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Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

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Genotypic association analysis using discordant-relative-pairs.

T Yan¹, Y-N Yang, X Cheng

¹Department of Statistics and Finance, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.

Annals of Human Genetics

|December 2, 2008

Summary

This summary is machine-generated.

Family-based designs are valuable for disease-gene association studies, avoiding population stratification. This study evaluates trade-offs in relative-pair designs, finding power increases with pair distance.

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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

Area of Science:

Genetics
Biostatistics
Population Genetics

Background:

Family-based designs are standard for disease-gene association studies, mitigating population stratification and admixture.
Late-onset diseases pose challenges for parental genotype acquisition, necessitating discordant-relative-pair designs.
Relative-pair designs, including sibling and cousin pairs, offer varying degrees of protection against population stratification.

Purpose of the Study:

To investigate the trade-off between population structure control and over-matching in relative-pair designs for disease-gene association.
To evaluate the performance of established statistical tests under population stratification and admixture.
To identify optimal relative-pair designs and statistical methods for robust disease-gene association analysis.

Main Methods:

Utilized McNemar's test, matched Cochran-Armitage trend tests (CATTs), matched maximum efficient robust test (MERT), and Bhapkar's test.
Assessed test validity in the presence of population stratification (PS) and admixture.
Conducted numerical simulations to compare the power and robustness of different tests across various relative-pair relatedness levels.

Main Results:

McNemar's test, CATTs, MERT, and Bhapkar's test are valid under population stratification but not admixture.
These tests demonstrated robust power, with no single test uniformly outperforming others.
Statistical power generally increased with greater distance (less relatedness) between relative pairs in simulations.

Conclusions:

Relative-pair designs offer a viable approach for disease-gene association studies, particularly when parental genotypes are unavailable.
The choice of statistical test and the degree of relatedness in relative pairs significantly impact study power and reliability.
Further research and application to real-world datasets are warranted to refine these methods for complex disease genetics.