评估开源罕见变异分析管道的功能和可用性
Cristian Riccio1,2, Max L Jansen1,2, Felix Thalén1,2
1Cardio-CARE, Medizincampus Davos, Herman-Burchard-Str. 12, 7265 Davos Wolfgang, Switzerland.
Briefings in bioinformatics
|February 5, 2025
概括
分析罕见的遗传变异是复杂的. 本次审查确定了17个管道,并建议使用STAARpipeline,REGENIE,Ravages和OrdinalGWAS等特定工具进行不同的复杂特征遗传分析.
科学领域:
- 遗传学和基因组学 在
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 大规模测序研究越来越多地发现罕见的遗传变异.
- 稀有变异对于理解复杂的特征至关重要,但难以通过计算分析.
- 缺乏全面的概述阻碍了选择适当的罕见变异分析工具.
研究的目的:
- 系统地审查和评估可用的开源罕见变异分析管道.
- 为研究人员提供关于选择适合其特定遗传分析的工具的指导.
- 确定未来管道开发的差距和机会.
主要方法:
- 在MEDLINE和谷歌学者的系统文献搜索,截至2023年11月27日.
- 包括接受队列/病例控制基因型数据和分组变异的开源管道.
- 根据功能和可用性标准对17条已确定管道进行评估.
主要成果:
- 确定了17个罕见变异分析管道,支持各种特征类型,关联测试和变异权重方案.
- 目前没有单一的管道为所有数据类型提供全面的可扩展性和灵活性.
- 建议使用特定的管道:STAARpipeline (用户友好),REGENIE (可扩展,可维护),Ravages (多项式特征) 和OrdinalGWAS (顺序性特征).
结论:
- 目前罕见变异分析管道的景观是多样化的,没有一个适合所有人的解决方案.
- 工具的选择应以特定的分析需求,特征类型和所需的可扩展性为指导.
- 需要开发一个高度灵活,可扩展和用户友好的管道,以充分利用罕见变体来发现复杂的特征.
更多相关视频
09:34Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
33.5K
04:58Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
Published on: December 13, 2024
2.1K
相关概念视频
Single Pipe Systems
In pipe flow analysis, problems are typically categorized into three types — Type I, Type II, and Type III — based on the known parameters and the desired outcome. Each type of problem addresses specific engineering requirements using fluid properties, pipe characteristics, and operational conditions.
In a Type I problem, fluid properties (density and viscosity), pipe characteristics (including diameter, length, and surface roughness), and the flow rate or average velocity are known. The...
In a Type I problem, fluid properties (density and viscosity), pipe characteristics (including diameter, length, and surface roughness), and the flow rate or average velocity are known. The...
Multiple Pipe Systems
Multipipe systems consist of complex configurations of interconnected pipes designed to transport fluids efficiently across intricate networks. They are essential in engineering applications requiring precise control over flow distribution, pressure, and head loss. They are categorized into series, parallel, loop, and network configurations, each distinguished by unique flow characteristics and applications.
Series Configuration
In a series configuration, fluid flows sequentially from one pipe...
Series Configuration
In a series configuration, fluid flows sequentially from one pipe...
Design Example: Analyzing Capacity Contours for Flood Risk Assessment
Flood risk assessment involves careful planning and analysis to ensure the safety of communities near water retention structures. Capacity contours are a vital tool in this process, as they illustrate the potential spread of water at specific levels in a given area. In the context of building a bund across a small valley, these contours play a critical role in evaluating the safety of nearby residential areas.In this example, the bund is intended to store stormwater in the valley. The engineers...
Methods to Assess Microbial Communities
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
