title: Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data.
abstract: Microarrays have enabled the determination of how thousands of genes are expressed to coordinate function within single organisms. Yet applications to natural or engineered communities where different organisms interact to produce complex properties are hampered by theoretical and technological limitations. Here we describe a general method to accurately identify low-abundant targets in systems containing complex mixtures of homologous targets. We combined an analytical predictor of nonspecific probe-target interactions (cross-hybridization) with an optimization algorithm that iteratively deconvolutes true probe-target signal from raw signal affected by spurious contributions (cross-hybridization, noise, background, and unequal specific hybridization response). The method was capable of quantifying, with unprecedented specificity and accuracy, ribosomal RNA (rRNA) sequences in artificial and natural communities. Controlled experiments with spiked rRNA into artificial and natural communities demonstrated the accuracy of identification and quantitative behavior over different concentration ranges. Finally, we illustrated the power of this methodology for accurate detection of low-abundant targets in natural communities. We accurately identified Vibrio taxa in coastal marine samples at their natural concentrations (<0.05% of total bacteria), despite the high potential for cross-hybridization by hundreds of different coexisting rRNAs, suggesting this methodology should be expandable to any microarray platform and system requiring accurate identification of low-abundant targets amid pools of similar sequences.
authors.affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Luisa A
authors.initials: LA
authors.lastname: Marcelino
authors.forename: Vadim
authors.initials: V
authors.lastname: Backman
authors.forename: Andres
authors.initials: A
authors.lastname: Donaldson
authors.forename: Claudia
authors.initials: C
authors.lastname: Steadman
authors.forename: Janelle R
authors.initials: JR
authors.lastname: Thompson
authors.forename: Sarah Pacocha
authors.initials: SP
authors.lastname: Preheim
authors.forename: Cynthia
authors.initials: C
authors.lastname: Lien
authors.forename: Eelin
authors.initials: E
authors.lastname: Lim
authors.forename: Daniele
authors.initials: D
authors.lastname: Veneziano
authors.forename: Martin F
authors.initials: MF
authors.lastname: Polz
mesh_terms: D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D012335:RNA, Ribosomal / Q000032:analysis*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*; D014733:Vibrio / Q000145:classification / Q000235:genetics / Q000302:isolation & purification
chemical_list: D012335:RNA, Ribosomal