Entangled mate sequencing

• US 10,385,391 B2
• Filed: 09/22/2010
• Issued: 08/20/2019
• Est. Priority Date: 09/22/2009
• Status: Active Grant

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Roth, Frederick P., Mellor, Joseph C., Lu, Yong, Chee, Mark
• Primary Examiner(s): Vivlemore, Tracy
• Assistant Examiner(s): Kaup, Sahana S
• Application Number:
  US13/497,069
• Publication Number:
  US 20120245039A1
• Time in Patent Office: 3,254 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• 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 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target

Abstract

Methods and compositions are provided for performing a set of N DNA sequencing reaction cycles whereby sequence information is obtained for approximately 2*N nucleotide bases.

Claims

1. A method of determining nucleotide sequence identities of heterogeneous, tethered nucleic acid template sequences comprising the steps of:

providing a mosaic target nucleic acid sequence including a first template nucleic acid sequence and a second template nucleic acid sequence, wherein the first and second template nucleic acid sequences are tethered and heterogeneous and of relatively homogeneous length;

simultaneously reading the first template nucleic acid sequence and the second template nucleic acid sequence to obtain a mixed entangled sequencing signal representative of each of the first template nucleic acid sequence and the second template nucleic acid sequence; and

disentangling the mixed sequencing signal into its constituent individual template sequences by matching the mixed entangled sequencing signal to its closest match in a reference collection of known sequence signatures wherein the mixed entangled sequencing signal is obtained by annealing a first primer sequence to a portion of the first template nucleic acid sequence and a second primer sequence to a portion of the second template nucleic acid sequence;

extending the annealed primers simultaneously; and

sequentially determining the identity of each set of two bases extended from the 3′

ends of the first and second primers to obtain mixed base signatures and using said mixed base signatures to obtain a mixed nucleic acid sequence signature of the tethered first and second template nucleic acid sequences, wherein the identity of each set of two bases extended from the 3′

ends of the first and second primers is sequentially determined by nucleotide addition sequencing.

2. The method of claim 1, wherein the heterogeneous, tethered nucleic acid template sequences represent one or more of a genome, a proteome, a transcriptome or a cellular pathway.

21. The method of claim 1, wherein the step of determining the sequence is performed by comparing the nucleic acid sequence signature to a reference collection of seed sequences.

3. A method of determining nucleotide sequence identities of tethered, heterogeneous nucleic acid template sequences comprising the steps of:

providing a heterogeneous library of mosaic target nucleic acid sequences, in which a plurality include a first template nucleic acid sequence and a second template nucleic acid sequence, wherein the first and second template nucleic acid sequences are tethered and heterogeneous and of relatively homogeneous length;

simultaneously reading the first template nucleic acid sequence and the second template nucleic acid sequence to obtain a mixed entangled sequencing signal representative of each of the first template nucleic acid sequence and the second template nucleic acid sequence; and

disentangling the mixed sequencing signal into its constituent individual template sequences by matching the mixed entangled sequencing signal to its closest match in a reference collection of known sequence signatures wherein the mixed entangled sequencing signal is obtained by annealing a first primer sequence to a portion of the first template nucleic acid sequence and a second primer sequence to a portion of the second template nucleic acid sequence;

extending the annealed primers simultaneously; and

sequentially determining the identity of each set of two bases extended from the 3′

ends of the first and second primers to obtain mixed base signatures and using said mixed base signatures to obtain a mixed nucleic acid sequence signature of the tethered first and second template nucleic acid sequences, wherein the identity of each set of two bases extended from the 3′

ends of the first and second primers is sequentially determined by nucleotide addition sequencing.

4. The method of claim 3, wherein the first template nucleic acid sequence is a barcode sequence and the second template nucleic acid sequence is a genomic sequence.

5. The method of claim 3, wherein the reference collection is in a database.

6. The method of claim 3, wherein the plurality includes the first template nucleic acid sequence, the second template nucleic acid sequence, and a third template nucleic acid sequence wherein the first, second and third template nucleic acid sequences are tethered and heterogeneous and of relatively homogeneous length;

simultaneously reading the first template nucleic acid sequence, the second template nucleic acid sequence and the third template nucleic acid sequence to obtain a mixed entangled sequencing signal representative of each of the first template nucleic acid sequence the second template nucleic acid sequence and the third template nucleic acid sequence; and

disentangling the mixed sequencing signal into its constituent individual template sequences by matching the mixed entangled sequencing signal to its closest match in a reference collection of known sequence signatures.

