使用Affymetrix SNP阵列对基因组畸变进行可视化分析。

Visualization of genomic aberrations using Affymetrix SNP arrays.

作者信息

Müller André, Holzmann Karlheinz, Kestler Hans A

机构信息

Internal Medicine I, University of Ulm, D-89069 Ulm, Germany.

出版信息

Bioinformatics. 2007 Feb 15;23(4):496-7. doi: 10.1093/bioinformatics/btl608. Epub 2006 Nov 30.

DOI:10.1093/bioinformatics/btl608

PMID:17138589

Abstract

MOTIVATION

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.

AVAILABILITY

IdeogramBrowser and its source code are freely available under a creative commons license and can be obtained from http://www.informatik.uni-ulm.de/ni/staff/HKestler/ideo/. IdeogramBrowser is a platform independent Java application.

摘要

动机

DNA拷贝数畸变在不同类型的癌症中经常被发现。基于微阵列方法的最新进展拓宽了我们对这类畸变数量和结构的认识。高密度单核苷酸多态性（SNP）微阵列提供了极高的分辨率，每个基因组多达50万个SNP。由于数据量巨大，在大型数据集中检测常见畸变是一项巨大挑战。我们描述了一种新型开源软件工具——IdeogramBrowser，它是专门为与Affymetrix SNP阵列配合使用而设计的。它提供了多个畸变图谱的交互式核型可视化，并直接链接到基因卡片。共识区域与基因表示的可视化允许对数据进行探索性评估。