Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.
Forensic Sci Int Genet. 2012 May;6(3):341-9. doi: 10.1016/j.fsigen.2011.07.010. Epub 2011 Sep 9.
There is growing evidence that the histone-DNA complexes found in nucleosomes offer protection from DNA degradation processes, including apoptotic events in addition to bacterial and environmental degradation. We sought to locate human nucleosome regions and build a catalogue of SNPs sited near the middle of these genomic segments that could be combined into a single PCR multiplex specifically for use with extremely degraded human genomic DNA samples. Using recently optimized bio-informatics tools for the reliable identification of nucleosome sites based on sequence motifs and their positions relative to known promoters, 1395 candidate loci were collected to construct an 18-plex single base extension assay. Genotyping performance of the nucleosome SNPs was tested using artificially degraded DNA and 24 casework samples where the likely state of degradation of DNA was established by comparison to profile completeness in four other forensic assays: a standard 15-plex STR identification test, a miniaturized STR multiplex and two autosomal SNP multiplexes. The nucleosome SNP assay gave genotyping success rates 6% higher than the best existing forensic SNP assay: the SNPforID Auto-2 29-plex and significantly higher than the mini-STR assay. The nucleosome SNPs we located and combined therefore provide a new type of marker set that can be used to supplement existing approaches when the analysed DNA is likely to be extremely degraded and may fail to give sufficient STR genotypes for a reliable identification.
越来越多的证据表明，核小体中的组蛋白-DNA 复合物提供了对 DNA 降解过程的保护，包括凋亡事件，以及细菌和环境降解。我们试图定位人类核小体区域，并构建一个 SNP 目录，这些 SNP 位于这些基因组片段的中间附近，可组合成一个单一的 PCR 多重扩增，专门用于极度降解的人类基因组 DNA 样本。我们使用最近优化的生物信息学工具，根据序列基序及其相对于已知启动子的位置，可靠地识别核小体位点，收集了 1395 个候选基因座，构建了一个 18 重单碱基延伸测定法。通过使用人工降解 DNA 和 24 个案例样本测试核小体 SNP 的基因分型性能，这些案例样本的 DNA 降解状态是通过与其他四种法医分析的谱完整性进行比较来确定的：标准的 15 重 STR 识别测试、微型 STR 多重扩增和两个常染色体 SNP 多重扩增。核小体 SNP 分析的基因分型成功率比现有的最佳法医 SNP 分析（SNPforID Auto-2 29 重扩增）高出 6%，明显高于微型 STR 分析。因此，我们定位和组合的核小体 SNP 提供了一种新型的标记集，当分析的 DNA 可能极度降解且可能无法提供足够的 STR 基因型以进行可靠鉴定时，可以用于补充现有方法。
