CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.
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DOI：
10.1186/1471-2105-11-74
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发表时间：
2010-02-04
影响因子：
3
通讯作者：
White PS
中科院分区：
文献类型：
--
作者：
Gai X;Perin JC;Murphy K;O'Hara R;D'arcy M;Wenocur A;Xie HM;Rappaport EF;Shaikh TH;White PS
最近的研究表明，拷贝数变异（CNVs）是常见的高等真核生物，并与相当一部分的遗传和获得性风险的各种人类疾病。高分辨率基因组监测平台的日益可用性为快速评估研究和临床样本的CNV含量以及确定已鉴定变体的潜在致病性提供了机会。然而，目前几乎没有用于准确和有效的CNV检测和评估的信息学工具。我们开发了一套软件工具和资源（CNV Workshop），用于从各种SNP阵列平台进行全基因组自动CNV检测。CNV研讨会包括三个主要组成部分：从基因组阵列数据中检测、注释和呈现结构变异。CNV检测利用循环二进制分割算法的稳健和基因型特异性扩展，并支持使用其他检测算法。预测的CNV在MySQL数据库中捕获，该数据库支持基于队列的项目，并包含安全的用户身份验证层和用户/管理员角色。为了帮助确定致病性，检测到的CNV还自动注释基因内容、已知疾病基因座和基于基因的文献参考。通过基于Web的表示层可以轻松地查询、排序、过滤和可视化结果，该表示层包括CNV内容和相关公共数据的基于GBrowse的图形表示，与UCSC基因组浏览器的集成，以及每个CNV的基因组属性的表格显示。据我们所知，CNV Workshop代表了第一个用于检测、注释和评估结构变异的生物学和临床意义的连贯和方便的平台。CNV Workshop已成功用于健康个体和疾病队列的基因组变异评估，是协调多个相关项目的理想平台。可在网站上查阅：http://sourceforge.net/projects/cnv
Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects. Available on the web at: http://sourceforge.net/projects/cnv
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影响因子：
64.8
作者：
Cook, Edwin H., Jr.;Scherer, Stephen W.
通讯作者：
Scherer, Stephen W.
影响因子：
30.8
作者：
Iafrate, AJ;Feuk, L;Lee, C
通讯作者：
Lee, C
影响因子：
7
作者：
Shaikh, Tamim H.;Gai, Xiaowu;Hakonarson, Hakon
通讯作者：
Hakonarson, Hakon
影响因子：
7
作者：
Fiegler, Heike;Redon, Richard;Carter, Nigel P.
通讯作者：
Carter, Nigel P.
影响因子：
2.1
作者：
Olshen, AB;Venkatraman, ES;Wigler, M
通讯作者：
Wigler, M