Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues.
Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues.
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DOI：
10.1371/journal.pone.0092553
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Jamal R
中科院分区：
文献类型：
--
作者：
Ali Hassan NZ;Mokhtar NM;Kok Sin T;Mohamed Rose I;Sagap I;Harun R;Jamal R
对选定样本的多个基因组数据集进行综合分析可以更好地洞察整体数据，并可以增强我们对癌症的了解。本研究的目的是阐明结直肠癌（CRC）样本及其相应非癌组织中拷贝数变异（CNV）与基因表达之间的关联。使用 Illumina HumanOmni1-Quad 检测对来自同一患者的 64 配对 CRC 样本进行 CNV 分析，并使用多重连接探针扩增方法进行验证。使用 Affymetrix Human Gene 1.0 ST 阵列对来自同一组患者的 15 个配对样本进行全基因组表达谱分析。然后将从两个阵列结果获得的重要基因重叠。为了确定分子途径，将数据映射到 KEGG 数据库。比较原发性肿瘤和非癌性上皮的全基因组 CNV 分析揭示了 1638 个基因的增加和 36 个基因的损失。在肿瘤样本中，显着的增益主要出现在20号染色体20q12位置，频率为45.31%。与该细胞带相关的基因的例子有 PTPRT、EMILIN3 和 CHD6。在 8 号染色体 8p23.2 位置检测到丢失数量最多，在所有肿瘤样本中发生率为 17.19%。在此细胞带中发现的基因包括 CSMD1 和 DLC1。全基因组表达谱显示，与非癌症样本相比，CRC 中有 709 个基因上调，699 个基因下调。这两个数据集的整合确定了 56 个重叠基因，这些基因位于 8、20 和 22 号染色体上。MLPA 证实，与参考样本相比，CRC 样本在 20 号染色体上的增益最高。通过综合分析在转录组背景下解释 CNV 数据可能会提供关于 CRC 基因组景观的更深入的知识。
Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.
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影响因子：
24.5
作者：
Deng N;Goh LK;Wang H;Das K;Tao J;Tan IB;Zhang S;Lee M;Wu J;Lim KH;Lei Z;Goh G;Lim QY;Tan AL;Sin Poh DY;Riahi S;Bell S;Shi MM;Linnartz R;Zhu F;Yeoh KG;Toh HC;Yong WP;Cheong HC;Rha SY;Boussioutas A;Grabsch H;Rozen S;Tan P
通讯作者：
Tan P
影响因子：
3.8
作者：
Hawthorn L;Luce J;Stein L;Rothschild J
通讯作者：
Rothschild J
影响因子：
14.9
作者：
Huang V;Place RF;Portnoy V;Wang J;Qi Z;Jia Z;Yu A;Shuman M;Yu J;Li LC
通讯作者：
Li LC
影响因子：
3.7
作者：
Jasmine F;Rahaman R;Dodsworth C;Roy S;Paul R;Raza M;Paul-Brutus R;Kamal M;Ahsan H;Kibriya MG
通讯作者：
Kibriya MG
影响因子：
168.9
作者：
Cunningham, David;Atkin, Wendy;Starling, Naureen
通讯作者：
Starling, Naureen