Molecular redundant sequencing

• US 9,051,611 B2
• Filed: 08/14/2013
• Issued: 06/09/2015
• Est. Priority Date: 07/26/2007
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Christians, Fred, Turner, Stephen
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US13/967,070
• Publication Number:
  US 20140017690A1
• Time in Patent Office: 664 Days
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing

Abstract

Methods, systems and compositions where a target nucleic acid includes a registration sequence disposed therein for identification of the number or relative position of determined sequence from the template sequence. Particularly preferred aspects include a registration sequence in a circular template nucleic acid sequence which is, in turn, used in sequence by incorporation processes that rely upon template dependent, polymerase mediated primer extension in the identification of the sequence of the template.

Claims

1. A method of sequencing nucleic acid fragments within a genetic target material, comprising:

fractionating the genetic target material into separate fractions;

tagging each of said separate fractions with known exogenous registration sequences, wherein nucleic acid fragments in a single fraction are tagged with an identical known exogenous registration sequence and wherein nucleic acid fragments in said separate fractions are tagged with different known exogenous registration sequences; and

further wherein the exogenous registration sequences provide identification of which separate fraction a given nucleic acid fragment was derived from, thereby generating tagged fragments in each of said separate fractions;

circularizing the tagged fragments;

pooling the tagged fragments from all of said separate fractions;

sequencing the tagged fragments until the exogenous registration sequence has been sequenced at least twice, thereby generating sequence reads, each of which comprises at least two exogenous registration sequence portions and at least one tagged fragment sequence portion.

2. The method of claim 1, further comprising using said at least two exogenous registration sequence portions of each of said sequence reads to both (i) determine which of said separate fractions of the genetic target material corresponds to each of said tagged fragment sequence portions, and (ii) identify a sequence context of the tagged fragment sequence portion based on its position within a tagged fragment relative to the exogenous registration sequence portion.

3. The method of claim 1, wherein said sequencing is performed using a sequencing process that is nondestructive to the fragments sequence.

4. The method of claim 3, wherein said sequencing process comprises identifying bases upon incorporation in a template-directed, polymerase-mediated primer extension reaction, wherein the fragments comprise the template.

5. The method of claim 3, wherein said sequencing process comprises sequencing a product of rolling circle replication of the target nucleic acid sequence.

6. The method of claim 3, wherein said sequencing process comprises a Sanger sequencing process.

7. The method of claim 1, wherein the genetic target material is a genome.

8. The method of claim 7, wherein the separate fractions comprise fragments from different chromosomes of the genome.

9. A method of determining a nucleic acid sequence for a plurality of target nucleic acids, comprising:

providing the plurality of target nucleic acids in separate fractions, wherein each of said separate fractions comprises a different subset of said target nucleic acids, wherein each different subset comprises target nucleic, acids from a genomic region of interest;

tagging the target nucleic acids in the multiple separate fractions with exogenous registration sequences such that all of the target nucleic acids in a single fraction comprise the same exogenous registration sequence that is different from the exogenous registration sequences used to tag the target nucleic acids in other fractions, and further wherein said exogenous registration sequences tag said target nucleic acids at selected locations relative to a first sequence of nucleotides in said target nucleic acids;

sequencing the target nucleic acids to generate sequence reads comprising both target sequence information and exogenous registration sequence information such that the first sequence of nucleotides and registration sequence are sequenced multiple times;

aligning the sequence reads based at least in part upon the exogenous registration sequence information, thereby providing an aligned set of sequence reads for each of said separate fractions; and

determining a consensus sequence from said aligned set of sequence reads to determine a nucleic acid sequence for each first sequence of nucleotides in each different subset of target nucleic acids.

10. The method of claim 9, wherein the target nucleic acids are circular nucleic acids.

11. The method of claim 9, wherein said sequencing is performed using a sequencing process that is nondestructive to the fragments sequence.

12. The method of claim 9, wherein said sequencing comprises sequencing the target nucleic acids at least five times.

13. The method of claim 9, wherein said aligning is performed by a computer.

14. A composition, comprising:

a set of nucleic acid synthesis complexes comprising;

a set of circular nucleic acid templates comprising different length fragments of a nucleic acid region of interest, each having a common 5′

-terminal sequence, wherein each of the circular nucleic acid templates comprises one of said different length fragments and one exogenous registration sequence, wherein the 5′

-end of said fragment is linked to a 3′

-end of the exogenous registration sequence, and the 3′

-end of said fragment is linked to a 5′

-end of the exogenous registration sequence;

a primer sequence annealed to at least a portion of the exogenous registration sequence in each of said circular nucleic acid templates, and

a nucleic acid polymerase bound to each of said circular nucleic acid templates at said primer sequence; and

a plurality of types of nucleotides or nucleotide analogs.

15. The composition of claim 14, wherein the plurality of types of nucleotides or nucleotide analogs comprise detectable labels.

16. A method of sequencing a nucleic acid region of interest, the method comprising:

providing a nucleic acid region of interest;

fragmenting the nucleic acid region of interest to produce a nested set of fragments of the nucleic acid region of interest, wherein the nested set comprises fragments of varying lengths, and further wherein each fragment in the nested set comprises a common 5′

-terminal sequence and a variable 3′

-terminal sequence, such that each terminates at a different point in the nucleic acid region of interest depending on its length;

circularizing each fragment in the nested set of fragments by linking a 3′

-end of an exogenous registration sequence to the 5′

-end of each fragment in the nested set and linking a 5′

-end of the exogenous registration sequence to the 3′

-end of each fragment in the nested set, thereby generating circular nucleic acid templates of varying sizes;

sequencing each of the circular nucleic acid templates, thereby generating sequence reads comprising sequence information for the variable 3′

-terminal sequences; and

assembling the sequence reads based upon the sequence information for the variable terminal sequences and the varying sizes of the circular nucleic acid templates.

17. The method of claim 16, wherein said sequencing process comprises identifying bases during incorporation in a template-directed, polymerase-mediated primer extension reaction performed on the circular nucleic acid templates, wherein a polymerase synthesizes a nascent strand in a direction from the exogenous registration sequence toward the variable 5′

-terminal sequences.

18. The method of claim 16, wherein a primer is annealed to the exogenous registration sequence prior to said sequencing.

19. The method of claim 16, further comprising subjecting the fragments in the nested set to a size-based separation prior to said circularizing.

20. The method of claim 16, wherein overlapping sequence portions exist between two or more of said sequence reads, and further wherein said assembling further comprises using said overlapping sequence portions.