CPBayes - Bayesian Meta Analysis for Studying Cross-Phenotype Genetic Associations

A Bayesian meta-analysis method for studying cross-phenotype genetic associations. It uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. CPBayes is based on a spike and slab prior. The methodology is available from: A Majumdar, T Haldar, S Bhattacharya, JS Witte (2018) <doi:10.1371/journal.pgen.1007139>.

Last updated 4 years ago

4.26 score 3 stars 12 scripts 293 downloads

MPGE - A Two-Step Approach to Testing Overall Effect of Gene-Environment Interaction for Multiple Phenotypes

Interaction between a genetic variant (e.g., a single nucleotide polymorphism) and an environmental variable (e.g., physical activity) can have a shared effect on multiple phenotypes (e.g., blood lipids). We implement a two-step method to test for an overall interaction effect on multiple phenotypes. In first step, the method tests for an overall marginal genetic association between the genetic variant and the multivariate phenotype. The genetic variants which show an evidence of marginal overall genetic effect in the first step are prioritized while testing for an overall gene-environment interaction effect in the second step. Methodology is available from: A Majumdar, KS Burch, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020) <doi:10.1101/2020.07.06.190256>.

Last updated 4 years ago

3.70 score 1 stars 1 scripts 218 downloads

eGST - Leveraging eQTLs to Identify Individual-Level Tissue of Interest for a Complex Trait

Genetic predisposition for complex traits is often manifested through multiple tissues of interest at different time points in the development. As an example, the genetic predisposition for obesity could be manifested through inherited variants that control metabolism through regulation of genes expressed in the brain and/or through the control of fat storage in the adipose tissue by dysregulation of genes expressed in adipose tissue. We present a method eGST (eQTL-based genetic subtyper) that integrates tissue-specific eQTLs with GWAS data for a complex trait to probabilistically assign a tissue of interest to the phenotype of each individual in the study. eGST estimates the posterior probability that an individual's phenotype can be assigned to a tissue based on individual-level genotype data of tissue-specific eQTLs and marginal phenotype data in a genome-wide association study (GWAS) cohort. Under a Bayesian framework of mixture model, eGST employs a maximum a posteriori (MAP) expectation-maximization (EM) algorithm to estimate the tissue-specific posterior probability across individuals. Methodology is available from: A Majumdar, C Giambartolomei, N Cai, MK Freund, T Haldar, T Schwarz, J Flint, B Pasaniuc (2019) <doi:10.1101/674226>.

Last updated 6 years ago

3.70 score 1 scripts 163 downloads