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Integrating Genetic Data in Target Trial Emulations

This repository contains the supporting code for the manuscript "Integrating genetic data in target trial emulations improves their design and informs the value of polygenic scores for prognostic and predictive enrichment", available on medRxiv with DOI: 10.1101/2024.11.05.24316763.

Overview

This repository provides code to accompany the manuscript, offering transparency on the analysis steps undertaken. The analyses are designed for use with the FinnGen cohort and leverage proprietary datasets specific to this study.

Repository Structure

  • scripts/: R scripts for data preprocessing, trial emulation, and analysis.
  • scripts_MR/: R scripts related to Mendelian Randomization (MR) analyses.

Prerequisites

The code requires access to FinnGen-specific data and is intended for use within the FinnGen research environment.

Required Software and Packages

  • R (version 4.0 or higher)
  • R packages:
    • dplyr
    • ggplot2
    • TwoSampleMR
    • data.table
    • survival

Usage

  1. Data Access:

    • Approved access to the FinnGen dataset is required.
  2. Running Analyses:

    • Use the provided scripts to replicate the analyses described in the manuscript.
  3. Mendelian Randomization Analyses:

    • MR analysis scripts can be found in the scripts_MR/ folder.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Acknowledgments

We acknowledge the FinnGen project and all collaborators who contributed to this research.

Citation

If you use any part of this repository in your work, please cite the following manuscript:

German, J. et al. (2024). Integrating genetic data in target trial emulations improves their design and informs the value of polygenic scores for prognostic and predictive enrichment. medRxiv. DOI: 10.1101/2024.11.05.24316763.

Contact

For questions or further information, please contact the corresponding authors listed in the manuscript.

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