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DescriptionTP53 germline mutation carrier estimation and cancer risk predictions
Development Information
GitHub wwylab/LFSPRO
LanguageR, C++
Current version2.0.0
PlatformsPlatform independent
LicenseGPL v3
Last updatedNew features in 2.0.0: lfspro.mode is added to replace lfspro to account for additional utilities in cancer-specific and multiple primary cancer risk predictions. Simply specify parameter ‘mode’ to call desired functions.
Citation Peng, G., Bojadzieva, J., Ballinger, M. L., Li, J., Blackford, A. L., Mai, P. L., Savage, S. A., Thomas, D. M., Strong, L. C., … Wang, W. (2017). Estimating TP53 Mutation Carrier Probability in Families with Li-Fraumeni Syndrome Using LFSPRO. Cancer Epidemiology, Biomarker and Prevention, 26(6), 837-844. 
Shin, S. J., Ning, J., Bojadzieva, J., Strong, L. C., and Wang, W. (2018). Bayesian estimation of a semiparametric recurrent event model with applications to the penetrance estimation of multiple primary cancers in Li-Fraumeni syndrome. Biostatistics, 00, 1–16. 
Shin, S. J., Yuan, Y., Strong, L. C., Bojadzieva, J., and Wang, W. (2018). Bayesian Semiparametric Estimation of Cancer-Specific Age-at-Onset Penetrance With Application to Li-Fraumeni Syndrome. Journal of the American Statistical Association, 1–12. 
Help and Support
Contact Wenyi Wang 


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 criteria2,3.


Source File: LFSPRO_2.0.0.tar.gz

Mac OS: LFSPRO_2.0.0.tgz


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


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


For MacOS:


For Windows,


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:

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



family information data example

family information data example

Cancer information Data

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


cancer information data example

cancer information data example

Package Illustration

The following code briefly illustrates how to used the package. Check the manual for details. <- c("fam1","fam2","fam2","fam2","fam2")
id <- c(1,1,2,100,200) <- data.frame(, id)

# LFS classic criteria
# Chompret criteria

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


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: (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.

Output of '1st.cs'

Output of 'mpc'


Here you can download the standard R documentation for LFSPRO.


How to use LFSPRO in R


  1. Li FP, Fraumeni JF, Jr., Mulvihill JJ, et al. A cancer family syndrome in twenty-four kindreds. Cancer research. Sep 15 1988;48(18):5358-5362. [return]
  2. Chompret A, Abel A, Stoppa-Lyonnet D, et al. Sensitivity and predictive value of criteria for p53 germline mutation screening. Journal of medical genetics. Jan 2001;38(1):43-47. [return]
  3. Tinat J, Bougeard G, Baert-Desurmont S, et al. 2009 version of the Chompret criteria for Li Fraumeni syndrome. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. Sep 10 2009;27(26):e108-109; author reply e110. [return]