Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease

Code used to generate figures and tables in Uddin, M. M. et al. 2022 Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease.

CHIP calling

CHIP calling was done using the pipeline described in Bick, et al. 2021 (Terra workflow:https://app.terra.bio/#workspaces/terra-outreach/CHIP-Detection-Mutect2)

EWAS

EWAS was performed using CpGassoc R package Scripts

Meta-Analysis

Meta-analysis was performed using METAL software Scripts

Mendelian randomization (MR)

Mendelian randomization was performed using GSMR from GCTA software Scripts

Enrichment analyses

Enrichment and functional annotation analyses were performed using custom R scripts (coming soon)

Citation

• Uddin, M. M., N. Q. Nguyen, B. Yu, J. Brody, A. Pampana, T. Nakao, M. Fornage, J. Bressler, N. Sotoodehnia, J. Weinstock, M. Honigberg, D. Nachun, R. Bhattacharya, G. Griffin, V. Chander, R. Gibbs, J. Rotter, C. Liu, A. Baccarelli, D. Chasman, E. Whitsel, D. Kiel, J. Murabito, E. Boerwinkle, B. Ebert, S. Jaiswal, J. Floyd, A. Bick, C. Ballantyne, B. Psaty, P. Natarajan and K. Conneely (2022). "Clonal hematopoiesis of indeterminate potential, DNA methylation, and risk for coronary artery disease." Nat Commun.