Penetrance Estimation in Family-based Studies with the penetrance R package

Reliable methods for penetrance estimation are critical to improving clinical decision making and risk assessment for hereditary cancer syndromes. Penetrance is defined as the proportion of individuals who carry a genetic variant (i.e., genotype) that causes a trait and show symptoms of that trait, such as cancer (i.e., phenotype). We introduce penetrance, an open-source R package, to estimate age-specific penetrance from pedigree data. The package employs a Bayesian estimation approach, allowing for the incorporation of prior knowledge through the specification of priors for the parameters of the carrier distribution. It also includes options to impute missing ages during the estimation process, addressing incomplete age data in pedigree datasets. Our software provides a flexible and user-friendly tool for researchers to estimate penetrance in complex family-based studies, facilitating improved genetic risk assessment.