Design considerations for array CGH to oligonucleotide arrays
Article first published online: 14 SEP 2005
Copyright © 2005 Wiley-Liss, Inc.
Cytometry Part A
Special Issue: Honoring the Lifetime Achievements of Mack J. Fulwyler
Volume 67A, Issue 2, pages 129–136, October 2005
How to Cite
Baldocchi, R. A., Glynne, R. J., Chin, K., Kowbel, D., Collins, C., Mack, D. H. and Gray, J. W. (2005), Design considerations for array CGH to oligonucleotide arrays. Cytometry, 67A: 129–136. doi: 10.1002/cyto.a.20161
- Issue published online: 20 SEP 2005
- Article first published online: 14 SEP 2005
- Manuscript Accepted: 23 MAR 2005
- Manuscript Revised: 22 MAR 2005
- Manuscript Received: 5 MAR 2005
- USPHS. Grant Numbers: CA58207, CA 64602
- comparative genomic hybridization;
- multiplex polymerase chain reaction;
- genomic amplification;
- single nucleotide polymorphism
Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)–amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome.
In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon.
In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate.
Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity. © 2005 International Society for Analytical Cytology