This is a joint work with Benjamin Rodriguez-Santiago (qGenomics) and Luis Pérez-Jurado (UPF). MAD is a software tool to detect mosaic events from SNP arrays using BAF and LRR values. The algorithm is based on a segmentation procedure which uses the main features of GADA (and R package to detect CNVs). To install MAD, start R and enter:
[generic]
source(“http://www.creal.cat/media/upload/arxius/jr/CREAL_install/install.R”)
creal.install(“mad”)
[/generic]
The methodological paper has been accepted in BMC Bioinformatics and can be found here. An example about how to use the software is described in the vignette. The algorithm has been used to discover mosaic alterations in a large collaborative study:
> *Jacobs KB, Yeager M, Zhou W, … Gonzalez JR, … Rothman N, Pérez-Jurado LA, Chanock SJ. Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet. 2012 May 6;44(6):651-8*