Qiao Ying, Liu Xudong, Harvard Chansonette, Nolin Sarah L, Brown W Ted, Koochek Maryam, Holden Jeanette J A, Lewis M E Suzanne, Rajcan-Separovic Evica
Department of Pathology, UBC, Children's and Women's Health Centre of BC, Vancouver, British Columbia, Canada.
BMC Genomics. 2007 Jun 12;8:167. doi: 10.1186/1471-2164-8-167.
Genomic copy number variants (CNVs) involving >1 kb of DNA have recently been found to be widely distributed throughout the human genome. They represent a newly recognized form of DNA variation in normal populations, discovered through screening of the human genome using high-throughput and high resolution methods such as array comparative genomic hybridization (array-CGH). In order to understand their potential significance and to facilitate interpretation of array-CGH findings in constitutional disorders and cancers, we studied 27 normal individuals (9 Caucasian; 9 African American; 9 Hispanic) using commercially available 1 Mb resolution BAC array (Spectral Genomics). A selection of CNVs was further analyzed by FISH and real-time quantitative PCR (RT-qPCR).
A total of 42 different CNVs were detected in 27 normal subjects. Sixteen (38%) were not previously reported. Thirteen of the 42 CNVs (31%) contained 28 genes listed in OMIM. FISH analysis of 6 CNVs (4 previously reported and 2 novel CNVs) in normal subjects resulted in the confirmation of copy number changes for 1 of 2 novel CNVs and 2 of 4 known CNVs. Three CNVs tested by FISH were further validated by RT-qPCR and comparable data were obtained. This included the lack of copy number change by both RT-qPCR and FISH for clone RP11-100C24, one of the most common known copy number variants, as well as confirmation of deletions for clones RP11-89M16 and RP5-1011O17.
We have described 16 novel CNVs in 27 individuals. Further study of a small selection of CNVs indicated concordant and discordant array vs. FISH/RT-qPCR results. Although a large number of CNVs has been reported to date, quantification using independent methods and detailed cellular and/or molecular assessment has been performed on a very small number of CNVs. This information is, however, very much needed as it is currently common practice to consider CNVs reported in normal subjects as benign changes when detected in individuals affected with a variety of developmental disorders.
近期发现涉及超过1 kb DNA的基因组拷贝数变异（CNV）在人类基因组中广泛分布。它们代表了正常人群中新发现的一种DNA变异形式，是通过使用高通量和高分辨率方法（如阵列比较基因组杂交（array-CGH））筛查人类基因组而发现的。为了了解其潜在意义并便于解释在先天性疾病和癌症中array-CGH的发现，我们使用市售的1 Mb分辨率BAC阵列（Spectral Genomics）对27名正常个体（9名白种人；9名非裔美国人；9名西班牙裔）进行了研究。通过荧光原位杂交（FISH）和实时定量PCR（RT-qPCR）对部分CNV进行了进一步分析。
在27名正常受试者中总共检测到42种不同的CNV。其中16种（38%）此前未被报道。42种CNV中的13种（31%）包含OMIM中列出的28个基因。对正常受试者中的6种CNV（4种先前报道的和2种新的CNV）进行FISH分析，结果证实了2种新CNV中的1种以及4种已知CNV中的2种的拷贝数变化。通过FISH检测的3种CNV进一步通过RT-qPCR进行了验证，并获得了可比数据。这包括最常见的已知拷贝数变异之一的克隆RP11-100C24，通过RT-qPCR和FISH均未检测到拷贝数变化，以及对克隆RP11-89M16和RP5-1011O17缺失的确认。
我们在27名个体中描述了16种新的CNV。对一小部分CNV的进一步研究表明，array与FISH/RT-qPCR结果存在一致和不一致的情况。尽管迄今为止已报道了大量的CNV，但使用独立方法进行定量以及详细的细胞和/或分子评估仅在极少数CNV上进行过。然而，这些信息非常必要，因为目前在患有各种发育障碍的个体中检测到正常受试者中报道的CNV时，通常将其视为良性变化。
