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使用点阵寡核苷酸的高分辨率微阵列比较基因组杂交分析

High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides.

作者信息

Carvalho B, Ouwerkerk E, Meijer G A, Ylstra B

机构信息

Department of Pathology, VU University Medical Centre, de Boelelaan 1117, 1081HV Amsterdam, The Netherlands.

出版信息

J Clin Pathol. 2004 Jun;57(6):644-6. doi: 10.1136/jcp.2003.013029.

DOI:10.1136/jcp.2003.013029
PMID:15166273
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1770328/
Abstract

BACKGROUND

Currently, comparative genomic hybridisation array (array CGH) is the method of choice for studying genome wide DNA copy number changes. To date, either amplified representations of bacterial artificial chromosomes (BACs)/phage artificial chromosomes (PACs) or cDNAs have been spotted as probes. The production of BAC/PAC and cDNA arrays is time consuming and expensive.

AIM

To evaluate the use of spotted 60 mer oligonucleotides (oligos) for array CGH.

METHODS

The hybridisation of tumour cell lines with known chromosomal aberrations on to either BAC or oligoarrrays that are mapped to the human genome.

RESULTS

Oligo CGH was able to detect amplifications with high accuracy and greater spatial resolution than other currently used array CGH platforms. In addition, single copy number changes could be detected with a resolution comparable to conventional CGH.

CONCLUSIONS

Oligos are easy to handle and flexible, because they can be designed for any part of the genome without the need for laborious amplification procedures. The full genome array, containing around 30000 oligos of all genes in the human genome, will represent a big step forward in the analysis of chromosomal copy number changes. Finally, oligoarray CGH can easily be used for any organism with a fully sequenced genome.

摘要

背景

目前，比较基因组杂交芯片（array CGH）是研究全基因组DNA拷贝数变化的首选方法。迄今为止，细菌人工染色体（BAC）/噬菌体人工染色体（PAC）的扩增产物或cDNA已被点样作为探针。BAC/PAC和cDNA芯片的制作既耗时又昂贵。

目的

评估点样的60聚体寡核苷酸（oligos）在array CGH中的应用。

方法

将具有已知染色体畸变的肿瘤细胞系与定位到人类基因组的BAC芯片或寡核苷酸芯片进行杂交。

结果

与目前使用的其他array CGH平台相比，寡核苷酸CGH能够以更高的准确性和更高的空间分辨率检测扩增。此外，单拷贝数变化能够以与传统CGH相当的分辨率被检测到。

结论

寡核苷酸易于操作且灵活，因为它们可以针对基因组的任何部分进行设计，而无需繁琐的扩增程序。包含人类基因组中所有基因的约30000个寡核苷酸的全基因组芯片，将在染色体拷贝数变化分析方面向前迈出一大步。最后，寡核苷酸芯片CGH可轻松用于任何具有全基因组序列的生物体。

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