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Updated: Jun 14, 2025

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

在存在相位不确定性的情况下,对等位基因特异性表达的贝叶斯估计

Xue Zou, Zachary W Gomez, Timothy E Reddy

bioRxiv : the preprint server for biology

|August 30, 2024

概括

BEASTIE使用贝叶斯模型精确量化等位基特异性表达 (ASE),提高了RNA-Seq数据的准确性. 这种方法克服了当前分析的局限性,提高了遗传变异的识别.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
分子生物学分子生物学

背景情况:

对等位基因特异性表达 (ASE) 分析检测出母系和父系等位基因之间的不平衡基因表达.
ASE失衡可能源于cis作用因素,如突变或调控变异.
现有的ASE估计方法有局限性,包括依赖单个变体,分阶段假设和偏差.

研究的目的:

使用RNA-Seq数据和基因型开发精确的贝叶斯层次模型,用于基因水平的ASE量化.
为了应对ASE分析中的挑战,例如映射偏差,基因型错误和分阶段错误.

主要方法:

开发了BEASTIE,这是贝叶斯的层次模型,用于ASE量化.
从Genome-in-a-Bottle NA12878中纳入经验阶段化错误率,以考虑阶段化错误.
通过模拟数据和1000个基因组项目的现实数据验证了BEASTIE.

主要成果:

BEASTIE在基因层面实现了精确的ASE量化.
与现有方法相比,该模型显示出更高的精度,特别是在高分相误差的情况下.
BEASTIE有效地识别了其他方法可能错过的罕见遗传变异.

结论:

BEASTIE提供了一个强大的,准确的方法来量化ASE.
该工具增强了发现基因变异和基失衡模式的发现.
BEASTIE作为Python源代码和Docker图像可以免费使用.

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A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

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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

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Hardy-Weinberg Principle

Hardy-Weinberg Principle

Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.

Epistasis Analysis

Epistasis Analysis

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...