The penetrance R package for estimation of age specific risk in family-based studies.

Motivation: Reliable tools and software for penetrance (age-specific risk among those who carry a genetic variant) estimation are critical to improving clinical decision making and risk assessment for hereditary syndromes. However, there is a lack of easily usable software for penetrance estimation in family-based studies that implements a Bayesian estimation approach.

Results: We introduce penetrance, an open-source R package available on CRAN, to estimate age-specific penetrance using family-history pedigree data. The package uses 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 information which is not uncommon in pedigree datasets. Our open-source software provides a flexible and user-friendly tool for researchers to estimate penetrance in complex family-based studies, facilitating improved genetic risk assessment in hereditary syndromes.

Availability and implementation: The penetrance package is freely available on CRAN. Source code and documentation are available at https://github.com/nicokubi/penetrance.