Design considerations for array CGH to oligonucleotide arrays

R. A. Baldocchi, R. J. Glynne, Kwang-Yung Chin, D. Kowbel, C. Collins, D. H. Mack, Joe Gray

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Background: 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. Methods: 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. Results: 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. Conclusion: 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.

Original languageEnglish (US)
Pages (from-to)129-136
Number of pages8
JournalCytometry Part A
Volume67
Issue number2
DOIs
StatePublished - Oct 2005
Externally publishedYes

Fingerprint

Oligonucleotide Array Sequence Analysis
Oligonucleotides
Polymerase Chain Reaction
Single Nucleotide Polymorphism
Genome
Microarray Analysis
Sequence Homology
DNA

Keywords

  • Comparative genomic hybridization
  • Genomic amplification
  • Microarrays
  • Multiplex polymerase chain reaction
  • Single nucleotide polymorphism

ASJC Scopus subject areas

  • Hematology
  • Cell Biology
  • Pathology and Forensic Medicine
  • Biophysics
  • Endocrinology

Cite this

Baldocchi, R. A., Glynne, R. J., Chin, K-Y., Kowbel, D., Collins, C., Mack, D. H., & Gray, J. (2005). Design considerations for array CGH to oligonucleotide arrays. Cytometry Part A, 67(2), 129-136. https://doi.org/10.1002/cyto.a.20161

Design considerations for array CGH to oligonucleotide arrays. / Baldocchi, R. A.; Glynne, R. J.; Chin, Kwang-Yung; Kowbel, D.; Collins, C.; Mack, D. H.; Gray, Joe.

In: Cytometry Part A, Vol. 67, No. 2, 10.2005, p. 129-136.

Research output: Contribution to journalArticle

Baldocchi, RA, Glynne, RJ, Chin, K-Y, Kowbel, D, Collins, C, Mack, DH & Gray, J 2005, 'Design considerations for array CGH to oligonucleotide arrays', Cytometry Part A, vol. 67, no. 2, pp. 129-136. https://doi.org/10.1002/cyto.a.20161
Baldocchi RA, Glynne RJ, Chin K-Y, Kowbel D, Collins C, Mack DH et al. Design considerations for array CGH to oligonucleotide arrays. Cytometry Part A. 2005 Oct;67(2):129-136. https://doi.org/10.1002/cyto.a.20161
Baldocchi, R. A. ; Glynne, R. J. ; Chin, Kwang-Yung ; Kowbel, D. ; Collins, C. ; Mack, D. H. ; Gray, Joe. / Design considerations for array CGH to oligonucleotide arrays. In: Cytometry Part A. 2005 ; Vol. 67, No. 2. pp. 129-136.
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