相关实验视频

Updated: Jan 12, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

mtDeOxoGer:一种基于机器学习的策略,有效过高通量mtDNA测序数据中的氧化损伤引起的人工突变

Shanshan Guo¹, Shengjing Li², Tianlei Sun³

¹State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, 710032, China; Translational Medicine Center, Clinical Experimental Center, Shaanxi Provincial People's Hospital and Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, 710032, China.

Free radical biology & medicine

|November 3, 2025

概括

线粒体DNA (mtDNA) 测序精度得到了新的机器学习工具的改进,该工具可以过氧化损伤文物. 这种方法提高了在癌症研究中检测真实mtDNA突变的可靠性.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

线粒体DNA (mtDNA) 突变在瘤中很常见,下一代测序 (NGS) 增强了检测.
氧化工件,特别是超声波DNA碎片化的氧化工件,通过模仿低频突变来损害mtDNA NGS的准确性.
氧化损伤对mtDNA测序的影响比核DNA的理解要少.

研究的目的:

系统地评估mtDNA NGS数据中的氧化损伤文物.
开发一种机器学习策略,以提高mtDNA突变检测的准确性.
在mtDNA库准备中识别氧化工件的来源.

主要方法:

对私人和公共mtDNA NGS数据集的分析,重点关注8-oxoguanine病变.
超声波DNA碎片化参数和基于酶的碎片化的实验验证.
开发和应用一个逻辑回归模型 (mtDeOxoGer) 结合变异性等位基因频率,链方向偏差,GC含量和序列上下文.

主要成果:

低频率的C>A和G>T替代被确定为mtDNA NGS中常见的工件.
超声波碎片被证实是氧化工件的主要来源,受温度,强度和周期数的影响.
该mtDeOxoGer模型有效地区分了真实的mtDNA突变和氧化工件.

结论:

完善mtDNA测序方法对于准确的遗传研究至关重要.
开发的机器学习策略为提高mtDNA突变检测可靠性的实际框架.
这种方法支持更可靠的线粒体遗传学研究癌症和其他疾病.

关键词:

机器学习机器学习线粒体DNA是线粒体的DNA.这是下一代测序.氧化工艺品的氧化工艺品超声波碎片化的超声波

更多相关视频

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution

Author Spotlight: High-Throughput Image-Based Quantification of Mitochondrial DNA Synthesis and Distribution

Published on: May 5, 2023

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

Published on: February 10, 2023

相关概念视频

Mismatch Repair

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...

Mismatch Repair

Mismatch Repair

Spontaneous and Induced Mutations

Spontaneous and Induced Mutations

Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).

Nucleotide Excision Repair

Nucleotide Excision Repair

DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...