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

BMC Bioinformatics
Ronald van EijkJan Oosting

Abstract

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. 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. 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.

References

Oct 5, 2001·Trends in Genetics : TIG·P DevileeC J Cornelisse
Feb 17, 2005·Diagnostic Molecular Pathology : the American Journal of Surgical Pathology, Part B·Marcory C van DijkJudith W Jeuken
Mar 8, 2007·Journal of the National Cancer Institute·Liesbeth HameetmanPancras C W Hogendoorn
Apr 17, 2007·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Sibel Kantarci, Patricia K Donahoe
Dec 5, 2008·Electrophoresis·Piotr KozlowskiDavid J Kwiatkowski

❮ Previous
Next ❯

Citations

Jun 21, 2011·BMC Bioinformatics·Alejandro CáceresJuan R González
Jun 8, 2012·Genes, Chromosomes & Cancer·Danielle MeijerJudith V G M Bovée
Aug 26, 2010·Genes, Chromosomes & Cancer·Alexander B MohsenyAnne-Marie Cleton-Jansen
Feb 20, 2018·Molecular Biology Reports·Régis Afonso Costa, Héctor N Seuánez
Jun 23, 2020·Oncology Letters·Hülya YaziciRegina M Santella
May 22, 2019·Gastric Cancer : Official Journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association·Lindsay C HewittHeike I Grabsch

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
electrophoresis
chromosomal aberrations

Software Mentioned

Access
Delphi
Genescan Analysis Genotyper
MLPAinter
Windows XP
Office Access
GeneMapper
Genemarker
Microsoft Access
MLPA

Related Concepts

Related Feeds

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.