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Title: Design Considerations for Array CGH to OligonucleotideArrays

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.

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
COLLABORATION - UCSF
OSTI Identifier:
925429
Report Number(s):
LBNL-62621
R&D Project: 443180; BnR: KP1104010; TRN: US200807%%352
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Cytometry Part A
Additional Journal Information:
Journal Volume: 67A; Journal Issue: 2; Related Information: Journal Publication Date: 2005
Country of Publication:
United States
Language:
English
Subject:
59; DESIGN; DETECTION; DNA; HYBRIDIZATION; NUCLEOTIDES; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; PROBES

Citation Formats

Baldocchi, R A, Glynne, R J, Chin, K, Kowbel, D, Collins, C, Mack, D H, and Gray, J W. Design Considerations for Array CGH to OligonucleotideArrays. United States: N. p., 2005. Web. doi:10.1002/cyto.a.20161.
Baldocchi, R A, Glynne, R J, Chin, K, Kowbel, D, Collins, C, Mack, D H, & Gray, J W. Design Considerations for Array CGH to OligonucleotideArrays. United States. https://doi.org/10.1002/cyto.a.20161
Baldocchi, R A, Glynne, R J, Chin, K, Kowbel, D, Collins, C, Mack, D H, and Gray, J W. Fri . "Design Considerations for Array CGH to OligonucleotideArrays". United States. https://doi.org/10.1002/cyto.a.20161.
@article{osti_925429,
title = {Design Considerations for Array CGH to OligonucleotideArrays},
author = {Baldocchi, R A and Glynne, R J and Chin, K and Kowbel, D and Collins, C and Mack, D H and Gray, J W},
abstractNote = {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.},
doi = {10.1002/cyto.a.20161},
url = {https://www.osti.gov/biblio/925429}, journal = {Cytometry Part A},
number = 2,
volume = 67A,
place = {United States},
year = {2005},
month = {3}
}