改进的多祖先精细映射识别出底层分子特征和疾病风险的cis-regulatory变异
Zeyun Lu1,2,3, Xinran Wang4,5, Matthew Carr4
1Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. zeyunlu@usc.edu.
Nature genetics
|July 21, 2025
概括
新的SuShiE模型提高了识别不同祖先分子特征的因果遗传变异的精度. 这种方法改善了分子定量特征位点 (molQTL) 研究和关联分析中的基因发现.
科学领域:
- 遗传学 遗传学 是一个
- 统计遗传学 统计遗传学
- 生物信息学是一种生物信息学.
背景情况:
- 对cis-molQTL (cis-molecular quantitative trait loci) 的统计精细映射对于识别因果变异至关重要.
- 现有的方法在准确性和处理多样化的祖先方面面临挑战.
研究的目的:
- 介绍共享单一效应的总和 (SuShiE) 模型,以改进多祖先的cis-molQTL精细映射.
- 提高因果性cis-molQTL与标记变异区分的准确性.
- 推断交叉祖先效应的大小相关性,并估计祖先特定的表达式预测权重.
主要方法:
- 开发了利用链接不平衡异质性的SuShiE模型.
- 通过广泛的模拟验证了SuShiE,并与现有方法进行了比较.
- 从TOPMed-MESA和GENOA研究中应用SuShiE到36,907个分子表型 (mRNA表达,蛋白质水平).
主要成果:
- 在模拟中,SuShiE的性能始终优于现有的精细映射方法.
- 与现有方法相比,SuShiE鉴定了cis-molQTL用于18.2%更多的基因,具有更高的功能丰富性.
- 分析揭示了跨祖先的一致的cis-molQTL架构,功能丧失不耐受基因具有显著的异质性.
- 根据SuShiE的相关性研究,白细胞特征的基因增加了25.4%.
结论:
- SuShiE显著提高了多祖先 cis-molQTL 精细映射的精度和功率.
- 该模型为不同种群中分子特征的遗传结构提供了新的见解.
- SuShiE在遗传关联研究中促进了更全面的基因发现.
相关概念视频
Genome-wide Association Studies-GWAS
14.3K
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...
14.3K
Cis-regulatory Sequences
10.1K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
10.1K
Modern Molecular Taxonomy
151
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
151
Polygenic Traits
66.5K
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...
66.5K
Single Nucleotide Polymorphisms-SNPs
15.9K
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,...
15.9K
X-linked Traits
55.3K
In most mammalian species, females have two X sex chromosomes and males have an X and Y. As a result, mutations on the X chromosome in females may be masked by the presence of a normal allele on the second X. In contrast, a mutation on the X chromosome in males more often causes observable biological defects, as there is no normal X to compensate. Trait variations arising from mutations on the X chromosome are called “X-linked”.
55.3K


