Design considerations for array CGH to oligonucleotide arrays.
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.


CONCLUSIONS
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.
Baldocchi
R A
RA
University of California at San Francisco Cancer Center, San Francisco, California, USA. russ.baldocchi@dakocytomation.com
Glynne
R J
RJ
Chin
K
K
Kowbel
D
D
Collins
C
C
Mack
D H
DH
Gray
J W
JW
D000782:Aneuploidy; D002890:Chromosomes, Human, Pair 20 / Q000235:genetics; D041321:Chromosomes, Human, X / Q000235:genetics; D005260:Female; D018628:Gene Dosage; D006801:Humans; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D016133:Polymerase Chain Reaction
D015345:Oligonucleotide Probes