LFSPRO

TP53 germline mutations are the main cause of Li-Fraumeni Syndrome . This package is designed to estimate probabilities that: 1) the counselee is a TP53 germline mutation carrier, 2) the counselee develops any cancer in future, 3) the counselee develops breast cancer, sarcoma or any other cancers in future, 4) the counselee develops a first or second primary cancer in future, on the basis of his/her family cancer history. The package also provides functions for using the LFS classic¹ and Chompret criteria^2,3.

Download

Source File: LFSPRO_2.0.0.tar.gz

Mac OS: LFSPRO_2.0.0.tgz

Windows: LFSPRO_2.0.0.zip

Note: Please let us know if you encounter any problems or issues in installing or downloading packages.

Installation

After downloading the R package, for Unix alike system type the following command in the command line to install the package:

R CMD INSTALL LFSPRO_2.0.0.tar.gz

For MacOS:

R CMD INSTALL LFSPRO_2.0.0.tgz

For Windows,

R CMD INSTALL LFSPRO_2.0.0.zip

Check here for details of R package installation.

The details about how to install R and LFSPRO package, please check the Documentation below.

Input Data Illustration

LFSPRO requires two data sets as input. One data set stores the pedigree information and the other stores the cancer information.

Family Information Data

The structure of the family information data is described below:

• fam.id: family id
• id: individual id
• fid: father’s id. If the individual is the founder of the pedigree, set his/her father’s id as NA.
• mid: mother’s id. If the individual is the founder of the pedigree, set his/her mother’s id as NA.
• gender: 0: female; 1: male
• age: if the individual is alive, it is his/her current age. Otherwise, it is age of death.

Example: For the pedigree shown below, it can be stored in the family information data file on its right:

Cancer information Data

The cancer information data stores the following information about the cancer:

• fam.id: family id
• id: individual id
• cancer.type: We classified the cancers into 11 groups as below according to NCCN Guidelines Version 1.2012 Li-Fraumeni Syndrome criteria.
• diag.age: The age when the individual was diagnosed with the cancer.

Example:

Package Illustration

The following code briefly illustrates how to used the package. Check the manual for details.

fam.id <- c("fam1","fam2","fam2","fam2","fam2")
id <- c(1,1,2,100,200)
counselee.id <- data.frame(fam.id, id)

# LFS classic criteria
lfsClassic(fam.data, cancer.data, counselee.id)
# Chompret criteria
lfsChompret2015(fam.data, cancer.data, counselee.id)

# "1st.all" predict the probability of carrying TP53 mutations
lfspro.mode(fam.data, cancer.data, counselee.id, "1st.all")
# "mpc" predict future risks of developing multiple primary cancers
lfspro.mode(fam.data, cancer.data, counselee.id, "mpc")
# "1st.cs" predict future risks of having breast cancer, sarcoma, other cancers, and death
lfspro.mode(fam.data, cancer.data, counselee.id, "1st.cs")

Output

LFSPRO will output the TP53 mutation carrier probability and/or future cancer risk for each counselee.

When mode is “1st.all”, it ouputs the TP53 mutation carrier probability for each counselee. It is a data frame with 3 variables: fam.id (family id), id (individual id) and pp (posterior probability that the counselee is a TP53 mutation carrier).

When mode is “1st.cs”, it outputs a list, contains a data frame of TP53 mutation carrier probability and a list of future risks of having breast cancer, sarcoma, other cancers and death for each counselee.

When mode is “mpc”, it outputs a data frame of TP53 mutation carrier probability and a data frame of future cancer risk prediction of developing multiple primary cancer for each counselee.

Documentation

Here you can download the standard R documentation for LFSPRO.

Manual

How to use LFSPRO in R

Reference