Nucleic acid sequencing and process

• US 20100105052A1
• Filed: 10/05/2009
• Published: 04/29/2010
• Est. Priority Date: 10/29/2007
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Reid, Clifford, Sparks, Andrew, Dahl, Fredrik, DRMANAC, Radoje, Callow, Matthew J.
• Granted Patent: US 8,518,640 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation

Abstract

The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.

Claims

1. A method of determining the identification of a first nucleotide at a detection position of a target sequence comprising a plurality of detection positions, said method comprising:

(a) providing a surface comprising a plurality of concatemers, wherein each concatemer comprises a plurality of monomers and each monomer comprises;

i) a first target domain of said target sequence comprising a first set of target detection positions;

ii) at least a first adaptor comprising;

1) a first anchor site; and

2) a second adjacent anchor site;

b) hybridizing a first anchor probe to said first anchor site;

c) hybridizing a second anchor probe to said second anchor site, wherein said second anchor probe also hybridizes to sequences outside said second anchor site;

d) hybridizing at least a first sequencing probe to said first target domain, wherein said first sequencing probe comprises;

i) a first probe domain complementary to said target domain;

ii) a unique nucleotide at a first interrogation position; and

iii) a label;

under conditions wherein if said unique nucleotide is complementary to said first nucleotide, said sequencing probe hybridizes to said concatemer; and

e) ligating said anchor probes and said sequencing probe;

f) identifying said first nucleotide.

2. A method according to claim 1 wherein a set of sequencing probes are contacted with said surface, each sequencing probe comprising:

a) a first probe domain complementary to said target domain;

b) a unique nucleotide at a first interrogation position; and

c) a label;

wherein each label of said set corresponds to said unique nucleotide.

3. A method according to claim 1 wherein each of said monomers comprises a plurality of adaptors.

4. A method according to claim 3 wherein at least one of said adaptors comprises at least one Type IIs endonuclease recognition site.

5. A method according to claim 1 wherein steps b) e) are repeated to identify a second nucleotide at a second detection position.

6. A method according to claim 1, wherein said second anchor probe comprises a set of second anchor probes comprising at least three degenerate bases that hybridizes to said sequences outside said second anchor site.

7. A method according to claim 1, wherein said second anchor probe comprises at least one terminus that is selectively activatable for ligation.

8. A method according to claim 1 wherein said surface is functionalized.

9. A method according to claim 8 wherein said functionalized surface comprises functional moieties selected from the group consisting of amines, silanes, and hydroxyls.

10. A method according to claim 1 wherein said surface comprises a plurality of spatially distinct regions comprising said immobilized concatemers.

11. A method according to claim 1 wherein said concatemers are immobilized on said surface using capture probes.

12. A method according to claim 1 further comprising fragmenting genomic nucleic acid to form target sequences.

13. A method according to claim 1 wherein said target sequence is a genomic nucleic acid sequence.

14. A substrate according to claim 13 wherein said genomic nucleic acid sequences are human.

15. A method according to claim 1, wherein said ligating step (e) is driven to between about 20 percent and about 90 percent completion.