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


CONCLUSIONS
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.
Sanders
Mathijs A
MA
Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands. m.sanders@erasmusmc.nl
Verhaak
Roel G W
RG
Geertsma-Kleinekoort
Wendy M C
WM
Abbas
Saman
S
Horsman
Sebastiaan
S
van der Spek
Peter J
PJ
Löwenberg
Bob
B
Valk
Peter J M
PJ
D002897:Chromosomes, Human, Pair 7 / Q000235:genetics*; D003198:Computer Simulation; D018628:Gene Dosage; D020869:Gene Expression Profiling; D015894:Genome, Human / Q000235:genetics*; D005838:Genotype; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics; D019656:Loss of Heterozygosity / Q000235:genetics; D008390:Markov Chains; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software