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, 57 (6), 644-6

High Resolution Microarray Comparative Genomic Hybridisation Analysis Using Spotted Oligonucleotides

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High Resolution Microarray Comparative Genomic Hybridisation Analysis Using Spotted Oligonucleotides

B Carvalho et al. J Clin Pathol.

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.

Figures

Figure 1
Figure 1
Microarray comparative genomic hybridisation (CGH) profile of the BT474 cell line. (A) Bacterial/phage artificial chromosome polymerase chain reaction representations were used as probe DNAs spotted on to the glass slide; (B) oligonucleotides were used as probe DNAs spotted on to the glass slide. Moving average applied to the log2 ratio of the oligo CGH profile. The vertical bars indicate the spacing between the chromosomes.
Figure 2
Figure 2
Microarray comparative genomic hybridisation (CGH) profile of the long arm of chromosome 17 of the BT474 cell line. Grey triangles, bacterial/phage artificial chromosome polymerase chain reaction representations were used as probe DNAs spotted on to the glass slide; black squares, oligonucleotides were used as probe DNAs spotted on to the glass slide (log2 ratio without moving average). The horizontal bars indicate the two separate amplicons observed.
Figure 3
Figure 3
Microarray comparative genomic hybridisation profile of the GM00143 cell line with a trisomy of chromosome 18. Moving average applied to the log2 ratio. The vertical bars indicate spacing between the chromosomes.

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