Applications of single molecule sequencing

• US 20060046258A1
• Filed: 02/25/2005
• Published: 03/02/2006
• Est. Priority Date: 02/27/2004
• Status: Abandoned Application

• Current Assignee: California Institute of Technology, Fluidigm Corporation
• Original Assignee: Fluidigm Corporation
• Inventors: Quake, Stephen, Lapidus, Stanley N.
• Application Number:
  US11/067,102
• Publication Number:
  US 20060046258A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The invention provides methods for determining the presence of a disease by comparing a sequence from a single target molecule with a predetermined sequence that is associated with a specific disease.

Claims

1-16. -16. (canceled)

17. A method for detecting low abundance nucleic acids indicative of a disease state in a heterogeneous sample, the method comprising the steps of:

a) obtaining a biological sample suspected to contain a nucleic acid that would not be expected to be present in the sample if the individual from whom it was obtained were healthy;

b) conducting a sequencing reaction on nucleic acid in said sample; and

c) comparing nucleic acid sequences obtained in said conducting step to one or more reference sequences that represent nucleic acids that are not expected to be present in a sample obtained from a healthy individual, thereby to identify nucleic acids in said sample that are indicative of a disease state.

18. The method of claim 17, wherein said biological sample is blood or another body fluid.

19. The method of claim 17, wherein said biological sample is obtained from tissue.

20. The method of claim 17, wherein said reference sequences represent a mutation that is indicative of cancer or precancer.

21. The method of claim 17, wherein said reference sequences represent an infectious disease agent.

22. The method of claim 17, wherein said heterogeneous sample comprises nucleic acid derived from multiple cell types.

23. The method of claim 20, wherein said mutation is a mutation or a deletion.

24. The method of claim 17, wherein said biological sample is maternal blood.

25. The method of claim 24, wherein said reference nucleic acid is fetal DNA or RNA.

26. The method of claim 17, wherein said comparing step identifies the presence of nucleic acids derived from multiple organisms in a pooled sample.

27. A method for detecting a nucleic acid sequence in a heterogeneous sample, wherein said sample is suspected to contain a nucleic acid template that would not be expected to be present in said sample, the method comprising the steps of:

a) obtaining a heterogeneous sample, comprising a nucleic acid;

b) depositing said sample onto a substrate;

c) conducting a template dependent primer extension reaction on said sample, thereby obtaining sequence information for said heterogeneous sample; and

d) comparing a sequence obtained in said conducting step to a reference sequence, thereby detecting said nucleic acid template that would not be expected to be present in said sample.

28. The method of claim 27, wherein the sample is deposited onto the substrate such that at least a portion of nucleic acids contained in said sample are individually optically resolvable on said substrate.