Methods and apparatus to sequence a nucleic acid

• US 9,322,060 B2
• Filed: 10/16/2013
• Issued: 04/26/2016
• Est. Priority Date: 10/16/2012
• Status: Active Grant

• Current Assignee: Abbott Molecular Incorporated (Abbott Laboratories Incorporated)
• Original Assignee: Abbott Molecular Incorporated (Abbott Laboratories Incorporated)
• Inventors: Hayden, Mark A.
• Primary Examiner(s): Woolwine, Samuel
• Assistant Examiner(s): OYEYEMI, OLAYINKA A
• Application Number:
  US14/055,634
• Publication Number:
  US 20140106360A1
• Time in Patent Office: 923 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: B01J 2219/00 Chemical, physical or physico-chemical processes in general; Their relevant apparatus
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2563/159 Microreactors, e.g. emulsion PCR or sequencing, droplet PCR, microcapsules, i.e. non-liquid containers with a range of different permeability's for different reaction components

Abstract

Methods, systems, apparatus and machine readable media are disclosed to sequence nucleic acid. An example method includes subjecting a sequence of target nucleotide bases captured on a microtransponder to a plurality of sequencing reactions to build a sequence of labeled nucleotide bases that are complementary to and bound to the sequence of target nucleotide bases. The example method also includes identifying each labeled nucleotide base of the sequence of labeled nucleotide bases and each respective complementary target nucleotide base of the sequence of target nucleotide bases to which the labeled nucleotide base is bound after each sequencing reaction. In addition, each labeled nucleotide base of the sequence of labeled nucleotide bases and each respective complementary target nucleotide base of the sequence of target nucleotide bases to which the labeled nucleotide base is bound is associated with a microtransponder identification number.

Claims

1. A method comprising:

subjecting a sequence of target nucleotide bases captured on a microtransponder to a plurality of sequencing-by-synthesis reactions to sequentially add a sequence of single nucleotide bases that are complementary to and bound to the sequence of target nucleotide bases;

identifying each added nucleotide base after each sequencing reaction;

and associating each added nucleotide base of the sequence with an identification number of the microtransponder.

2. The method of claim 1, wherein the target nucleotide bases are captured via a capture probe.

3. The method of claim 1, wherein the target nucleotide bases comprise DNA or RNA.

4. The method of claim 1 further comprising clonally amplifying the target nucleotide bases.

5. The method of claim 4, wherein said clonally amplifying comprises an emulsion polymerase chain reaction prior to the sequencing reaction.

6. The method of claim 1, wherein at least one of the added nucleotide bases comprises a label.

7. The method of claim 6 wherein a single label is used for a plurality of added nucleotide bases.

8. The method of claim 6 wherein a plurality of different labels is used for each added nucleotide base to differentiate different added nucleotide bases.

9. The method of claim 1, wherein at least one of the added nucleotide bases comprises an optical label.

10. The method of claim 1, wherein at least one of the added nucleotide bases comprises an electrochemical label.

11. The method of claim 1, wherein identifying the added nucleotide base comprises detecting the added nucleotide base by employing a flow meter.

12. The method of claim 11, wherein said identifying comprises moving said microtransponder with said added base from a reaction station of an apparatus to an identification station of said apparatus using said flow meter.

13. The method of claim 12, wherein said identification station comprises a detector for detecting said added base, wherein said detector detects one or more of an optical signal, an electrical signal, and a chemical signal.

14. The method of claim 13, wherein said added base is detected by a change in fluorescence, luminescence, pH, heat, hydrogen ion concentration, pyrophosphate concentration, and radioactivity.

15. The method of claim 1 further comprising using a plurality of microtransponders for a multiplex assay containing more than one nucleic acid target.

16. The method of claim 1 further comprising performing at least a portion of the method in a microfluidic chip device.

17. A method comprising:

subjecting a sequence of target nucleotide bases captured on a microtransponder to a plurality of sequencing-by-synthesis reactions to sequentially add a sequence of single nucleotide bases that are complementary to and bound to the sequence of target nucleotide bases;

moving said microtransponder with each added nucleotide base from a reaction station of an apparatus to an identification station of said apparatus using a flow meter;

identifying each added nucleotide base after each sequencing reaction; and

moving said microtransponder from said identification station of said apparatus to said reaction station of said apparatus.

18. The method of claim 17 further comprising removing an extraneous sequencing reagent.