Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme
Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme
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DOI：
10.1016/j.cancergencyto.2003.09.012
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发表时间：
2004-05-01
影响因子：
--
通讯作者：
Nowak, NJ
中科院分区：
文献类型：
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作者：
Cowell, JK;Matsui, SI;Nowak, NJ
在脑肿瘤的分析中，识别基因的丢失和获得是有价值的。逐个基因座的分析表明，预后和化疗反应以及特定基因和基因座的丢失或获得之间存在相关性。这些方法是劳动密集型的，并且不能提供肿瘤细胞内遗传变化的全局视图。细菌人工染色体(BAC)阵列覆盖了基因组，平均分辨率低于1 MBP，允许在单个比较基因组杂交(CGH)实验中定义这些基因变化的总和。这些变化直接覆盖在人类基因组序列上，从而提供了由百万碱基位置和异常区域的基因含量所反映的扩增或缺失的程度。虽然这种基于阵列的CGH方法(CGHa)似乎可靠地检测到肿瘤基因变化的程度，但它还没有得到强有力的测试。我们使用光谱核型分析(SKY)和CGHa比较了四个新衍生的早期传代胶质瘤细胞系的遗传变化。用CGHa检测细胞系在Sky分析下的染色体变化。此外，CGHa检测到隐蔽的遗传得失，并解决了Sky无法解析的微妙标记染色体的性质，因此提供了与以前技术相比的明显优势。CGHa结果与原始肿瘤细胞系相比有显著的大体一致性，除了肿瘤样本中看到的变化的幅度通常比细胞系受到抑制，这是正常细胞污染肿瘤样本的结果。CGHa揭示了原始肿瘤中没有的细胞系的变化，反之亦然，即使在尽可能早的传代时进行分析，这突出了细胞对体外培养的适应。CGHa被证明是识别肿瘤细胞基因变化的高精度和高效率的方法。这种方法可以准确地识别与人类基因组序列直接相关的肿瘤中细微的、新颖的遗传异常。CGHa远超常规中期CGH提供的分辨率和信息，不依赖于肿瘤的体外培养进行中期扩散。(C)2004 Elsevier Inc.保留所有权利。
Identification of genetic losses and gains is valuable in analysis of brain tumors. Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci. These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells. Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than I MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment. These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region. Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested. We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa. Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa. In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies. There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample. CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture. CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells. This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence. CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads. (C) 2004 Elsevier Inc. All rights reserved.