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Open Access Software

MLPAstats: An R GUI package for the integrated analysis of copy number alterations using MLPA data

Alejandro Cáceres12*, Lluís Armengol3, Sergi Villatoro4 and Juan R González125*

Author Affiliations

1 Center for Research in Environmental Epidemiology, Doctor Aiguader 88, Barcelona 08003, Spain

2 Institut Municipal d'Investigació Mèdica, Doctor Aiguader 88, Barcelona 08003, Spain

3 Quantitative Genomic Medicine Laboratories, Doctor Aiguader 88, Barcelona 08003, Spain

4 Center for Genomic Regulation, Doctor Aiguader 88, Barcelona 08003, Spain

5 CIBER Epidemiología y Salud Pública, Doctor Aiguader 88, Barcelona 08003, Spain

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BMC Bioinformatics 2011, 12:147  doi:10.1186/1471-2105-12-147

Published: 11 May 2011

Abstract

Background

Multiplex-Dependent Probe Amplification (MLPA) is a cost-effective experimental method for candidate gene studies, aimed at the identification of copy number alterations. The analysis of such genetic variants, from electropherogram peak intensities, involves two main stages. First, peak normalization for each probe is required to remove the contribution of probe size to peak intensity. Second, the statistical significance of peak alteration between case and control samples is estimated. A number of methods have been proposed in each step with varying levels of complexity and precision. However, there is no single framework from which the results of each method and possible combinations at each step can be assessed.

Results

We present MLPAstats, an R package designed to integrate the methods for exploring different analysis scenarios in a reliable way. A GUI has been developed to allow researchers to find their optimal analysis strategy.

Conclusions

MLPAstats is an analysis tool that promotes the use of cost-effective MLPA suitable for candidate gene studies. Its R implementation allows future methods to be easily incorporated, while its GUI will facilitate its use by non-expert analysts. A vignette describing a set-by-step tutorial is also available with the package.