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Open Access Software

MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification

Ronald van Eijk1, Paul HC Eilers2, Remco Natté1, Anne-Marie Cleton-Jansen1, Hans Morreau1, Tom van Wezel and Jan Oosting1*

Author Affiliations

1 Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands

2 Department of Biostatistics, Erasmus University Medical Center, Rotterdam, The Netherlands

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BMC Bioinformatics 2010, 11:67  doi:10.1186/1471-2105-11-67

Published: 29 January 2010

Abstract

Background

Multiplex Ligation-Dependent Probe Amplification (MLPA) is an application that can be used for the detection of multiple chromosomal aberrations in a single experiment. In one reaction, up to 50 different genomic sequences can be analysed. For a reliable work-flow, tools are needed for administrative support, data management, normalisation, visualisation, reporting and interpretation.

Results

Here, we developed a data management system, MLPAInter for MLPA interpretation, that is windows executable and has a stand-alone database for monitoring and interpreting the MLPA data stream that is generated from the experimental setup to analysis, quality control and visualisation. A statistical approach is applied for the normalisation and analysis of large series of MLPA traces, making use of multiple control samples and internal controls.

Conclusions

MLPAinter visualises MLPA data in plots with information about sample replicates, normalisation settings, and sample characteristics. This integrated approach helps in the automated handling of large series of MLPA data and guarantees a quick and streamlined dataflow from the beginning of an experiment to an authorised report.