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US 8,771,940 B2Granted
Array for detecting microbes
AssigneeThe Regents of the University of California
InventorsGary L. Andersen, Todd D. DeSantis
Life of this patent
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Abstract
The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.
Claims28
A method comprising:
- applying a sample comprising nucleic acids derived from a plurality of microorganisms representing a plurality of operational taxonomic units (OTUs) to a system, the system comprising
- (i) a first probe set comprising a plurality of different first nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present only within a first OTU,
- (ii) a second probe set comprising a plurality of different second nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present in more than one OTU but collectively are present only in a second OTU, wherein the second OTU is different than the first OTU, and
- (iii) a third probe set consisting of a plurality of different third nucleic acid probes for detecting a third OTU, wherein the third nucleic acid probes are complementary to 16S rRNA or rDNA sequences collectively present in the third OTU and another OTU, and are selected to minimize the number of putative cross-reactive OTUs, wherein the third OTU is different from the second OTU and the first OTU;
- and
- detecting hybridization between the nucleic acids derived from the plurality of microorganisms and the first, second and third probe sets, and identifying the presence and/or the quantity of microorganisms from the first, second and third OTUs based on the hybridization.
3 more elements
A method comprising:
- applying a sample comprising nucleic acids derived from a plurality of microorganisms representing a plurality of operational taxonomic units (OTUs) to a system, the system comprising:
- (i) a first probe set comprising at least 11 different first nucleic acid probes, each of said first nucleic acid probes being complementary to a 16S rRNA or rDNA sequence present only in a first OTU,
- (ii) a second probe set comprising at least 11 different second nucleic acid probes, each of said second nucleic acid probes being complementary to a 16S rRNA or rDNA sequence present in a plurality of OTUs but collectively are present only in a second OTU, wherein the second OTU is different than the first OTU,
- (iii) a third probe set consisting of at least 11 different third nucleic acid probes for detecting a third OTU, wherein the third nucleic acid probes are complementary to 16S rRNA or rDNA sequences collectively present in the third OTU and another OTU, wherein the third OTU is different from the second OTU and the first OTU, wherein the different third nucleic acid probes are selected to minimize the number of putative cross-reactive OTUs;
- and
- detecting hybridization between the nucleic acids derived from the plurality of microorganisms and the first, second and third probe sets, and identifying the presence and/or the quantity of microorganisms from the first, second and third OTUs based on the hybridization.
3 more elements
A method comprising:
- applying a sample comprising nucleic acids derived from a plurality of microorganisms representing a plurality of operational taxonomic units (OTUs) to a system, the system comprising
- (i) a first probe set comprising a plurality of different first nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present only within a first OTU,
- (ii) a second probe set comprising a plurality of different second nucleic acid probes, each of which is complementary to a 16S rRNA or rDNA sequence that is present in more than one OTU but collectively are present only in a second OTU, wherein the second OTU is different than the first OTU, and
- (iii) a third probe set consisting of a plurality of different third nucleic acid probes for detecting a third OTU, wherein the third nucleic acid probes are complementary to 16S rRNA or rDNA sequences collectively present in the second OTU and the third OTU, and are selected to minimize the number of putative cross-reactive OTUs, wherein the third OTU is different from the second OTU and the first OTU;
- and
- detecting hybridization between the nucleic acids derived from the plurality of microorganisms and the first, second and third probe sets, and identifying the presence and/or the quantity of microorganisms from the first, second and third OTUs based on the hybridization.
3 more elements
Dependencies are inferred from the claim text.