Biology:FluChip

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The FluChip is a low-density DNA microarray for the identification of influenza viruses, originally developed at the University of Colorado at Boulder in the laboratory of Professor Kathy Rowlen[1] in collaboration with the Centers for Disease Control and Prevention (CDC) in Atlanta.

The project was funded in 2003 by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. The original FluChip [2][3] was designed to detect both influenza A and B viruses utilizing three gene targets: the HA (Hemagglutinin), NA (Neuraminidase), and M (matrix) gene segments. Numerous short DNA capture sequences were designed,[4] and used to both type and subtype influenza A viruses by taking advantage of genetic similarities and differences. The overall assay consisted of RT-PCR amplification of influenza RNA, subsequent runoff transcription using the PCR product as template, and hybridization of fluorescently-labeled fragmented RNA to the microarray surface. The overall pattern of fluorescence intensities were utilized to type and subtype the influenza virus(es) present.

MChip

various influenza A subtypes.

When it was discovered that the M gene segment alone contained enough genetic diversity between subtypes to provide subtype information, subsequent work focused on exploring this as a subtyping assay for influenza A (‘MChip’). MChip was utilized to examine hundreds of specimens, focusing on the ability to discriminate human H1N1, human H3N2, and avian influenza (H5N1) subtypes, and resulted in high clinical sensitivity and specificity as detailed in several published studies.[5] [6] [7] [8] Other influenza A viruses of interest that have been recently examined with MChip are the 1918 ‘Spanish flu’ strain, [9] and a variety of pandemic H1N1/09 virus specimens. [10] InDevR Inc. (Boulder, CO) licensed the FluChip technology from the University of Colorado and CDC in 2009, [11] and is developing the application for use in a forthcoming molecular diagnostics platform.

References

  1. ↑ "The "Flu Chip"- a New Way to Diagnose the Flu". http://www.niaid.nih.gov/topics/flu/research/diagnosticprogress/pages/fluchip.aspx. 
  2. ↑ Townsend, Michael B.; Dawson, Erica D.; Mehlmann, Martin; Smagala, James A.; Dankbar, Daniela M.; Moore, Chad L.; Smith, Catherine B.; Cox, Nancy J. et al. (2006). "Experimental Evaluation of the FluChip Diagnostic Microarray for Influenza Virus Surveillance". Journal of Clinical Microbiology 44 (8): 2863–2871. doi:10.1128/JCM.00134-06. PMID 16891504. 
  3. ↑ Mehlmann, Martin; Dawson, Erica D.; Townsend, Michael B.; Smagala, James A.; Moore, Chad L.; Smith, Catherine B.; Cox, Nancy J.; Kuchta, Robert D. et al. (2006). "Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus". Journal of Clinical Microbiology 44 (8): 2857–2862. doi:10.1128/JCM.00135-06. PMID 16891503. 
  4. ↑ Smagala, James A.; Dawson, Erica D.; Mehlmann, Martin; Townsend, Michael B.; Kuchta, Robert D.; Rowlen, Kathy L. (2005). "ConFind: a Robust Tool for Conserved Sequence Identification". Bioinformatics 21 (24): 4420–4422. doi:10.1093/bioinformatics/bti719. PMID 16239306. 
  5. ↑ Dawson, Erica D.; Moore, Chad L.; Smagala, James A.; Dankbar, Daniela M.; Mehlmann, Martin; Townsend, Michael B.; Smith, Catherine B.; Cox, Nancy J. et al. (2006). "MChip: A Tool for Influenza Surveillance". Analytical Chemistry 78 (22): 7610–7615. doi:10.1021/ac061739f. PMID 17105150. 
  6. ↑ Dawson, Erica D.; Moore, Chad L.; Dankbar, Daniela M.; Mehlmann, Martin; Townsend, Michael B.; Smagala, James A.; Smith, Catherine B.; Cox, Nancy J. et al. (2007). "Identification of A/H5N1 Influenza Viruses sing a Single Gene Diagnostic Microarray". Analytical Chemistry 79 (1): 378–384. doi:10.1021/ac061920o. PMID 17194164. 
  7. ↑ Mehlmann, Martin; Bonner, Aleta B.; Williams, John V.; Dankbar, Daniela M.; Moore, Chad L.; Kuchta, Robert D.; Podsiad, Amy B.; Tamerius, John D. et al. (2007). "Comparison of the MChip to Viral Culture, Reverse Transcription-PCR, and the QuickVue Influenza A+B Test for Rapid Diagnosis of Influenza". Journal of Clinical Microbiology 45 (4): 1234–1237. doi:10.1128/JCM.02202-06. PMID 17301287. 
  8. ↑ Dawson, Erica D.; Rowlen, Kathy L. (February 2010). FluChip: Robust Sequence Selection Method for a Diagnostic Influenza Microarray. in Influenza: Molecular Virology, Wang, Q. and Tao, Y. J., eds. Norfolk, UK, Caister Academic Press. ISBN 978-1-904455-57-8. 
  9. ↑ Moore, Chad L.; Smagala, James A.; Smith, Catherine B.; Dawson, Erica D.; Cox, Nancy J.; Kuchta, Robert J.; Rowlen, Kathy L. (2007). "Evaluation of MChip with Historic Subtype H1N1 Influenza A Viruses, Including the 1918 "Spanish Flu" Strain". Journal of Clinical Microbiology 45 (11): 3807–3810. doi:10.1128/JCM.01089-07. PMID 17855577. 
  10. ↑ "Press Release May 5, 2009". http://www.eurekalert.org/pub_releases/2009-05/uoca-ifd050509.php. 
  11. ↑ "Press Release April 28, 2009". http://www.eurekalert.org/pub_releases/2009-04/uoca-ftl042809.php. 

External links



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