VIPR: A probabilistic algorithm for analysis of microbial detection microarrays
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PROVIDER: PRJNA126409 | ENA |
REPOSITORIES: ENA
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Project description:The development of rapid and sensitive assays capable of detecting a wide range of infectious agents is critical for the effective diagnosis of diseases that have multiple etiologies. In recent years, many microarray-based diagnostics have been developed to identify viruses present in clinical specimens in a highly parallel fashion. Unfortunately, the rate of development of algorithms to interpret data generated from such platforms has not been commensurate. In particular, none of the existing interpretive algorithms is capable of utilizing empirical training data in a Bayesian framework. We have developed an interpretive algorithm, VIPR (Viral Identification using a PRobabilistic algorithm), to capitalize on our ability to generate positive control data for analysis of microbial diagnostic arrays. To illustrate this approach, we have focused on the analysis of viruses that cause hemorrhagic fever (HF). To assess the efficacy of VIPR, we hybridized 33 viruses to 100 microarrays and applied our algorithm to this dataset. A microarray composed of nearly 15,000 oligonucleotides was designed using a custom viral taxonomy-based strategy. The performance of VIPR was assessed by performing a leave-one-out cross validation. VIPR was able to identity the infecting virus with an accuracy of 94%. VIPR outperformed previously described algorithms for the set of HF viruses tested. Bayesian interpretative algorithms such as VIPR should be considered for diagnostic microarray applications.
2011-04-19 | GSE21407 | GEO
Project description:The development of rapid and sensitive assays capable of detecting a wide range of infectious agents is critical for the effective diagnosis of diseases that have multiple etiologies. In recent years, many microarray-based diagnostics have been developed to identify viruses present in clinical specimens in a highly parallel fashion. Unfortunately, the rate of development of algorithms to interpret data generated from such platforms has not been commensurate. In particular, none of the existing interpretive algorithms is capable of utilizing empirical training data in a Bayesian framework. We have developed an interpretive algorithm, VIPR (Viral Identification using a PRobabilistic algorithm), to capitalize on our ability to generate positive control data for analysis of microbial diagnostic arrays. To illustrate this approach, we have focused on the analysis of viruses that cause hemorrhagic fever (HF). To assess the efficacy of VIPR, we hybridized 33 viruses to 100 microarrays and applied our algorithm to this dataset. A microarray composed of nearly 15,000 oligonucleotides was designed using a custom viral taxonomy-based strategy. The performance of VIPR was assessed by performing a leave-one-out cross validation. VIPR was able to identity the infecting virus with an accuracy of 94%. VIPR outperformed previously described algorithms for the set of HF viruses tested. Bayesian interpretative algorithms such as VIPR should be considered for diagnostic microarray applications. In this study, 33 viruses including virtually every known hemorrhagic fever virus and a selection of their close relatives were grown in culture and hybridized to 102 microarrays. In addition, 8 uninfected samples were hybridized (110 total hybridizations). These hybridizations were used to test a novel algorithm for diagnosing the infecting virus from a hybridization pattern.
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Project description: Not available
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Project description:A prototype oligonucleotide microarray was designed to detect and identify viable bacterial species with the potential to grow of common beer spoilage microorganisms from the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Probes targeted the intergenic spacer regions (ISR) between 16S and 23S rRNA, which were amplified in a combination of reverse transcriptase (RT) and polymerase chain reaction (PCR) prior to hybridization. This method allows the detection and discrimination of single bacterial species in a complex sample. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non-growing bacteria. The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage microorganisms within mixed population. Keywords: microarray, oligonucleotide, species-specific, detection, beer spoilage bacteria
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Project description:Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1,000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the lower signal:noise ratio inherent in oligonucleotide-based hybridization assays. We have developed wuHMM, an algorithm for mapping CNVs from array comparative genomic hybridization (aCGH) platforms comprised of 385,000 to more than 3 million probes. wuHMM is unique in that it can utilize sequence divergence information to reduce the false positive rate (FPR). We apply wuHMM to 385K-aCGH, 2.1M-aCGH, and 3.1M-aCGH experiments comparing the 129X1/SvJ and C57BL/6J inbred mouse genomes. We assess wuHMM’s performance on the 385K platform by comparison to the higher resolution platforms and we independently validate 10 CNVs. The method requires no training data and is robust with respect to changes in algorithm parameters. At a FPR of less than 10%, the algorithm can detect CNVs with five probes on the 385K platform and three on the 2.1M and 3.1M platforms, resulting in effective resolutions of 24 kb, 2-5 kb, and 1 kb, respectively. Keywords: CNV detection algorithm development and assessment
2008-03-12 | GSE10511 | GEO