MixDeR:用于法医遗传谱系的SNP混合解卷工作流
Rebecca Mitchell1, Michelle Peck2, Erin Gorden2
1National Bioforensic Analysis Center, National Biodefense Analysis and Countermeasures Center, Operated by Battelle National Biodefense Institute for the US. Department of Homeland Security Science and Technology Directorate, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
Forensic science international. Genetics
|January 25, 2025
概括
MixDeR是一个新的R包和Shiny应用程序,可以解构混合单核酸多态 (SNP) 配置文件. 这使得两人混合物可以用于法医遗传谱系 (FGG) 应用.
科学领域:
- 法医科学 法医科学 法医科学
- 遗传学 是一个遗传学.
- 生物信息学是一种生物信息学.
背景情况:
- 下一代测序 (NGS) 能够使用单核酸多态 (SNP) 进行法医DNA分析.
- 法医遗传谱系 (FGG) 应用越来越重要,但在混合DNA样本方面面临着挑战.
- 目前的FGG算法主要设计用于单个来源的配置文件,限制了复杂的法医样本的分析.
研究的目的:
- 开发一个计算工作流程来解构FGG的混合SNP配置文件.
- 为了在法医案例工作中分析两个人的DNA混合物.
- 为扩大FGG能力的实验室创建一个用户友好的工具.
主要方法:
- 开发了MixDeR,一个R包和SNP配置文件解卷的Shiny应用程序.
- 集成的MixDeR与ForenSeq Kintelligence®基因型数据和EuroForMix (EFM) 进行解卷.
- 过的EFM输出生成与GEDmatch® PRO兼容的单源基因型.
- 包括用于工作流测试和验证的可选指标.
主要成果:
- MixDeR成功地解卷了两个人的SNP混合物.
- 工作流产生推断的单源基因型,格式为FGG数据库搜索.
- R包和Shiny应用程序为实验室提供了一个灵活的离线解决方案.
- 可选的验证指标有助于评估工作流的性能.
结论:
- 通过分析混合DNA样本,MixDeR提高了FGG的实用性.
- 该工具可用于具有不同级别生物信息专业知识的实验室.
- MixDeR支持在案例工作中扩展法医遗传谱系应用.
相关概念视频
Comparing Copy Number Variations and SNPs
17.1K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.1K
Single Nucleotide Polymorphisms-SNPs
13.9K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
13.9K
Genome-wide Association Studies-GWAS
12.4K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
12.4K


