A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

Background: Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly defined since it has been only studied systematically in one large-scale study and by using non optimal adhoc SNP array data analysis tools, uncovering rather large alterations (> 1 Mb) and affecting a high proportion of cells. Here we propose a novel methodology, Mosaic Alteration Detection-MAD, by providing a software tool that is effective for capturing previously described alterations as wells as new variants that are smaller in size and/or affecting a low percentage of cells. Results: The developed method identified all previously known mosaic abnormalities reported in SNP array data obtained from controls, bladder cancer and HapMap individuals. In addition MAD tool was able to detect new mosaic variants not reported before that were smaller in size and with l...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Juan R. González, Benjamin Rodriguez-Santiago, Alejandro Cáceres, Roger Pique-Regi, Nathaniel Rothman, Stephen J. Chanock, Lluís Armengol, Luis A. Perez-Jurado
• Keywords: Biometrics, BMCBI 2011, Data Analysis Tools, Nucleotide Polymorphisms, Sensitivity And Specificity