钟来检测有腐烂迹象的样本。从死者身上采集颅骨以获得一个训练数据集(n = 86)和两个独立测试集(无腐烂迹象:n = 44,有腐烂迹象:n = 48)。使用大规模平行测序(MPS)分析了ELOVL2、KLF14、PDE4C、RPA2、TRIM59和ZYG11A中6个CpG位点的DNAm。采用高效液相色谱法(HPLC)分析了 D-Asp 和 Pen 的含量。根据脊回归法建立的年龄预测模型得出,测试集中的平均绝对误差(MAEs)/均方根误差(RMSE)分别为 5.5 年/6.6 年(DNAm)、7.7 年/9.3 年(Pen)和 11.7 年/14.6 年(D-Asp)。不难发现,DNAm、D-Asp 和 Pen 模型在分解尸体样本中的准确度普遍较低(MAE:7.4-11.8 年,RMSE:10.4-15.4 年)。准确性降低的原因可能是对每种分子钟有不同影响的多种因素。为了确认分解引起的一般变化,一个以分解样本为训练集的可能年龄预测试验模型提高了留空交叉验证的准确性(MAE:6.6-12 年,RMSE:8.1-15.9 年)。在没有分解迹象的测试集上,将所有三种分子年龄钟结合起来得出的 MAE 和 RMSE 结果与单纯的 DNA 甲基化分析结果相当。不过,对于分解样本,将所有三个时钟结合在一起的结果可能会有所改善,尤其是在分解程度很高而 DNA 含量很低的样本中出现异常值时,可以减少偏差。结果表明,在特定情况下对不同分子钟进行组合分析具有普遍的潜力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Molecular age prediction using skull bone samples from individuals with and without signs of decomposition: a multivariate approach combining analysis of posttranslational protein modifications and DNA methylation

Molecular age prediction using skull bone samples from individuals with and without signs of decomposition: a multivariate approach combining analysis of posttranslational protein modifications and DNA methylation

The prediction of the chronological age of a deceased individual at time of death can provide important information in case of unidentified bodies. The methodological possibilities in these cases depend on the availability of tissues, whereby bones are preserved for a long time due to their mineralization under normal environmental conditions. Age-dependent changes in DNA methylation (DNAm) as well as the accumulation of pentosidine (Pen) and D-aspartic acid (D-Asp) could be useful molecular markers for age prediction. A combination of such molecular clocks into one age prediction model seems favorable to minimize inter- and intra-individual variation. We therefore developed (I) age prediction models based on the three molecular clocks, (II) examined the improvement of age prediction by combination, and (III) investigated if samples with signs of decomposition can also be examined using these three molecular clocks. Skull bone from deceased individuals was collected to obtain a training dataset (n = 86), and two independent test sets (without signs of decomposition: n = 44, with signs of decomposition: n = 48). DNAm of 6 CpG sites in ELOVL2, KLF14, PDE4C, RPA2, TRIM59 and ZYG11A was analyzed using massive parallel sequencing (MPS). The D-Asp and Pen contents were analyzed by high performance liquid chromatography (HPLC). Age prediction models based on ridge regression were developed resulting in mean absolute errors (MAEs)/root mean square errors (RMSE) of 5.5years /6.6 years (DNAm), 7.7 years /9.3 years (Pen) and 11.7 years /14.6 years (D-Asp) in the test set. Unsurprisingly, a general lower accuracy for the DNAm, D-Asp, and Pen models was observed in samples from decomposed bodies (MAE: 7.4–11.8 years, RMSE: 10.4–15.4 years). This reduced accuracy could be caused by multiple factors with different impact on each molecular clock. To acknowledge general changes due to decomposition, a pilot model for a possible age prediction based on the decomposed samples as training set improved the accuracy evaluated by leave-one-out-cross validation (MAE: 6.6–12 years, RMSE: 8.1–15.9 years). The combination of all three molecular age clocks did reveal comparable MAE and RMSE results to the pure analysis of the DNA methylation for the test set without signs of decomposition. However, an improvement by the combination of all three clocks was possible for the decomposed samples, reducing especially the deviation in case of outliers in samples with very high decomposition and low DNA content. The results demonstrate the general potential in a combined analysis of different molecular clocks in specific cases.

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来源期刊
CiteScore
5.80
自引率
9.50%
发文量
165
审稿时长
1 months
期刊介绍: The International Journal of Legal Medicine aims to improve the scientific resources used in the elucidation of crime and related forensic applications at a high level of evidential proof. The journal offers review articles tracing development in specific areas, with up-to-date analysis; original articles discussing significant recent research results; case reports describing interesting and exceptional examples; population data; letters to the editors; and technical notes, which appear in a section originally created for rapid publication of data in the dynamic field of DNA analysis.
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