Cheung Sau W, Shaw Chad A, Yu Wei, Li Jiangzham, Ou Zhishuo, Patel Ankita, Yatsenko Svetlana A, Cooper Mitchell L, Furman Patti, Stankiewicz Pawel, Lupski James R, Chinault A Craig, Beaudet Arthur L
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Genet Med. 2005 Jul-Aug;7(6):422-32. doi: 10.1097/01.gim.0000170992.63691.32.
We developed a microarray for clinical diagnosis of chromosomal disorders using large insert genomic DNA clones as targets for comparative genomic hybridization (CGH).
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.
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.
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.
我们开发了一种微阵列，用于使用大插入基因组DNA克隆作为比较基因组杂交（CGH）的靶标来进行染色体疾病的临床诊断。
该阵列包含362个经荧光原位杂交（FISH）验证的克隆，这些克隆跨越了与40多种已知人类基因组疾病相关的基因组区域，以及41条临床相关人类染色体端粒中每条的代表性亚端粒克隆。几乎所有缺失或重复基因组区域都包含三到四个克隆，每个亚端粒区域包含三个或更多克隆。我们通过检测25名先前在遗传诊所确诊并通过传统细胞遗传学研究的患者的基因组DNA，以盲法测试了染色体微阵列分析（CMA）。开发了一个用R统计编程语言实现的新型软件包，用于标准化、可视化和推断。
CMA结果与先前的细胞遗传学和FISH结果完全一致。对于逐个克隆分析，灵敏度估计为96.7%，特异性为99.1%。这种选定的人类基因组阵列的主要优点包括：对临床相关基因组区域进行检测，能够在单次分析中检测多种重复和缺失综合征，能够检测中期FISH可能无法检测到的重复，以及通过细胞遗传学实验室目前可用的传统FISH测试轻松确认疑似基因组变化。
该阵列是端粒FISH和位点特异性FISH的有吸引力的替代方法，但它不包括每条染色体臂的均匀覆盖，也不打算替代标准核型。CMA的局限性包括无法检测平衡的染色体变化和低水平的嵌合体。
