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“基因型颜色”：单核苷酸多态性（SNPs）和拷贝数变异（CNVs）的颜色可视化。

"GenotypeColour": colour visualisation of SNPs and CNVs.

作者信息

Barlati Sergio, Chiesa Sergio, Magri Chiara

机构信息

Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, Brescia University, Viale Europa 11, 25123 Brescia, Italy.

出版信息

BMC Bioinformatics. 2009 Feb 4;10:49. doi: 10.1186/1471-2105-10-49.

DOI:10.1186/1471-2105-10-49
PMID:19193232
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2640356/
Abstract

BACKGROUND

The volume of data available on genetic variations has increased considerably with the recent development of high-density, single-nucleotide polymorphism (SNP) arrays. Several software programs have been developed to assist researchers in the analysis of this huge amount of data, but few can rely upon a whole genome variability visualisation system that could help data interpretation.

RESULTS

We have developed GenotypeColour as a rapid user-friendly tool able to upload, visualise and compare the huge amounts of data produced by Affymetrix Human Mapping GeneChips without losing the overall view of the data.Some features of GenotypeColour include visualising the entire genome variability in a single screenshot for one or more samples, the simultaneous display of the genotype and Copy Number state for thousands of SNPs, and the comparison of large amounts of samples by producing "consensus" images displaying regions of complete or partial identity. The software is also useful for genotype analysis of trios and to show regions of potential uniparental disomy (UPD). All information can then be exported in a tabular format for analysis with dedicated software. At present, the software can handle data from 10 K, 100 K, 250 K, 5.0 and 6.0 Affymetrix chips.

CONCLUSION

We have created a software that offers a new way of displaying and comparing SNP and CNV genomic data. The software is available free at http://www.med.unibs.it/~barlati/GenotypeColour and is especially useful for the analysis of multiple samples.

摘要

背景

随着高密度单核苷酸多态性（SNP）芯片技术的近期发展，可获取的基因变异数据量大幅增加。已开发出多种软件程序来协助研究人员分析这海量数据，但很少有软件依赖于有助于数据解读的全基因组变异性可视化系统。

结果

我们开发了GenotypeColour，这是一个快速且用户友好的工具，能够上传、可视化并比较Affymetrix人类图谱基因芯片产生的海量数据，同时不会丢失数据的整体视图。GenotypeColour的一些功能包括在单个屏幕截图中可视化一个或多个样本的全基因组变异性，同时显示数千个SNP的基因型和拷贝数状态，以及通过生成显示完全或部分相同区域的“共识”图像来比较大量样本。该软件对于三联体的基因型分析以及显示潜在单亲二体（UPD）区域也很有用。然后所有信息都可以以表格形式导出，以便使用专用软件进行分析。目前，该软件可以处理来自10K、100K、250K、5.0和6.0 Affymetrix芯片的数据。

结论

我们创建了一个软件，它提供了一种显示和比较SNP和CNV基因组数据的新方法。该软件可在http://www.med.unibs.it/~barlati/GenotypeColour免费获取，对多个样本的分析特别有用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/de94cb92cee3/1471-2105-10-49-8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/a40e2382a7df/1471-2105-10-49-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/50ed0230ad94/1471-2105-10-49-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/b77ce5404cdd/1471-2105-10-49-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/40c3973de77e/1471-2105-10-49-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/25cd7c431e82/1471-2105-10-49-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/bc6816e9935f/1471-2105-10-49-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/66fec4e66378/1471-2105-10-49-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/de94cb92cee3/1471-2105-10-49-8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/a40e2382a7df/1471-2105-10-49-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/50ed0230ad94/1471-2105-10-49-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/b77ce5404cdd/1471-2105-10-49-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/40c3973de77e/1471-2105-10-49-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/25cd7c431e82/1471-2105-10-49-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/bc6816e9935f/1471-2105-10-49-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/66fec4e66378/1471-2105-10-49-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a254/2640356/de94cb92cee3/1471-2105-10-49-8.jpg

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