LFSPROShiny: An Interactive R/Shiny App for Prediction and Visualization of Cancer Risks in Families With Deleterious Germline TP53 Mutations

Authors

Nam H Nguyen
Elissa B Dodd-Eaton
Gang Peng
Jessica L Corredor
Wenwei Jiao
Jacynda Woodman-Ross
Banu K Arun
Wenyi Wang

Publication Date

2-1-2024

Journal

JCO Clinical Cancer Informatics

Abstract

Purpose: LFSPRO is an R library that implements risk prediction models for Li-Fraumeni syndrome (LFS), a genetic disorder characterized by deleterious germline mutations in the TP53 gene. To facilitate the use of these models in clinics, we developed LFSPROShiny, an interactive R/Shiny interface of LFSPRO that allows genetic counselors (GCs) to perform risk predictions without any programming components and further visualize the risk profiles of their patients to aid the decision-making process.

Methods: LFSPROShiny implements two models that have been validated on multiple LFS patient cohorts: a competing risk model that predicts cancer-specific risks for the first primary and a recurrent-event model that predicts the risk of a second primary tumor. Starting with a visualization template, we keep regular contact with GCs, who ran LFSPROShiny in their counseling sessions, to collect feedback and discuss potential improvement. On receiving the family history as input, LFSPROShiny renders the family into a pedigree and displays the risk estimates of the family members in a tabular format. The software offers interactive overlaid side-by-side bar charts for visualization of the patients' cancer risks relative to the general population.

Results: We walk through a detailed example to illustrate how GCs can run LFSPROShiny in clinics from data preparation to downstream analyses and interpretation of results with an emphasis on the utilities that LFSPROShiny provides to aid decision making.

Conclusion: Since December 2021, we have applied LFSPROShiny to over 100 families from counseling sessions at the MD Anderson Cancer Center. Our study suggests that software tools with easy-to-use interfaces are crucial for the dissemination of risk prediction models in clinical settings, hence serving as a guideline for future development of similar models.

Keywords

Humans, Genetic Predisposition to Disease, Germ Cells, Germ-Line Mutation, Li-Fraumeni Syndrome, Mobile Applications, Tumor Suppressor Protein p53

DOI

10.1200/CCI.23.00167

PMID

38346271

PMCID

PMC10871774

PubMedCentral® Posted Date

2-12-2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes