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Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
Powerful tests for association on quantitative trait loci incorporating imprinting effects
Fan Xia1, Ji-Yuan Zhou, Wing Kam Fung
1Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, Hong Kong.
Journal of Human Genetics
|April 5, 2013
Summary
This study introduces novel family-based association tests, Q-C-TDTI(c) and Q-C-MAX(c), for quantitative traits, incorporating genomic imprinting without Hardy-Weinberg equilibrium assumptions. These methods offer robust performance and accommodate complex family data structures.
Area of Science:
- Epigenetics
- Statistical Genetics
- Human Genetics
Background:
- Genomic imprinting is a key epigenetic mechanism influencing complex traits.
- Existing association studies for quantitative traits incorporating imprinting often rely on Hardy-Weinberg equilibrium or limited family data.
- There is a need for flexible methods that accommodate complex family structures and diverse genotypic data.
Purpose of the Study:
- To develop novel family-based association tests for quantitative traits that incorporate genomic imprinting.
- To address limitations of existing methods by not assuming Hardy-Weinberg equilibrium and accommodating incomplete parental genotypes and multiple siblings.
- To offer robust and versatile statistical tools for genetic association studies.
Main Methods:
- Proposed two novel classes of tests: Q-C-TDTI(c) and Q-C-MAX(c).
- Q-C-TDTI(c) utilizes a two-stage approach: first, testing imprinting effects with Q-C-PAT(c), then selecting an appropriate transmission disequilibrium test statistic.
- Q-C-MAX(c) involves taking the maximum of three transmission disequilibrium test statistics.
- Methods accommodate family data with missing parental genotypes and multiple siblings, without assuming trait distribution.
Main Results:
- Simulation results demonstrate that the proposed Q-C-TDTI(c) and Q-C-MAX(c) tests are robust to population stratification.
- The new tests exhibit superior performance compared to existing methods across various scenarios.
- The Q-C-TDTI(c) test was successfully applied to analyze data from the Framingham Heart Study.
Conclusions:
- The developed Q-C-TDTI(c) and Q-C-MAX(c) tests provide powerful and versatile tools for family-based association studies of quantitative traits, particularly when considering genomic imprinting.
- These methods overcome key limitations of previous approaches, enhancing the ability to study complex traits.
- The application to the Framingham Heart Study highlights the practical utility of these novel statistical tests in real-world genetic research.
Related Concept Videos
02:30Genomic 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...
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
01:22Imprinting
Behavioral imprinting is observed in some newborn animals and occurs when they develop strong and specific attachments to another animal (usually a parent) following brief, early-life exposures. Offspring imprint onto parents within a brief period after birth or hatching; this time window is called the critical period. Once imprinting occurs, the bond established between the parents and their offspring is usually long-lasting.
01:49Multiple Allele Traits
The Concept of Multiple Allelism
01:19X-linked Traits
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”.
01:19X-linked Traits
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”.
01:23Behavioral Genetics and Its Designs
Behavior genetics explores how genetic inheritance influences human behavior. It focuses on how genes, passed from parents to offspring, contribute to the development of behavioral traits and tendencies. This branch of genetics seeks to understand the complex interplay between inherited genetic factors and environmental influences in shaping our behaviors.
The primary methodologies used in behavior genetics include family studies, twin studies, and adoption studies, each providing unique...
The primary methodologies used in behavior genetics include family studies, twin studies, and adoption studies, each providing unique...