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使用DADA2去除微型MPS数据,并将其应用于两人DNA混合分析

Ye-Lim Kwon¹, Jiwon Kim², Su Min Joo²

¹Department of Forensic Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.

Forensic science international. Genetics

|May 10, 2025

概括

使用Divisive Amplicon Denoising Algorithm 2 (DADA2) 的计算错误纠正显著降低了微haplotype (microhap) 大规模并行测序 (MPS) 数据中的噪声. 这提高了在法医DNA混合分析中检测小等位基因的准确性.

科学领域:

法医遗传学法医遗传学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

大规模并行测序 (MPS) 在法医遗传学中推进了微型 (microhap) 研究.
MPS数据包含PCR和测序错误,使得DNA混合物中小等位基因检测复杂化.
分割式片排斥算法2 (DADA2) 已被建立用于微生物片序列变体 (ASV) 推断,但在法医中未得到充分探索.

研究的目的:

评估DADA2在法医应用中对微型MPS数据的无效性.
评估DADA2无声化对单一来源和混合DNA样本的基因型一致性和降噪的影响.

主要方法:

开发了一个内部MPS面板,用于24个多用途的微软.
实施了一个基于DADA2的管道,用于删除微型MPS数据.
对单个来源 (1 ng DNA) 和两人DNA混合物 (不同比例,低至10 pg小DNA) 的评估消毒性能.

主要成果:

消毒将平均噪声从1.2%降低到0.1%,在单一来源样本中,基因型一致性为99.5%.
达达2与异合基因对抗,因单个基因而异.
DADA2管道在混合物中减少了噪声单元类型的10倍 (1:10到1:100的比率).
在1:100比率 (10 pg小DNA) 中,噪声在≤2个标记物中被检测出来.

结论:

基于DADA2的计算错误纠正显示了法医微型错误分析的巨大潜力.
排毒提高了检测小等位基因和估计复杂DNA混合物中的贡献者的准确性.
需要进一步精细化,以应对异合性等位基因中单个基因差异的挑战.

关键词:

计算错误的纠正 - 计算错误的纠正分析DNA混合物的分析.拒绝这种行为,就是拒绝.大规模并行测序.微型型是指微型型.

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