| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS | REGISTER |
|
|
|
|
|||||||||||||
|
|
|||||||||||||||
SHORT REPORT |
1 Department of Pathology, VU University Medical Centre, de Boelelaan 1117, 1081HV Amsterdam, The Netherlands
2 Microarray Core Facility, Medical Faculty, VU University Medical Centre, van der Boechorststraat 7-9, 1081BT Amsterdam, The Netherlands
Correspondence to:
Dr B Ylstra
Microarray Core Facility, Medical Faculty, VU University Medical Centre, van der Boechorststraat 7-9, 1081BT Amsterdam, The Netherlands; b.ylstra{at}vumc.nl
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 30 000 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.
Keywords: omparative genomic hybridisation array; microarray; oligonucleotides
Abbreviations: BAC, bacterial artificial chromosome; CGH, comparative genomic hybridisation; CHORI, Children’s Hospital Oakland Research Institute; oligo, oligonucleotide; PAC, phage artificial chromosome; PCR, polymerase chain reaction
This article has been cited by other articles:
|
|
 |
|
  S. Derks, C. Postma, B. Carvalho, S. M. van den Bosch, P. T.M. Moerkerk, J. G. Herman, M. P. Weijenberg, A. P. de Bruine, G. A. Meijer, and M. van Engeland Integrated analysis of chromosomal, microsatellite and epigenetic instability in colorectal cancer identifies specific associations between promoter methylation of pivotal tumour suppressor and DNA repair genes and specific chromosomal alterations Carcinogenesis, February 1, 2008; 29(2): 434 - 439. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Conde, D. Montaner, J. Burguet-Castell, J. Tarraga, I. Medina, F. Al-Shahrour, and J. Dopazo ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling Nucleic Acids Res., July 13, 2007; 35(suppl_2): W81 - W85. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. S. Maydan, S. Flibotte, M. L. Edgley, J. Lau, R. R. Selzer, T. A. Richmond, N. J. Pofahl, J. H. Thomas, and D. G. Moerman Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization Genome Res., March 1, 2007; 17(3): 337 - 347. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. K Gruvberger-Saal, H. E Cunliffe, K. M Carr, and I. A Hedenfalk Microarrays in breast cancer research and clinical practice - the future lies ahead Endocr. Relat. Cancer, December 1, 2006; 13(4): 1017 - 1031. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. P. Harkin Genomics and the Impact of New Technologies on the Management of Colorectal Cancer Oncologist, October 1, 2006; 11(9): 988 - 991. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Ylstra, P. van den IJssel, B. Carvalho, R. H. Brakenhoff, and G. A. Meijer BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH) Nucleic Acids Res., January 26, 2006; 34(2): 445 - 450. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. van den IJssel, M. Tijssen, S.-F. Chin, P. Eijk, B. Carvalho, E. Hopmans, H. Holstege, D. K. Bangarusamy, J. Jonkers, G. A. Meijer, et al. Human and mouse oligonucleotide-based array CGH Nucleic Acids Res., December 16, 2005; 33(22): e192 - e192. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. van de Wiel, J. L. Costa, K. Smid, C. B.M. Oudejans, A. M. Bergman, G. A. Meijer, G. J. Peters, and B. Ylstra Expression Microarray Analysis and Oligo Array Comparative Genomic Hybridization of Acquired Gemcitabine Resistance in Mouse Colon Reveals Selection for Chromosomal Aberrations Cancer Res., November 15, 2005; 65(22): 10208 - 10213. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. E.L.M. Vissers, J. A. Veltman, A. G. van Kessel, and H. G. Brunner Identification of disease genes by whole genome CGH arrays Hum. Mol. Genet., October 15, 2005; 14(suppl_2): R215 - R223. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Nannya, M. Sanada, K. Nakazaki, N. Hosoya, L. Wang, A. Hangaishi, M. Kurokawa, S. Chiba, D. K. Bailey, G. C. Kennedy, et al. A Robust Algorithm for Copy Number Detection Using High-Density Oligonucleotide Single Nucleotide Polymorphism Genotyping Arrays Cancer Res., July 15, 2005; 65(14): 6071 - 6079. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Harbig, R. Sprinkle, and S. A. Enkemann A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array Nucleic Acids Res., February 18, 2005; 33(3): e31 - e31. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Cardoso, L. Molenaar, R. X. de Menezes, C. Rosenberg, H. Morreau, G. Moslein, R. Fodde, and J. M. Boer Genomic profiling by DNA amplification of laser capture microdissected tissues and array CGH Nucleic Acids Res., October 28, 2004; 32(19): e146 - e146. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS | REGISTER |
| Journal of Clinical Pathology | Molecular Pathology |
