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- To meet a growing bioinformatics challenge, a free website has been developed by a multidisciplinary team from the Medical College of Wisconsin
and Children's Research Institute in Milwaukee to significantly improve diagnostic testing and worldwide genetic tracking of human and animal influenza viruses.
The possibility of a pandemic has worried researchers and health officials since the onset of the avian or bird flu virus, and they have been scrambling to find ways to speed detection of various forms of influenza.
, unveiled at two recent health conferences, features a searchable database containing all accessible genetic sequences of influenza A, B, and C.
It is automatically updated weekly and also facilitates a rapid response whenever new virus strains emerge to cause either annual epidemics or the next pandemic.
Kelly Henrickson, a professor of pediatrics and microbiology at the Medical College, said with the widespread availability of rapid genetic testing for influenza in clinics and laboratories, considerable resources are spent on bioinformatics annually by researchers and funding agencies that are trying to improve influenza diagnostics.
Since the 1997 Hong Kong bird flu outbreak, Henrickson said the focus of the scientific community has intensified on all aspects of influenza. As a result, there has been a significant increase in the amount of genomic data for influenza, which is now greater than 46,000 genetic sequences and is growing by hundreds monthly.
This website came out of our need to have bioinformatics to help the molecular diagnostics of influenza, and so my teams challenge is to develop these state-of-the-art molecular diagnostics, and you need good bioinformatics to do that," he said. "So this tool was developed to make our lives easier.
Other members of the interdisciplinary team that developed the website are: pediatric research technologist Michael E. Bose, M.S.; assistant professor of pediatrics Jiang Fan, M.D.; bioinformatics center applications manager Andrew Patzer; physiology genetics data specialist Jack Littrel; and pediatric infections disease lab supervisor Andrea J. Kraft, M.S. Bioinformatics tools
Although the National Institutes of Health
has funded bioinformatics enhancements for a number of infectious diseases, including influenza, Henrickson said available tools are limited and are not as much help to clinicians and researchers working on molecular diagnostics for influenza.
According to the Medical College, the new website will be constantly updated to keep pace with emergence of new virus strains, and should reduce the resources being spent worldwide on duplicate efforts.
To illustrate its functionality in quickly aligning genetic sequences, the Medical College said the website has a simple pop-up query screen that allows all of the more than 46,000 sequences in its database to be searched, or probed, with a set of criteria. The criteria might include gene segment, year, species, geographic location, and subtype.
This feature not only aligns genetic sequences, it displays the consensus sequence with the percentage of match, mismatch, and gap at each position for rapid identification of the strain being tested.
The website's other important tools include a program that can automatically design primers and probes for the resulting consensus sequence, and a program that links the user and consensus sequence to a database containing the majority of published and already developed influenza primers and probes. The program displays data aligned to the consensus sequence using colored primer/probe sequences that, when clicked on, produce the complete reference for the user.
The website has garnered some international attention, having been presented at two recent gatherings: Seasonal & Pandemic Influenza, 2007 in Arlington, Va., and IX International Symposium on Respiratory viral infections in Hong Kong.
Henrickson said the website was well received at those gatherings, and he believes it will help labs that are doing novel molecular diagnostic work and those doing routine diagnostic development and need to keep their assays, or diagnostic tests, updated. It will help the little guys more because they dont have a couple of hundred thousand dollars to spend to do this well, he said. So this gives equal advantage to everyone developing molecular diagnostics around the world.
Work to develop the site was partially funded by the National Institute of Allergy and Infectious Diseases
. Expect next-generation site
In its existing form, the website focuses on influenza virus information, but other pathogens that cause respiratory tract infections, such as RSV and parainfluenza virus, will be added in the near future.
The website is an example of multidisciplinary research now favored by federal granting agencies. Earlier this year, the Medical College and Children's Research Institute dedicated a new, $140 million biomedical and translational research facility. The 298,000 research center, a collaborative project of the two organizations, provides shared research space and two wings of laboratories, one for Children's Research Institute and the other for the Medical College's Translational and Biomedical Research Center.Related stories
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