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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Two-stage family-based designs for sequencing studies.

Zhao Yang¹, Duncan C Thomas¹

¹Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089-9234, USA.

BMC Proceedings

|December 19, 2014

Summary

Family-based sequencing studies can identify and prioritize novel disease-causing genetic variants. This approach leverages variant sharing within families to distinguish causal from non-causal variants, improving genetic discovery in large populations.

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Area of Science:

Genetics
Epidemiology
Bioinformatics

Background:

Next-generation sequencing costs are decreasing but remain prohibitive for large epidemiological studies.
Identifying causal genetic variants among millions of rare variants presents a significant challenge.

Purpose of the Study:

To explore the utility of family-based designs for sequencing substudies.
To identify novel genetic variants and prioritize them based on their likelihood of causality.
To compare the statistical efficiency of different family-based designs.

Main Methods:

Utilizing family-based designs to exploit variant cosegregation with disease.
Introducing a score test criterion for prioritizing functional variants.
Applying methods to simulated sequence data from the Genetic Analysis Workshop 18.

Main Results:

Family-based designs can effectively distinguish causal from non-causal variants by analyzing cosegregation.
A score test criterion aids in prioritizing variants for their functional potential.
Comparison of 1-stage and 2-stage family-based designs was performed.

Conclusions:

Family-based sequencing substudies offer a valuable strategy for genetic variant discovery and prioritization in large-scale studies.
Exploiting cosegregation within families enhances the ability to identify true disease-causing variants.
The proposed score test provides a method for assessing variant causality.