title: SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels.
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.
  
  
  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.
authors.affiliation: Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands. m.sanders@erasmusmc.nl
authors.forename: Mathijs A
authors.initials: MA
authors.lastname: Sanders
authors.forename: Roel G W
authors.initials: RG
authors.lastname: Verhaak
authors.forename: Wendy M C
authors.initials: WM
authors.lastname: Geertsma-Kleinekoort
authors.forename: Saman
authors.initials: S
authors.lastname: Abbas
authors.forename: Sebastiaan
authors.initials: S
authors.lastname: Horsman
authors.forename: Peter J
authors.initials: PJ
authors.lastname: van der Spek
authors.forename: Bob
authors.initials: B
authors.lastname: Löwenberg
authors.forename: Peter J M
authors.initials: PJ
authors.lastname: Valk
mesh_terms: 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