Premium
Design considerations for array CGH to oligonucleotide arrays
Author(s) -
Baldocchi R. A.,
Glynne R. J.,
Chin K.,
Kowbel D.,
Collins C.,
Mack D. H.,
Gray J. W.
Publication year - 2005
Publication title -
cytometry part a
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.316
H-Index - 90
eISSN - 1552-4930
pISSN - 1552-4922
DOI - 10.1002/cyto.a.20161
Subject(s) - oligonucleotide , amplicon , biology , sense (electronics) , microbiology and biotechnology , oligomer restriction , polymerase chain reaction , dna microarray , dna nanoball sequencing , dna , genetics , computational biology , gene , genomic library , chemistry , base sequence , gene expression
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. © 2005 International Society for Analytical Cytology