Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 100, Issue 20, Pages 11237-11242Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1534744100
Keywords
design; modeling; microarray design
Categories
Ask authors/readers for more resources
High-density oligonucleotide microarrays enable simultaneous mon toring of expression levels of tens of thousands of transcripts. For accurate detection and quantitation of transcripts in the presence of cellular mRNA, it is essential to design microarrays whose oligonucleotide probes produce hybridization intensities that accurately reflect the concentration of original mRNA. We present a model-based approach that predicts optimal probes by using sequence and empirical information. We constructed a thermodynamic model for hybridization behavior and determined the influence of empirical factors on the effective fitting parameters. We designed Affymetrix GeneChip probe arrays that contained all 25-mer probes for hundreds of human and yeast transcripts and collected data over a 4,000-fold concentration range. Multiple linear regression models were built to predict hybridization intensities! of each probe at given target concentrations, and each inter city profile is summarized by a probe response metric. We selected probe sets to represent each transcript that were optimize I with respect to responsiveness, independence (degree to which probe sequences are nonoverlapping), and uniqueness (lack of similarity to sequences in the expressed genomic background). We 5 how that this approach is capable of selecting probes with high sensitivity and specificity for high-density oligonucleotide array,
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available