SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.
SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.
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DOI：
10.1371/journal.pone.0001093
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发表时间：
2007-10-31
期刊：
影响因子：
3.7
通讯作者：
Hayward NK
中科院分区：
文献类型：
--
作者：
Nancarrow DJ;Handoko HY;Stark MS;Whiteman DC;Hayward NK
全基因组，单核苷酸多态性（SNP）微阵列的最新应用来研究癌症中的DNA拷贝数畸变，为鉴定基因组变化提供了无与伦比的灵敏度。在某些情况下，这些变化的复杂性使它们难以解释，尤其是当肿瘤样品被正常（基质）组织污染时。当前的自动评分算法需要大量的手动数据检查和校正，尤其是在评估未培养的肿瘤标本时。为了解决这些限制，我们开发了一种视觉工具来帮助分析DNA拷贝数数据。模拟的DNA拷贝数（SIDCON）是一种基于电子表格的应用程序，旨在在存在或不存在基质污染的情况下模拟所有已知类型的肿瘤DNA拷贝数变化的B贵族和LOGR图的外观。该系统允许用户确定基质污染的水平，并指定最多3种不同的DNA拷贝数畸变，最多可达5000个数据点（代表单个SNP）。这允许用户灵活地评估简单或复杂的DNA拷贝数组合。我们证明了如何使用该效用来估计肿瘤样品内基质污染的水平，以及它在解密我们在一系列肿瘤中观察到的复杂异质拷贝数变化时的应用。我们认为，该工具对在该地区工作的其他工具（既可以用作培训工具）有用，并有助于解释复杂的拷贝数更改。
The recent application of genome-wide, single nucleotide polymorphism (SNP) microarrays to investigate DNA copy number aberrations in cancer has provided unparalleled sensitivity for identifying genomic changes. In some instances the complexity of these changes makes them difficult to interpret, particularly when tumour samples are contaminated with normal (stromal) tissue. Current automated scoring algorithms require considerable manual data checking and correction, especially when assessing uncultured tumour specimens. To address these limitations we have developed a visual tool to aid in the analysis of DNA copy number data. Simulated DNA Copy Number (SiDCoN) is a spreadsheet-based application designed to simulate the appearance of B-allele and logR plots for all known types of tumour DNA copy number changes, in the presence or absence of stromal contamination. The system allows the user to determine the level of stromal contamination, as well as specify up to 3 different DNA copy number aberrations for up to 5000 data points (representing individual SNPs). This allows users great flexibility to assess simple or complex DNA copy number combinations. We demonstrate how this utility can be used to estimate the level of stromal contamination within tumour samples and its application in deciphering the complex heterogeneous copy number changes we have observed in a series of tumours. We believe this tool will prove useful to others working in the area, both as a training tool, and to aid in the interpretation of complex copy number changes.
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