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Updated: Jun 17, 2026

Large-Scale Multi-Omics Genome-Wide Association Studies (Mo-GWAS): Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
Growth mixture modeling as an exploratory analysis tool in longitudinal quantitative trait loci analysis
Su-Wei Chang1, Seung Hoan Choi, Ke Li
1Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, USA. shuchang@ams.sunysb.edu.
Growth mixture modeling shows promise for genome-wide association studies (GWAS) in identifying quantitative trait loci (QTLs). While the likelihood-ratio test was unreliable, direct and Bayesian tests effectively identified genetic markers associated with traits, even when near, not directly at, the gene.
Area of Science:
- Genetics
- Statistical Genetics
- Bioinformatics
Background:
- Longitudinal quantitative trait loci (QTL) detection is crucial in genome-wide association studies (GWAS).
- Growth mixture modeling (GMM) offers a potential framework for analyzing longitudinal genetic data.
- Common software packages like Mplus and SAS TRAJ are used, but their performance in this context requires evaluation.
Purpose of the Study:
- To evaluate the performance of GMM in identifying longitudinal QTLs within a GWAS framework.
- To compare the effectiveness of different statistical tests (likelihood-ratio, direct coefficient, Bayesian chi-square) within GMM for QTL detection.
- To assess the impact of marker proximity to the causal gene on statistical power.
Main Methods:
- Simulated 200 replicates of longitudinal data for GWAS.
- Applied GMM using Mplus and SAS TRAJ software.
- Utilized three statistical tests: likelihood-ratio test, direct test of genetic model coefficients, and chi-square test based on posterior Bayesian probability.
Main Results:
- Mplus exhibited computational limitations for this application.
- Tests applied to non-trait-related genes showed sensitivity to departures from Hardy-Weinberg equilibrium.
- The likelihood-ratio test was unsuitable due to deviations from expected asymptotic distributions for non-associated markers.
- Direct and Bayesian chi-square tests demonstrated satisfactory performance.
- Substantial power was achieved using markers located near the causal gene.
Conclusions:
- GMM is a potentially valuable tool for GWAS in identifying longitudinal QTLs.
- The direct test of genetic coefficients and the Bayesian probability chi-square test are recommended over the likelihood-ratio test for GMM-based GWAS.
- Marker proximity to the causal gene impacts statistical power, with nearby markers offering considerable power for detection.
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