Method for detecting a biological entity in a sample

• US 20040096879A1
• Filed: 07/30/2003
• Published: 05/20/2004
• Est. Priority Date: 02/18/2000
• Status: Active Grant

• Current Assignee: Leidos, Inc. (Leidos Holdings, Inc.)
• Original Assignee: Science Applications International Corporation
• Inventors: Robinson, Doreen, Schaudies, Robert Paul
• Granted Patent: US 7,070,935 B2
• Time in Patent Office: Days
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels

Abstract

The invention relates to the detection of a biological entity in a sample. More particularly, the invention relates to detection of specific pathogens from a possible presence of hundreds to thousands of distinct biological species. The invention provides new assays that can detect the presence of one or more biological entity in a sample out of a possible number of hundreds to thousands of distinct biological species. The method according to the invention for detecting a biological entity in a sample comprises randomly amplifying nucleic acids in the sample to produce labeled nucleic acids; hybridizing the labeled nucleic acids to an array of predetermined nucleic acids; and detecting the labeled nucleic acids that have hybridized to the array.

Claims

1. A method for detecting a biological entity in a sample, comprising randomly amplifying nucleic acids in the sample to produce labeled nucleic acids;

hybridizing the labeled nucleic acids to an array of predetermined nucleic acids; and

detecting the labeled nucleic acids that have hybridized to the array.

2. The method of claim 1, wherein the amplification step comprises a polymerase chain reaction.

3. The method of claim 1, wherein the amplification step utilizes random primers four to nine nucleotides in length.

4. The method of claim 1, wherein the array of predetermined nucleic acids are immobilized on a surface.

5. The method of claim 1, wherein the labeled nucleic acids are enzymatically detected.

6. The method of claim 1, wherein the labeled nucleic acids are biotinylated.

7. The method of claim 1, wherein the labeled nucleic acids are fluorescently labeled.

8. The method of claim 1, wherein the labeled nucleic acids are labeled with digoxigenin.

9. The method of claim 1, wherein the labeled nucleic acids are labeled with radiolabel.

10. The method of claim 4, wherein the surface is an opaque membrane.

11. The method of claim 4, wherein the surface is silica-based.

12. The method of claim 1, wherein the predetermined nucleic acid sequences are at predetermined positions on the array.

13. The method of claim 1, wherein the sample comprises multiple biological entities.

14. The method of claim 1, wherein the biological entity is a pathogen.

15. The method of claim 1, wherein the predetermined nucleic acids are more than 30 nucleotides in length.