Design considerations for array CGH to oligonucleotide arrays
| Autor: | Baldocchi Russell A, Joe W. Gray, D. H. Mack, David Kowbel, C. Collins, Koei Chin, Richard Glynne |
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| Rok vydání: | 2005 |
| Předmět: |
Chromosomes
Human X Histology DNA-encoded chemical library Oligonucleotide Chromosomes Human Pair 20 Gene Dosage Nucleic Acid Hybridization Cell Biology Amplicon Biology Aneuploidy Polymerase Chain Reaction Molecular biology Pathology and Forensic Medicine law.invention law Multiplex polymerase chain reaction Sense (molecular biology) Humans Female DNA microarray Oligonucleotide Probes Polymerase chain reaction Oligonucleotide Array Sequence Analysis Comparative genomic hybridization |
| Zdroj: | Cytometry Part A. :129-136 |
| ISSN: | 1552-4930 1552-4922 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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