Use of hidden correlations in short oligonucleotide array data are insufficient for accurate quantification of nucleic acid targets in complex target mixtures

作     者：Rule, Rebecca A. Pozhitkov, Alex E. Noble, Peter A. 

作者机构：Univ Washington Seattle WA 98195 USA Univ So Mississippi Coll Marine Sci Ocean Springs MS 39566 USA 

出 版 物：《JOURNAL OF MICROBIOLOGICAL METHODS》 (微生物学方法杂志)

年 卷 期：2009年第76卷第2期

页      面：188-195页

核心收录：

学科分类：0710[理学-生物学] 1007[医学-药学(可授医学、理学学位)] 100705[医学-微生物与生化药学] 07[理学] 071005[理学-微生物学] 10[医学] 

基　　金：US National Oceanic and Atmospheric Administration [NAO3NOS4260216] Royalty Research Fund Provost Bridge Funding Program 

主　　题：Microbial ecology Optimization algorithm Cross-hybridization Free energy rRNA Nonspecific hybridizations Oligonucleotide arrays 

摘      要：Nonspecific target binding (i.e., cross-hybridization) is a major challenge for interpreting oligonucleotide microarray results because it is difficult to determine what portion of the signal is due to binding of complementary (specific) targets to a probe versus that due to binding of nonspecific targets. Solving this challenge would be a major accomplishment in microarray research potentially allowing quantification of targets in biological samples. Marcelino et al. recently described a new approach that reportedly solves this challenge by iteratively deconvoluting true specific signal from raw signal, and quantifying ribosomal (rRNA) sequences in artificial and natural communities (i.e., Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data, Proc. Natl. Acad. Sci. 103, 13629-13634). We evaluated their approach using high-density oligonucleotide microarrays and Latin-square designed experiments consisting of 6 and 8 rRNA targets in 16 different artificial mixtures. Our results show that contrary to the claims in the article, the hidden correlations in the microarray data are insufficient for accurate quantification of nucleic acid targets in complex artificial target mixtures. (c) 2008 Elsevier B.V. All rights reserved.