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

BackgroundMultiplex 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.ResultsHere, 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.ConclusionsMLPAinter 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.

[1]  P. Devilee,et al.  Ever since Knudson. , 2001, Trends in genetics : TIG.

[2]  K. Aldape,et al.  Detection of 1p and 19q loss in oligodendroglioma by quantitative microsatellite analysis, a real-time quantitative polymerase chain reaction assay. , 2001, The American journal of pathology.

[3]  N. Carter,et al.  Array Comparative Genomic Hybridization Analysis of Colorectal Cancer Cell Lines and Primary Carcinomas , 2004, Cancer Research.

[4]  P. Donahoe,et al.  Congenital diaphragmatic hernia (CDH) etiology as revealed by pathway genetics , 2007, American journal of medical genetics. Part C, Seminars in medical genetics.

[5]  Peter Devilee,et al.  BRCA1 genomic deletions are major founder mutations in Dutch breast cancer patients , 1997, Nature Genetics.

[6]  A. Hills,et al.  Detection of subtelomere imbalance using MLPA: validation, development of an analysis protocol, and application in a diagnostic centre , 2007, BMC Medical Genetics.

[7]  L. Samuelsson,et al.  Multiplex ligation-dependent probe amplification (MLPA) detects large deletions in the MECP2 gene of Swedish Rett syndrome patients. , 2003, Genetic testing.

[8]  D. Zwijnenburg,et al.  Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. , 2002, Nucleic acids research.

[9]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[10]  P. Eilers,et al.  Multiplex Ligation‐Dependent Probe Amplification for the Detection of 1p and 19q Chromosomal Loss in Oligodendroglial Tumors , 2005, Brain pathology.

[11]  Jordy Coffa,et al.  MLPAnalyzer: Data Analysis Tool for Reliable Automated Normalization of MLPA Fragment Data , 2008, Cellular oncology : the official journal of the International Society for Cellular Oncology.

[12]  A. Cleton-Jansen,et al.  The role of EXT1 in nonhereditary osteochondroma: identification of homozygous deletions. , 2007, Journal of the National Cancer Institute.

[13]  Cisca Wijmenga,et al.  Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays. , 2005, Cancer research.

[14]  E. Jordanova,et al.  Genome-wide allelic state analysis on flow-sorted tumor fractions provides an accurate measure of chromosomal aberrations. , 2008, Cancer research.

[15]  D. Ruiter,et al.  Multiplex Ligation-Dependent Probe Amplification for the Detection of Chromosomal Gains and Losses in Formalin-Fixed Tissue , 2005, Diagnostic molecular pathology : the American journal of surgical pathology, part B.

[16]  K. Klinger,et al.  Rapid detection of chromosome aneuploidies in uncultured amniocytes by using fluorescence in situ hybridization (FISH). , 1992, American journal of human genetics.

[17]  D. Kwiatkowski,et al.  New applications and developments in the use of multiplex ligation‐dependent probe amplification , 2008, Electrophoresis.

[18]  Tommy Gerdes,et al.  Automatic analysis of multiplex ligation‐dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection) , 2005, Electrophoresis.