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Association tests in nuclear families.

K D Siegmund¹, W J Gauderman

¹Department of Preventive Medicine, University of Southern California, Los Angeles, Calif 9089-9011, USA. kims@usc.edu

|July 28, 2001

Summary

This study introduces a new conditional likelihood method for testing linkage disequilibrium in families. The approach accurately detects genetic associations in families with multiple affected children.

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Area of Science:

Genetics
Statistical Genetics
Bioinformatics

Background:

Linkage disequilibrium (LD) analysis is crucial for identifying genetic variants associated with diseases.
Existing methods may be affected by familial correlation in disease status due to linkage.
Nuclear families with multiple affected offspring present unique challenges for LD testing.

Purpose of the Study:

To develop and evaluate a conditional likelihood approach for testing linkage disequilibrium in nuclear families.
To assess the robustness of the method against familial correlation in disease status.
To compare two variations of the conditional likelihood method.

Main Methods:

A conditional likelihood approach is presented, conditioning on the identity-by-descent (IBD) structure of sibling genotypes.
Two conditional likelihoods are compared: one conditioning on IBD and phase, the other on IBD alone.
A simulation study was conducted using sibships with two or three affected siblings.

Main Results:

The score tests derived from both conditional likelihoods maintained the correct test size in simulations.
Both methods demonstrated equivalent power to detect linkage disequilibrium at the 5% significance level.
The first likelihood is equivalent to allele-counting methods under the log-additive model.

Conclusions:

The proposed conditional likelihood approach is effective for testing linkage disequilibrium in nuclear families with multiple affected offspring.
The method is robust to familial correlation in disease status arising from linkage.
The two compared likelihoods offer valid and powerful approaches for LD detection.

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