Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays.

Yang Liu, Lee Sam, Jianrong Li, Yves A Lussier

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

BACKGROUND: To address the limitations of traditional virus and pathogen detection methodologies in clinical diagnosis, scientists have developed high-throughput oligonucleotide microarrays to rapidly identify infectious agents. However, objectively identifying pathogens from the complex hybridization patterns of these massively multiplexed arrays remains challenging. METHODS: In this study, we conceived an automated method based on the hypergeometric distribution for identifying pathogens in multiplexed arrays and compared it to five other methods. We evaluated these metrics: 1) accurate prediction, whether the top ranked prediction(s) match the real virus(es); 2) four accuracy scores. RESULTS: Though accurate prediction and high specificity and sensitivity can be achieved with several methods, the method based on hypergeometric distribution provides a significant advantage in term of positive predicting value with two to sixty folds the positive predicting values of other methods. CONCLUSION: The proposed multi-specie array analysis based on the hypergeometric distribution addresses shortcomings of previous methods by enhancing signals of positively hybridized probes.

Original languageEnglish (US)
JournalBMC Bioinformatics
Volume10 Suppl 2
DOIs
StatePublished - 2009
Externally publishedYes

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Oligonucleotides
Robust Methods
Pathogens
Microarrays
Oligonucleotide Array Sequence Analysis
Microarray
Hypergeometric Distribution
Viruses
Virus
Prediction
Throughput
High Throughput
Specificity
Fold
Probe
Sensitivity and Specificity
Metric
Methodology
Term

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays. / Liu, Yang; Sam, Lee; Li, Jianrong; Lussier, Yves A.

In: BMC Bioinformatics, Vol. 10 Suppl 2, 2009.

Research output: Contribution to journalArticle

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