7. The method of claim 3, wherein the mosaic target nucleic acid sequence includes 3 or more tethered, nucleic acid sequences.

8. The method of claim 3, wherein the mosaic target nucleic acid sequence is present on an array.

9. A method of determining nucleotide sequence identities of two tethered nucleic acid sequences comprising the steps of:

providing a heterogeneous library of mosaic target nucleic acid sequences, in which a plurality include a first template nucleic acid sequence and a second template nucleic acid sequence, wherein the first and second template nucleic acid sequences are tethered and heterogeneous and of relatively homogeneous length;

simultaneously reading the first template nucleic acid sequence, the second template nucleic acid sequence and the third template nucleic acid sequence to obtain a mixed entangled sequencing signal representative of each of the first template nucleic acid sequence the second template nucleic acid sequence and the third template nucleic acid sequence; and

disentangling the mixed sequencing signal into its constituent individual template sequences by matching the mixed entangled sequencing signal to its closest match in a reference collection of known sequence signatures

wherein the mixed entangled sequencing signal is obtained by annealing a first primer sequence to a portion of the first template nucleic acid sequence and a second primer sequence to a portion of the second template nucleic acid sequence;

extending the annealed primers simultaneously; and

sequentially determining the identity of each set of two bases extended from the 3′

ends of the first and second primers to obtain mixed base signatures and using said mixed base signatures to obtain a mixed nucleic acid sequence signature of the tethered first and second template nucleic acid sequences, wherein the identity of each set of two bases extended from the 3′

ends of the first and second primers is sequentially determined by nucleotide addition sequencing.

10. The method of claim 9, wherein the reference collection is a collection of sequence signatures and the second nucleic acid sequence is not present in the reference collection of sequence signatures.

11. The method of claim 9, wherein each mixed base signature sequence includes a set of two bases selected from the group consisting of AA, CC, GG, TT, AC, AG, AT, CG, CT and GT.

12. The method of claim 9, wherein the first and second template nucleic acid sequences are barcode sequences.

13. The method of claim 9, wherein the first and second template nucleic acid sequences are genomic sequences.

14. The method of claim 9, wherein the first and second primer sequences have the same sequence identity.

15. The method of claim 9, wherein the first and second primer sequences have a different sequence identity.

16. A method of identifying a cell having heterogeneous nucleic acid sequences comprising the steps of:

providing a cell having a mosaic target nucleic acid sequence including a first barcode sequence and a second barcode sequence, wherein the first and second barcode sequences are tethered and heterogeneous and of relatively homogeneous length;

simultaneously reading the first barcode sequence and the second barcode sequence to obtain a mixed entangled sequencing signal representative of each of the first barcode sequence and second barcode sequence;

disentangling the mixed sequencing signal into its constituent individual barcode sequences by matching the mixed entangled sequencing signal to its closest match in a reference collection of known sequence signatures;

wherein the mixed entangled sequencing signal is obtained by annealing a first primer sequence to a portion of the first template nucleic acid sequence and a second primer sequence to a portion of the second template nucleic acid sequence;

extending the annealed primers simultaneously;

sequentially determining the identity of each set of two bases extended from the 3′

ends of the first and second primers to obtain mixed base signatures and using said mixed base signatures to obtain a mixed nucleic acid sequence signature of the tethered first and second template nucleic acid sequences, wherein the identity of each set of two bases extended from the 3′

ends of the first and second primers is sequentially determined by nucleotide addition sequencing; and

determining the nucleotide sequence identity of one or both of the tethered first and second barcode sequences to identify the cell from the mixed nucleic acid barcode sequence signature.

17. The method of claim 16, wherein the cell is a yeast cell.

18. The method of claim 17, wherein the yeast cell contains two or more alterations.

19. The method of claim 16, wherein the heterogeneous nucleic acid sequences represent one or more of a genome, a proteome, a transcriptome or a cellular pathway.

20. The method of claim 16, wherein the heterogeneous nucleic acid sequences represent Homo sapiens nucleic acid sequences.