Development and validation of a CGH microarray for clinical cytogenetic diagnosis
Development and validation of a CGH microarray for clinical cytogenetic diagnosis
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DOI：
10.1097/01.gim.0000170992.63691.32
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发表时间：
2005-07-01
影响因子：
8.8
通讯作者：
Beaudet, AL
中科院分区：
文献类型：
--
作者：
Cheung, SW;Shaw, CA;Beaudet, AL
目的：利用大插入基因组DNA克隆作为比较基因组杂交(CGH)的靶点，研制了一种用于临床诊断染色体疾病的微阵列。方法：该阵列包含362个FISH验证的克隆，这些克隆跨越40多个已知的人类基因组疾病所涉及的基因组区域，以及41个临床相关的人类染色体端粒中每一个的代表性端粒下克隆。包括来自几乎所有缺失或复制基因组区域的三个或四个克隆，以及每个亚端粒区域的三个或更多克隆。我们以掩蔽的方式测试了染色体微阵列分析(CMA)，检测了25例患者的基因组DNA，这些患者以前是在遗传诊所确诊的，并进行了常规细胞遗传学研究。开发了一个用R统计编程语言实现的用于归一化、可视化和推理的新的软件包。结果：CMA结果与细胞遗传学和FISH结果完全一致。克隆分析的敏感性为96.7%，特异性为99.1%。这种选定的人类基因组阵列的主要优势包括：询问临床上相关的基因组区域，能够在一次分析中测试广泛的复制和缺失综合征，能够检测可能不被中期FISH检测到的复制，以及通过细胞遗传学实验室现有的常规FISH测试容易确认可疑的基因组变化。结论：该阵列是端粒FISH和位点特异性FISH的一种有吸引力的替代方案，但它不包括每条染色体臂上的均匀覆盖，也不打算取代标准的核型。CMA的局限性包括无法检测到平衡的染色体变化和低水平的嵌合体。
Purpose: We developed a microarray for clinical diagnosis of chromosomal disorders using large insert genomic DNA clones as targets for comparative genomic hybridization (CGH). Methods: The array contains 362 FISH-verified clones that span genomic regions implicated in over 40 known human genomic disorders and representative subtelomeric clones for each of the 41 clinically relevant human chromosome telomeres. Three or four clones from almost all deletion or duplication genomic regions and three or more clones for each subtelomeric region were included. We tested chromosome microarray analysis (CMA) in a masked fashion by examining genomic DNA from 25 patients who were previously ascertained in a genetic clinic and studied by conventional cytogenetics. A novel software package implemented in the R statistical programming language was developed for normalization, visualization, and inference. Results: The CMA results were entirely consistent with previous cytogenetic and FISH findings. For clone by clone analysis, the sensitivity was estimated to be 96.7% and the specificity was 99.1%. Major advantages of this selected human genome array include the following: interrogation of clinically relevant genomic regions, the ability to test for a wide range of duplication and deletion syndromes in a single analysis, the ability to detect duplications that would likely be undetected by metaphase FISH, and ease of confirmation of suspected genomic changes by conventional FISH testing currently available in the cytogenetics laboratory. Conclusion: The array is an attractive alternative to telomere FISH and locus-specific FISH, but it does not include uniform coverage across the arms of each chromosome and is not intended to substitute for a standard karyotype. Limitations of CMA include the inability to detect both balanced chromosome changes and low levels of mosaicism.