Department of Bioinformatics and Computational Biology

LFSPRO

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LFSPRO

LFSPRO
Overview
Description TP53 mutation carrier estimation for families with Li-Fraumeni syndrome.
Development Information
Language R, C++
Current Version 1.0.4
Platforms Platform independent
License GPL v3
Status Active
References
Citations Peng G, Bojadzieva J, Ballinger ML, Thomas DM, Strong LC, Wang W✉. Estimating TP53 Mutation Carrier Probability in Families with Li-Fraumeni Syndrome Using LFSPRO. Cancer Epidemiology, Biomarker and Prevention Jan 2017. DOI: 10.1158/1055-9965.EPI-16-0695.
News A new version is now available.
Help and Support
Contact Wenyi Wang


Germline TP53 mutation is a main cause for the Li-Fraumeni Syndrome. This package is designed to estimate the probability that the counselee carries a germ line TP53 deleterious mutation based on his/her family cancer history. We also provide functions for decision based on the commonly used clinical criteria: the classic [1] and Chompret criteria [2][3] in the package.

Contents


Download

LFSPRO is now available from inside the BayesMendel R package. You can download from here: BayesMendel version 2.1-2

Source File: LFSPRO_1.0.5.tar.gz

Mac OS: LFSPRO_1.0.5.tgz

Windows 10: LFSPRO_1.0.5.zip R packages for old versions of Windows are available upon request.

Warning: An error may occur when installing the package in Mac OS X Yosemite. It may caused by the incompatibility between R and the Yosemite system. Please let us know if you encounter any such problems.

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_1.0.5.tar.gz

For MacOS:

R CMD INSTALL LFSPRO_1.0.5.tgz

For Windows,

R CMD INSTALL LFSPRO_1.0.5.zip

Check here for details of R package installation.

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

Input Data Illustration

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

Pedigree Information Data

The structure of the pedigree 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: 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 pedigree information data file on its right:

pedigree
pedigree information file

Cancer information Data

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

  • fam.id: family id
  • id: individual id
  • cancer.type: cancer type. We divided all the cancers into 11 groups according to NCCCN Guidelines Version 1.2012 Li-Fraumeni Syndrome criteria. Check documentations for details.
  • diag.age: The age when the individual was diagnosed with cancer.

Example:

cancer information data file

Package Illustration

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

options(stringsAsFactors = FALSE)
fam.id <- c("fam1","fam2","fam2","fam2","fam2")
id <- c(0,0,2,100,200)
counselee.id <- data.frame(fam.id, id)
# LFS classic criteria
LFSClassic(fam.data, cancer.data, counselee.id)
# Chompret criteria
LFSChompret(fam.data, cancer.data, counselee.id)

allef.g <- list(c(0.9999,0.0001))
mRate.g <- 5e-4

# LFSPRO
LFSPRO(fam.data, cancer.data, LFSpenet.2010, counselee.id, allef.g, 1,mRate.g)

Output

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).

Documentation

Here you can download the standard R documentation for LFSPRO.

Manual

How to use LFSPRO in R

Reference

[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.
[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.
[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.