THESIAS

THESIAS estimates haplotype frequencies and tests haplotype effects in association studies of unrelated individuals to assess genetic influences on complex traits.

Key Features:

• Polymorphism Analysis: Supports analysis of polychotomous phenotypes and X-linked polymorphisms.
• Haplotype-Based Association Analysis: Simultaneously estimates haplotype frequencies and haplotype effects for association testing.
• Survival Outcome Analysis: Implements haplotype-based association analysis for censored survival data using a Stochastic-EM (SEM) algorithm within a Cox proportional hazards framework.
• Maximum Likelihood Estimation: Employs a maximum likelihood method to jointly estimate haplotype frequencies and their phenotypic effects.

Scientific Applications:

• Candidate gene association studies: Applied to investigate associations between candidate gene polymorphisms (for example, P-selectin gene polymorphisms) and disease outcomes such as myocardial infarction.
• Identification of risk or protective haplotypes: Reveals complex relationships between multiple genetic variants and phenotypic outcomes by identifying haplotypes associated with increased or decreased risk.

Methodology:

Haplotype frequency estimation from genotype data; simultaneous maximum likelihood estimation of haplotype frequencies and effects; association testing for binary, quantitative, and survival outcomes; implementation of a Stochastic-EM (SEM) algorithm for censored data within a Cox proportional hazards model.