TADA

Transmission And De novo Association Test

   

Motivation:

Each person inherits mutations from parents, some of which may predispose the person to certain diseases. Meanwhile, new mutations may occur spontaneously during the reproductive process, and if disrupting key genes, such “de novo” mutations may increase risks of disease. TADA (Transmission And De novo Association test) is a Bayesian model that effectively combines data from de novo mutations, inherited variants in families, and standing variants in the population (identified with case-control studies). This approach significantly increases the power of gene discovery, as we demonstrated through the studies of exome sequencing data of Autism Spectrum Disorder (ASD).

Before starting:

TADA is written in R and runs on any platform that supports R.  Make sure R is downloaded and installed on your computer. The R programming language is a freeware version of S-plus for Windows/Linux.  R can be downloaded from http://www.r-project.org.

Download:

TADA is written as a series of functions.  Click on this link to get your copy of the software: TADA.zip. Once downloaded issue the command source(“TADA.v1.2.R”) in R  to start using the software.

Documentation:

The software package contains extensive documentation. It can also be downloaded here.  

Revisions:

v1.1 fixes a bug that causes the program TADAnull to fail when entries for denovo.only are not the same across the different classes.  

Reference:

He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K (2013).  Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes. PLoS Genetics, 2013 Aug;9(8):e1003671.

   

Contact Information:

 

If you have problems running the software or you have come across a bug that we have not discovered during our testing you can contact:

 

Xin He

Lane Center of Computational Biology

Carnegie Mellon University

xinhe2@gmail.com