利用新一代测序(NGS)数据对常染色体 STR 等位基因进行序列分析和二级结构预测

IF 0.5 Q4 GENETICS & HEREDITY Human Gene Pub Date : 2024-03-04 DOI:10.1016/j.humgen.2024.201274
Hirak Ranjan Dash, Akash Ranga
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引用次数: 0

摘要

NGS 技术在法医 DNA 分析中的应用探索了 STR 标记中基于序列的等位基因。这样就可以对观察到的 STR 等位基因序列进行深入分析,以了解其性质、稳定性、遗传性以及在分析过程中可能产生的人工痕迹。本研究利用 NGS 技术对 20 个 STR 标记的 100 个等位基因序列进行了序列拓扑分析和二级结构预测。在本研究使用的 20 个 STR 标记中观察到的等位基因的 G + C 含量从 58.65 ± 1.367% (D2S1338) 到 7.62 ± 0.844% (D12ATA63)不等。发现 FGA 的单株平均精确质量和对株平均精确质量最高(25,963.248 ± 1623.271;27,501.720 ± 1712.691),而 D4S2408 产生的单株精确质量和对株精确质量最低(11,136.354 ± 1521.757;11,582.021 ± 1585.486)。不出所料,没有一个 STR 标记显示存在开放阅读框、密码子和 CRISPR 序列。三个 STR 标记(即 D2S1338、TH01 和 D5S2800)显示存在 Cac8I、TspGWI、TspDTI、AccI 和 Hpy8I 酶的限制位点。系统进化分析表明,D12ATA63 和 D19S433 标记之间的等位基因密切相关。在 D2S1338 的等位基因上预测出了稳定的假结,其平均能量为-0.76,假结中出现的核苷酸数最多,为 21.33,这表明该标记更容易产生扩增伪影。
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Sequence analysis and secondary structure prediction of autosomal STR alleles using next generation sequencing (NGS) data

The inception of NGS technology in forensic DNA analysis explores the sequence-based alleles in STR markers. This allows the in-depth analysis of observed STR allelic sequences to understand their nature, stability, inheritance, and possible generation of artifacts during their analysis. In the current study, 100 allelic sequences at 20 STR markers generated using the NGS technique were analyzed for their sequence topographies and prediction of secondary structures. The G + C content of the alleles observed in 20 STR markers used in this study varied from 58.65 ± 1.367% (D2S1338) to 7.62 ± 0.844% (D12ATA63). The average exact mass of one stand and for the opposite stand mass was found to be highest in FGA (25,963.248 ± 1623.271; 27,501.720 ± 1712.691), whereas, D4S2408 generated the lowest exact mass of one stand and for the opposite stand mass (11,136.354 ± 1521.757; 11,582.021 ± 1585.486). As expected, none of the STR markers showed the presence of open reading frames, Codons, and CRISPR sequences. Three STR markers viz. D2S1338, TH01, and D5S2800 showed the presence of restriction sites for Cac8I, TspGWI, TspDTI, AccI, and Hpy8I enzymes. Phylogenetic analysis reveals the close association of alleles between the D12ATA63 and D19S433 markers. Stable pseudoknots were predicted at alleles of D2S1338 showing an average energy of −0.76 with the highest number of nucleotides present in the pseudoknots i.e., 21.33, suggesting this marker is more prone to generate amplification artifacts.

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来源期刊
Human Gene
Human Gene Biochemistry, Genetics and Molecular Biology (General), Genetics
CiteScore
1.60
自引率
0.00%
发文量
0
审稿时长
54 days
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