Visualization of genomic aberrations using Affymetrix SNP arrays | Zendy

André Frotta Müller | Zendy; Karlheinz Holzmann | Zendy; Hans A. Kestler | Zendy

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Visualization of genomic aberrations using Affymetrix SNP arrays

Author(s) -

André Frotta Müller,

Karlheinz Holzmann,

Hans A. Kestler

Publication year - 2006

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl608

Subject(s) - visualization , computer science , java , snp , dna microarray , software , snp genotyping , computational biology , single nucleotide polymorphism , source code , snp array , mit license , biology , data mining , genetics , gene , genotype , programming language , operating system , gene expression

DNA copy number aberrations are frequently found in different types of cancer. Recent developments of microarray-based approaches have broadened the knowledge on number and structure of such aberrations. High-density single nucleotide polymorphism (SNP) microarrays provide an extremely high resolution with up to 500,000 SNPs per genome. Owing to the enormous amount of data the detection of common aberrations in large datasets is a great challenge. We describe a novel open source software tool--IdeogramBrowser--which was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards. Visualization of consensus regions together with gene representation allows the explorative assessment of the data.

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