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SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels

Mathijs A Sanders1, Roel GW Verhaak12, Wendy MC Geertsma-Kleinekoort1, Saman Abbas1, Sebastiaan Horsman3, Peter J van der Spek3, Bob Löwenberg1 and Peter JM Valk1*

Author Affiliations

1 Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands

2 Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA; The Broad Institute of M.I.T. and Harvard, Cambridge, USA

3 Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands

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BMC Genomics 2008, 9:41  doi:10.1186/1471-2164-9-41

Published: 25 January 2008

Abstract

Background

Accurate analyses of comprehensive genome-wide SNP genotyping and gene expression data sets is challenging for many researchers. In fact, obtaining an integrated view of both large scale SNP genotyping and gene expression is currently complicated since only a limited number of appropriate software tools are available.

Results

We present SNPExpress, a software tool to accurately analyze Affymetrix and Illumina SNP genotype calls, copy numbers, polymorphic copy number variations (CNVs) and Affymetrix gene expression in a combinatorial and efficient way. In addition, SNPExpress allows concurrent interpretation of these items with Hidden-Markov Model (HMM) inferred Loss-of-Heterozygosity (LOH)- and copy number regions.

Conclusion

The combined analyses with the easily accessible software tool SNPExpress will not only facilitate the recognition of recurrent genetic lesions, but also the identification of critical pathogenic genes.