Abstract
BackgroundAccurate 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.ResultsWe 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.ConclusionThe 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.
Highlights
Accurate analyses of comprehensive genome-wide single nucleotide polymorphisms (SNPs) genotyping and gene expression data sets is challenging for many researchers
Genotypes and copy numbers are displayed as sequential blocks of which color indicates genotype, horizontal coordinate indicates position on the chromosome and vertical coordinate indicates copy number (Figure 1)
The initial version of SNPExpress has already been successfully applied in showing segmental uniparental disomy as a recurrent mechanism for homozygous CEBPA mutations in acute myeloid leukemia [38]
Summary
Accurate analyses of comprehensive genome-wide SNP genotyping and gene expression data sets is challenging for many researchers. High-density genome-wide views of biological samples, using high-throughput DNA mapping and mRNA gene expression microarrays facilitate the identification of recurrent molecular lesions. Both types of microarrays, which are being produced by different manufacturers, e.g., Nimblegen, Agilent, Sequenom, Applied Biosystems, Illumina and Affymetrix, typically contain large numbers of small oligonucleotides that interrogate the genome. Available DNA arrays contain over 500.000 probe sets, while the gene expression arrays target over 20.000 genes. Efficient analysis of these large datasets remains a challenge for many researchers. SNPs are currently estimated to be present at a frequency of 1
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