路径多基因风险评分 (pPRS) 用于分析基因环境相互作用
W James Gauderman1, Yubo Fu1, Bryan Queme2
1Division of Biostatistics, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA.
bioRxiv : the preprint server for biology
|January 7, 2025
概括
路径定义的多基因风险评分 (pPRS) 提高了对复杂疾病的基因环境相互作用的检测. 这种方法在特定的遗传途径中确定了NSAID使用和结直肠癌风险之间的显著相互作用.
科学领域:
- 遗传学和流行病学
- 癌症研究 癌症研究
- 药物基因组学 药物基因组学
背景情况:
- 多基因风险评分 (PRS) 汇总遗传变异以估计疾病风险.
- PRS和环境因素 (PRS × E) 之间的相互作用为疾病生物学和有针对性的预防提供了洞察力.
- 标准PRS可能会由于包含非相互作用变体而稀释相互作用信号.
研究的目的:
- 探索路径定义PRS (pPRS) 对于检测PRS×E相互作用的实用性.
- 调查PRS与非类固醇抗炎药物 (NSAID) 在结直肠癌 (CRC) 风险中的相互作用.
- 确定特定的遗传途径,参与NSAIDs对CRC的保护作用.
主要方法:
- 利用最先进的工具来注释基因变异到pPRS构建的基因组路径.
- 进行模拟以比较pPRS × E相互作用测试与标准PRS × E相互作用测试的功率.
- 分析了CRC的大型队列研究 (N=78,253),检查了NSAID使用和pPRS之间的相互作用.
主要成果:
- 模拟表明,针对性的pPRS × E相互作用测试比整体的PRS × E相互作用测试产生的功率大得多.
- 在CRC队列中没有观察到有意义的整体PRS × NSAID相互作用 (p=0.41).
- 在TGF-β / 淋巴腺激素释放激素受体 (GRHR) 途径内的SNP中确定了显著的pPRS × NSAID相互作用 (p=0.0003).
- 与风险较低的人 (OR=0.84在第五百分点PRS) 相比,NSAIDs在已识别的途径内具有更高遗传风险的个体中对CRC的保护作用增加 (OR=0.70在第95百分点PRS).
结论:
- 路径定义的PRS显著提高了检测基因与环境相互作用的能力.
- NSAIDs对CRC的保护作用是通过TGF-β/GRHR等遗传通路进行的.
- 针对特定途径中具有高遗传风险的个体,可以优化基于NSAID的CRC预防策略.
相关概念视频
Gene-Environment Interactions
248
Gene expression is a dynamic process that is significantly influenced by environmental factors. This interaction underlies the complex nature of biological development and the phenotypic differences observed among individuals, even among those with identical genetic makeups. Factors such as radiation, temperature, behavior, nutrition, and stress play pivotal roles in determining how genes are expressed. The concept of the reaction range is central to understanding this interaction. It posits...
248
Polygenic Traits
64.7K
When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
64.7K
Background and Environment Affect Phenotype
6.4K
Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
6.4K
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
Pleiotropy
39.7K
Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
39.7K
Epistasis Analysis
4.9K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
4.9K


