Methods and systems for obtaining a single molecule consensus sequence

• US 9,600,626 B2
• Filed: 03/23/2016
• Issued: 03/21/2017
• Est. Priority Date: 03/28/2008
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Travers, Kevin, Otto, Geoff, Turner, Stephen, Heiner, Cheryl, Ma, Congcong
• Primary Examiner(s): Brusca, John S
• Application Number:
  US15/078,895
• Publication Number:
  US 20160321397A1
• Time in Patent Office: 363 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides
• CPC Class Codes: C12Q 2525/307 Circular oligonucleotides
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

Computer systems, computer readable media, and computer methods for obtaining, calling, and assembling nucleic acid sequences are presented. In some aspects the invention includes the sequencing of template constructs that comprise double stranded portions in partially contiguous constructs, to provide for single molecule consensus sequence determination through one or both of sequencing sense and antisense strands in the same molecule.

Claims

1. A method for determining a single molecule consensus sequence of a target nucleic acid, the method comprising:

performing a single molecule nucleic acid sequencing of a strand of a single target nucleic acid molecule, thereby obtaining data,

wherein the strand of the single target nucleic acid molecule comprises a first region comprising a first nucleic acid sequence connected through a linking nucleic acid segment to a second region, the second region comprising a second nucleic acid sequence, the first nucleic acid sequence being the complement of the second nucleic acid sequence, and

wherein the data comprises sequence data from the first region, the linking nucleic acid segment, and the second region; and

assembling the single molecule consensus sequence of the target nucleic acid using the data.

2. The method of claim 1 wherein the assembling is carried out using a hidden Markov model.

3. The method of claim 1 wherein the assembling makes use of local or global measures of the individual sequence qualities, sequence context, or characteristic features of the data.

4. The method of claim 1, wherein said performing comprises using an electrochemical system to perform the single molecule nucleic acid sequencing.

5. The method of claim 1, wherein said performing comprises using a nanopore sensor to perform the single molecule nucleic acid sequencing.

6. The method of claim 1, wherein said target nucleic acid comprises genomic DNA.

7. The method of claim 1, wherein the first region comprises at least 500 base pairs.

8. The method of claim 1, wherein said linking nucleic acid segment comprises a registration sequence.

9. The method of claim 8, wherein said registration sequence is used for alignment of the complement of the called first nucleic acid sequence and the called second nucleic acid sequence.

10. The method of claim 1, wherein said linking nucleic acid segment comprises a barcode sequence.

11. The method of claim 1, wherein the linking nucleic acid segment comprises a hairpin loop and wherein the method further comprising, prior to the performing, ligating the hairpin loop to a double-stranded nucleic acid molecule to produce the single target nucleic acid molecule.

12. The method of claim 1, the method further comprising:

subjecting a first portion of the data to a pulse recognition process to obtain pulse data; and

invoking a base calling process that uses the pulse data to call the first nucleic acid sequence, wherein the first nucleic acid sequence is used in the assembling to assemble the consensus sequence of the target nucleic acid.

13. The method of claim 12 wherein the first portion of data and the second portion of data are obtained from the same single physical location of the target nucleic acid.

14. The method of claim 1, wherein the data from the single target nucleic acid molecule comprises an amplitude pattern that provides sequence information of the target nucleic acid.

15. The method of claim 1, wherein the data from the single target nucleic acid molecule comprises a time-dependent amplitude pattern that provides sequence information of the single target nucleic acid.

16. The method of claim 1, wherein the data from the single target nucleic acid molecule comprises time-dependent amplitude data originating from a single physical location of the single target nucleic acid molecule, and the method further comprises:

calling the first nucleic acid sequence from a first portion of the data by analyzing time-dependent amplitude data in the first portion of the data, and

calling the second nucleic acid sequence from a second portion of the data by analyzing time-dependent amplitude data in the second portion of the data, wherein the first nucleic acid sequence and the second nucleic acid sequence is used in the assembling to assemble the consensus sequence of the target nucleic acid.

