Chip
Performing Highly Multiplexed Differential Diagnosis with Oligonucleotide Microarrays
A review of Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases.
Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
The collaborative efforts of an international assembly of scientists (2007) developed the GreeneChipPm, a panmicrobial microarray comprising 29,455 sixty-mer oligonucleotide probes for vertebrate viruses, bacteria, fungi, and parasites to facilitate rapid, unbiased, differential diagnosis of infectious diseases. The GreeneChipPm was fabricated using Agilent’s custom design service, developing viral probes that represented a minimum of 3 distinct genomic target regions for every family or genus of vertebrate virus in the ICTVdB. When possible, highly conserved regions within a coding sequence for an enzyme such as a polymerase and 2 other regions that corresponded to more variable structural proteins were selected. GreeneChipPm version 1.0 contained 29,495 probes that included previously developed probes, as well as 11,479 16S rRNA bacterial probes, 1,120 18S rRNA fungal probes, and 848 18S rRNA parasite probes. A total of 300 host immune response probes were added to arrays as a potential index to pathogenesis. Analysis of nasopharyngeal aspirates, blood, urine, and tissue from persons with various infectious diseases confirmed the presence of viruses and bacteria identified by other methods, and implicated Plasmodium falciparum in an unexplained fatal case of hemorrhagic feverlike disease during the Marburg hemorrhagic fever outbreak in Angola in 2004–2005. The advent of validated highly multiplexed microbiologic assays, such as the GreeneChipPm, will afford unprecedented opportunities for unbiased pathogen surveillance and discovery and reduction of illness and death caused by infectious disease.
Figure 1. Signal intensity for viral probes in blood (A) and the genomic location of positive Lake Victoria marburgvirus probes (B).
(A) Probe intensities were background corrected, log2-transformed, and converted to Z scores (and corresponding p values). Background distribution of signal fluorescence in the array was calculated by using fluorescence associated with 1,000 random null probes. Positive events were selected by applying a minimum p value per probe of 0.023 (2 standard deviations). Analysis of positive events with GreeneLAMP resulted in prediction of TaxID sample 11269 as the top prediction by the combined p value. Solid squares indicate Lake Victoria marburgvirus probes; open triangles indicate other probes. Ten of (90.9%) of 11 Lake Victoria marburgvirus probes were positive.
B) Sequence-based analysis identified GenBank accession no. DQ447653 (Lake Victoria marburgvirus–Angola2005 strain Ang1379c) with 10 positive probes (all 8 motifs) as the best match.
Figure 2. Analysis of 18S rRNA sequence (nt 291,256–292,364) recovered from the array after hybridization of sample Angola-460.
The phylogenetic tree was reconstructed with the neighbor-joining method applying a Kimura 2-parameter model with MEGA version 3.1. Number of nucleotide substitutions per site are indicated by the scale bar; bootstrap values (percentage of 1,000 pseudoreplicates) are given at relevant branches. Circles indicate Plasmodium falciparum sequences; inverted triangles indicate other known plasmodial pathogens of humans.
Title: Panmicrobial oligonucleotide array for diagnosis of infectious diseases.
Journal: Emerg Infect Dis [serial on the Internet]. 2007 Jan.
Authors: Gustavo Palacios, Phenix-Lan Quan, Omar J. Jabado, Sean Conlan, David L. Hirschberg, Yang Liu, Junhui Zhai, Neil Renwick, Jeffrey Hui, Hedi Hegyi, Allen Grolla, James E. Strong, Jonathan S. Towner, Thomas W. Geisbert, Peter B. Jahrling, Cornelia Büchen-Osmond, Heinz Ellerbrok, Maria Paz Sanchez-Seco, Yves Lussier, Pierre Formenty, Stuart T. Nichol, Heinz Feldmann, Thomas Briese, and W. Ian Lipkin.
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