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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...

Epigenetic Regulation

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...

Epigenetic Regulation

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.

Genomic Imprinting and Inheritance

Genomic Imprinting and Inheritance

Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...

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Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Published on: May 6, 2022

Gene-based mediation analysis in epigenetic studies.

Ruiling Fang¹, Haitao Yang², Yuzhao Gao¹

¹Shanxi Medical University.

Briefings in Bioinformatics

|July 2, 2020

Summary

This summary is machine-generated.

This study introduces gene-based high-dimensional mediation analysis (gHMA) to identify DNA methylation mediators in complex diseases. The proposed omnibus test (gHMA-O) robustly combines linear and nonlinear approaches for improved accuracy.

Keywords:

DNA methylation Kernel principal components high-dimensional mediation analysis nonlinear effect omnibus test

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Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

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Area of Science:

Genetics and Genomics
Biostatistics
Epigenetics

Background:

Mediation analysis is crucial for understanding indirect effects in research.
High-dimensional mediators, common in (epi)genomics, necessitate advanced analytical models.
Identifying DNA methylation as a mediator between exposure and disease outcome is key in epigenetic studies.

Purpose of the Study:

To develop and evaluate gene-based high-dimensional mediation analysis methods for epigenetic studies.
To identify important DNA methylations mediating the relationship between exposure and disease outcome.
To capture potential nonlinear mediation effects using kernel principal component analysis.

Main Methods:

Review of current high-dimensional mediation models.
Proposal of two gene-based analytical approaches: gHMA-L (linearity assumption) and gHMA-NL (nonlinearity assumption).
Development of an omnibus test (gHMA-O) combining gHMA-L and gHMA-NL for robustness.

Main Results:

gHMA-L excels under linear mediation assumptions, while gHMA-NL performs better with nonlinear assumptions.
The omnibus test (gHMA-O) demonstrates superior power and robustness by integrating both linear and nonlinear approaches.
Simulations confirm the effectiveness of the proposed methods under various scenarios.

Conclusions:

The proposed gene-based high-dimensional mediation analysis methods, particularly the omnibus test, offer powerful tools for epigenetic research.
These methods can identify key DNA methylation mediators in complex exposure-disease relationships, such as alcohol and ovarian cancer, or childhood maltreatment and mental health outcomes.