17. The method of claim 1, wherein the data from the single target nucleic acid molecule comprises time-dependent amplitude data originating from a single physical location of the target nucleic acid molecule, and the method further comprises:

calling the first nucleic acid sequence from a first portion of the data by analyzing amplitude data in the first portion of the data, and

calling the second nucleic acid sequence from a second portion of the data by analyzing amplitude data in the second portion of the data, wherein the first nucleic acid sequence and the second nucleic acid sequence is used in the assembling to assemble the consensus sequence of the target nucleic acid.

18. The method of claim 1, the method further comprising:

calling the first nucleic acid sequence of the first region of the target nucleic acid molecule from a first portion of the data; and

calling the second nucleic acid sequence of the second region of the target nucleic acid molecule from a second portion of the data; and

wherein

the assembling comprises assembling the consensus sequence of the target nucleic acid using the data from either (i) an alignment of the called first nucleic acid sequence with the complement of the called second nucleic acid sequence, or (ii) an alignment of the called second nucleic acid sequence with a complement of the called first nucleic acid sequence.

19. The method of claim 18, wherein the first portion of the data and the second portion of the date originate from the same single physical location of the target nucleic acid.

20. A sequencing system for determining a single molecule consensus sequence of a target nucleic acid, wherein the sequencing system comprises:

a reagent system that comprises a target nucleic acid molecule, wherein the target nucleic acid molecule comprises a strand having a first region comprising a first nucleic acid sequence connected through a linking nucleic acid segment to a second region, the second region comprising a second nucleic acid sequence, the first nucleic acid sequence being the complement of the second nucleic acid sequence; and

an analytical system that comprises nontransitory instructions for performing single molecule nucleic acid sequencing of the strand of the single target nucleic acid molecule thereby obtaining data,

wherein the data comprises sequence data from the first region, the linking nucleic acid segment, and the second region, and

wherein the data is assembled to obtain a single molecule consensus sequence of the target nucleic acid.

21. The sequencing system of claim 20 wherein the single molecule consensus sequence is determined by the analytical system using a hidden Markov model.

22. The sequencing system of claim 20 wherein the single molecule consensus sequence is determined by the analytical system using local or global measures of the individual sequence qualities, sequence context, or characteristic features of the data.

23. The sequencing system of claim 20, wherein said reagent system comprises an electrochemical system.

24. The sequencing system of claim 20, wherein said reagent system comprises a nanopore sensor.

25. The sequencing system of claim 20, wherein said target nucleic acid comprises genomic DNA.

26. The sequencing system of claim 20, wherein the first region comprises at least 500 base pairs.

27. The sequencing system of claim 20, wherein said linking nucleic acid segment comprises a registration sequence.

28. The sequencing system of claim 27, wherein said registration sequence is used for alignment of the complement of the called first nucleic acid sequence and called second nucleic acid sequence by the analytical system.

29. The sequencing system of claim 20, wherein said linking nucleic acid segment comprises a barcode sequence.

30. The sequencing system of claim 20 wherein the the linking nucleic acid segment comprises a hairpin loop and wherein the target nucleic acid is produced by ligating a hairpin loop to a double-stranded nucleic acid molecule.

31. The sequencing system of claim 20, wherein the analytical system is configured to perform a method that comprises:

calling the first nucleic acid sequence of the first region of the target nucleic acid molecule from a first portion of the data;

calling the second nucleic acid sequence of the second region of the target nucleic acid molecule from a second portion of the data; and

assembling the consensus sequence of the target nucleic acid using the data from either (i) an alignment of the called first nucleic acid sequence with the complement of the called second nucleic acid sequence, or (ii) an alignment of the called second nucleic acid sequence with a complement of the called first nucleic acid sequence.

32. The sequencing system of claim 31, wherein the first portion of the data and the second portion of the date originate from the same single physical location of the target nucleic acid.