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Intellectual Property Office

Improved Phylogenic Microarray Design and Analysis Tools IB-2733

APPLICATIONS OF TECHNOLOGY:

  • Monitoring water quality
  • Identifying opportunistic and pathogenic bacteria
  • Source tracking pollutants and pathogens
  • Monitoring bioremediation project progress as well as naturally-occurring or introduced organisms at the site
  • Studying microbial ecology of specific habitats
  • Identifying harmful (oil fouling) and beneficial (methane producing) organisms for energy producing companies

ADVANTAGES:

  • Improved accuracy compared to standard chip design methods and currently available microarrays and analysis
  • Analyzes microbial DNA samples from any environmental source
  • Simultaneously detects most known microorganisms
  • Detects low-abundance organisms that would be missed by conventional culturing or sequencing

ABSTRACT:

The Berkeley Lab team responsible for the PhyloChip, a Wall Street Journal 2008 Technology Innovation Award winner and one of R&D Magazine’s Top 100 Technologies for 2008, has invented a more accurate method for designing a high-density microarray that identifies, classifies, and gives relative changes in concentration from sample-to-sample.

As the number of different classes of organisms simultaneously detected by microarray hybridization increases, the number of potential cross-hybridizations of a target to competing probes rapidly increases. To design these high density microarrays, the Berkeley Lab technology uses a novel suite of software tools and selection criteria to utilize information from public sequence databases, e.g., the Lab’s Greengenes 16S rRNA sequence database, to identify probes that maximize confidence of accurate detection of a single organism or identification of a target.

The design method enables the researchers to identify a set of least cross-hybridizing probes that can be used to calculate the relative abundance of a specific organism at differing levels of taxonomic identification. A newly developed combination of analysis algorithms, software and other methods permits the accurate detection of multiple organisms and determination of relative abundance of organisms with maximum confidence.

STATUS:

  • Available for licensing or collaborative research.

To learn more about licensing a technology from LBNL see http://www.lbl.gov/Tech-Transfer/licensing/index.html.

REFERENCE NUMBER: IB-2733

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