Aggregate Mendelian Models
This repository contains code to reproduce the results presented in the paper
Liang, J. W., Knapp, S., Shannon, K. M., Bear, L. M., McCarthy, A. M., Idos, G. E., Hong, C., Gruber, S. B., Braun, D., & Parmigiani, G. (2022). Evaluating Mendelian risk prediction models that aggregate across genes and cancers.
PanelPROR package, Lee, G., et al. (2021)1. Download for non-clinical research purposes here.- Other R packages:
abind,knitr,pROC - Data from the USC-Stanford Hereditary Cancer Panel (HCP) Testing Study. Idos, G., et al. (2019)2.
- Data from the Center for Cancer Risk Assessment at Massachusetts General Hospital (MGH).
Additional details can be found in the sub-directory README files.
simulate_families/: Functions for simulating detailed pedigrees, including family history of cancer, genotypes, and tumor marker testing results.SEER: Repository for storing Surveillance, Epidemiology, and End Results (SEER) Program data downloaded from DevCan3.est_pen/: Code to estimate aggregate penetrances.simulations/: Code to run simulation studies.validation/: Code to validate PanelPRO models on the HCP and MGH cohorts.
1. Lee, G., Zhang, Q., Liang, J. W., Huang, T., Choirat, C., Parmigiani, G., & Braun, D. (2021). PanelPRO: A R package for multi-syndrome, multi-gene risk modeling for individuals with a family history of cancer. arXiv preprint arXiv:2010.13011.
2. Idos, G. E., Kurian, A. W., Ricker, C., Sturgeon, D., Culver, J. O., Kingham, K. E., ... & Levonian, P. (2019). Multicenter prospective cohort study of the diagnostic yield and patient experience of multiplex gene panel testing for hereditary cancer risk. JCO Precision Oncology, 3, 1-12.
3. Statistical Research and Applications Branch, National Cancer Institute. (2020). DevCan: Probability of Developing or Dying of Cancer Software. Version 6.7.8.