A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data

Roberts I.; Carter S.A.; Scarpini C.G.; Karagavriilidou K.; Barna J.C.J.; Calleja M.; Coleman N.

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A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data

机译：高通量计算框架，可从阵列比较基因组杂交数据中识别出显着的拷贝数畸变

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Reliable identification of copy number aberrations (CNA) from comparative genomic hybridization data would be improved by the availability of a generalised method for processing large datasets. To this end, we developed swatCGH, a data analysis framework and region detection heuristic for computational grids. swatCGH analyses sequentially displaced (sliding) windows of neighbouring probes and applies adaptive thresholds of varying stringency to identify the 10 of each chromosome that contains the most frequently occurring CNAs. We used the method to analyse a published dataset, comparing data preprocessed using four different DNA segmentation algorithms, and two methods for prioritising the detected CNAs. The consolidated list of the most commonly detected aberrations confirmed the value of swatCGH as a simplified high-throughput method for identifying biologically significant CNA regions of interest.

机译：通过可用于处理大型数据集的通用方法，可以改善从比较基因组杂交数据中可靠识别拷贝数畸变（CNA）的能力。为此，我们开发了swatCGH，数据分析框架和针对计算网格的区域检测启发式方法。 swatCGH分析相邻探针的顺序移位（滑动）窗口，并应用严格度不同的自适应阈值，以识别每个染色体中包含最频繁出现的CNA的10个。我们使用该方法分析已发布的数据集，比较使用四种不同的DNA分割算法预处理的数据，以及两种用于对检测到的CNA进行优先排序的方法。最常见检测到的像差的合并列表确认了swatCGH的价值，它是用于鉴定感兴趣的生物学上重要的CNA区域的简化的高通量方法。

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《Advances in Bioinformatics》 |2012年第2012期|共12页
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Roberts I.; Carter S.A.; Scarpini C.G.; Karagavriilidou K.; Barna J.C.J.; Calleja M.; Coleman N.;
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正文语种 eng
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1. A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data [J] . Roberts I., Carter S.A., Scarpini C.G., Advances in Bioinformatics . 2012,第Null期

机译：高通量计算框架，可从阵列比较基因组杂交数据中识别出显着的拷贝数畸变
2. Targeted array comparative genomic hybridisation (array CGH) identifies genomic imbalances associated with isolated congenital diaphragmatic hernia (CDH). [J] . Srisupundit K, Brady PD, Devriendt K, Prenatal Diagnosis . 2010,第12a13期

机译：靶向阵列比较基因组杂交（阵列CGH）可鉴定与孤立的先天性diaphragm肌疝（CDH）相关的基因组失衡。
3. Combined classical cytogenetics and array Comparative Genomic Hybridisation for genomic copy number analysis [J] . Meena Lall, Pushpa Saviour, Ratna Puri, Molecular cytogenetics . 2014,第Suppla1期

机译：组合古典细胞遗传学和阵列基因组拷贝数分析的比较基因组杂交
4. Framework for Identifying Common Aberrations in DNA Copy Number Data [C] . Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Research in Computational Molecular Biology; Lecture Notes in Bioinformatics; 4453 . 2007

机译：识别DNA拷贝数数据中常见像差的框架
5. A comparison of Hidden Markov Model based programs for detection of copy number variation in array comparative genomic hybridization data. [D] . Roberson, Andrea. 2010

机译：基于隐马尔可夫模型的程序比较，用于检测阵列比较基因组杂交数据中的拷贝数变异。
6. A High-Throughput Computational Framework for Identifying Significant Copy Number Aberrations from Array Comparative Genomic Hybridisation Data [O] . Ian Roberts, Stephanie A. Carter, Cinzia G. Scarpini, 2012

机译：一个高通量计算框架用于从阵列比较基因组杂交数据中识别出重要的拷贝数像差
7. Targeted array comparative genomic hybridisation (array CGH) identifies genomic imbalances associated with isolated congenital diaphragmatic hernia (CDH) [O] . Srisupundit, Kasemsri, Brady, Paul, Devriendt, Koenraad, 2010

机译：靶向阵列比较基因组杂交（阵列CGH）可确定与孤立的先天性diaphragm肌疝（CDH）相关的基因组失衡

A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data

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