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 language | English (US) |
|---|---|
| Pages (from-to) | 129-136 |
| Number of pages | 8 |
| Journal | Cytometry Part A |
| Volume | 67 |
| Issue number | 2 |
| DOIs | |
| State | Published - Oct 2005 |
| Externally published | Yes |
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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
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 journal › Article
}
TY - JOUR
T1 - Design considerations for array CGH to oligonucleotide arrays
AU - Baldocchi, R. A.
AU - Glynne, R. J.
AU - Chin, Kwang-Yung
AU - Kowbel, D.
AU - Collins, C.
AU - Mack, D. H.
AU - Gray, Joe
PY - 2005/10
Y1 - 2005/10
N2 - 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.
AB - 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.
KW - Comparative genomic hybridization
KW - Genomic amplification
KW - Microarrays
KW - Multiplex polymerase chain reaction
KW - Single nucleotide polymorphism
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UR - http://www.scopus.com/inward/citedby.url?scp=26444466177&partnerID=8YFLogxK
U2 - 10.1002/cyto.a.20161
DO - 10.1002/cyto.a.20161
M3 - Article
C2 - 16163695
AN - SCOPUS:26444466177
VL - 67
SP - 129
EP - 136
JO - Cytometry. Part A : the journal of the International Society for Analytical Cytology
JF - Cytometry. Part A : the journal of the International Society for Analytical Cytology
SN - 1552-4922
IS - 2
ER -