CNV-WebStore: Online CNV Analysis, Storage and Interpretation

Geert Vandeweyer,Wim Wuyts,Liesbeth Rooms,Edwin Reyniers,R Frank Kooy

doi:10.1186/1471-2105-12-4

Geert Vandeweyer, Wim Wuyts + Show 3 more

Open Access

https://doi.org/10.1186/1471-2105-12-4

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Journal: BMC bioinformatics	Publication Date: Jan 5, 2011
Citations: 103	License type: cc-by

Affiliation: Antwerp University Hospital

Abstract

BackgroundMicroarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV data management and interpretation system.ResultsWe present CNV-WebStore, an online platform to streamline the processing and downstream interpretation of microarray data in a clinical context, tailored towards but not limited to the Illumina BeadArray platform. Provided analysis tools include CNV analsyis, parent of origin and uniparental disomy detection. Interpretation tools include data visualisation, gene prioritisation, automated PubMed searching, linking data to several genome browsers and annotation of CNVs based on several public databases. Finally a module is provided for uniform reporting of results.ConclusionCNV-WebStore is able to present copy number data in an intuitive way to both lab technicians and clinicians, making it a useful tool in daily clinical practice.

Highlights

Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use copy number variation (CNV) data management and interpretation system
Data analysis approach To make a correct functional interpretation of CNV data, it is necessary to be able to start from a reliable set of candidate regions
By combining microarray data analysis with centralised storage, a comprehensive start point was created for data interpretation, the major task in current diagnostic usage of microarray data

Summary

Introduction

Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV data management and interpretation system. Before the development of array-based comparative genomic hybridisation, visual inspection of karyotypes under the microscope limited the detection of chromosomal aberrations to events larger than 5 to 10 Mb. A major breakthrough was achieved with the generation of BAC-arrays, initially consisting of about 2000 largeinsert clones spotted on a glass back plate [10]. BAC-arrays are gradually replaced by higher resolution platforms such as oligonucleotide- and SNP-arrays [11,12].

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