CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data
CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data
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DOI：
10.1177/1176935117746637
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发表时间：
2017-12-13
影响因子：
2
通讯作者：
Gusev, Yuriy
中科院分区：
文献类型：
--
作者：
Song, Lei;Bhuvaneshwar, Krithika;Gusev, Yuriy
CINdex Bioconductor软件包解决了高通量基因组分析的一个重要领域。它计算染色体不稳定性（CIN）指数，这是一种新的测量方法，定量表征全基因组拷贝数改变（CNA）作为CIN的测量。该软件包的优点是能够比较几组患者（病例组和对照组）之间的CIN指数值，这是转化研究中的典型用例。然后，差异变化的细胞带或染色体可以与位于受影响的基因组区域的基因以及途径相关联。这使得深入系统的基于生物学的网络分析和评估CNA对各种生物过程或临床结果的影响成为可能。该软件包已成功应用于结直肠癌的DNA拷贝数数据分析，作为多组学综合研究的一部分，以及用于分析其他几种癌症类型。源代码、沿着端到端教程和示例数据可在Bioconductor网站http://bioconductor.org/packages/CINdex/上免费获得。
The CINdex Bioconductor package addresses an important area of high-throughput genomic analysis. It calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN. The advantage of this package is an ability to compare CIN index values between several groups for patients (case and control groups), which is a typical use case in translational research. The differentially changed cytobands or chromosomes can then be linked to genes located in the affected genomic regions, as well as pathways. This enables in-depth systems biology-based network analysis and assessment of the impact of CNA on various biological processes or clinical outcomes. This package was successfully applied to analysis of DNA copy number data in colorectal cancer as a part of multi-omics integrative study as well as for analysis of several other cancer types. The source code, along with an end-to-end tutorial, and example data are freely available in Bioconductor at http://bioconductor.org/packages/CINdex/.