Methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction

1. A method for validating the integrity of a nucleic acid template in a multiplex sequencing reaction, the method comprising:

obtaining a template nucleic acid;

incorporating at least two of the same sequence identifiers into the template, wherein the sequence identifiers comprise four or more nucleotides;

sequencing the template to generate sequence reads, and

analyzing the sequence reads to determine if the two incorporated sequence identifiers remain associated with the template, thereby validating the integrity of the nucleic acid template in a multiplex sequencing reaction.

2. The method according to claim 1 , wherein a first identifier is incorporated into a 5′ portion of the template and a second identifier is incorporated into a 3′ portion of the template.

3. The method according to claim 2 , wherein after incorporation of the identifiers, the template has the following configuration from 5′ to 3′: a first known sequence; a first barcode sequence; a second known sequence; a target polynucleotide sequence; a third known sequence; a second barcode sequence; and a fourth known sequence.

4. The method according to claim 1 , wherein a first identifier is incorporated into a 5′ end of the template and a second identifier is incorporated into a 3′ end of the template.

5. The method according to claim 1 , wherein prior to sequencing, the template is attached to a substrate.

6. The method according to claim 2 , wherein the template is directly attached to the substrate.

7. The method according to claim 2 , wherein the template is indirectly attached to the substrate.

8. The method according to claim 5 , further comprising, amplifying the template.

9. The method according to claim 1 , wherein sequencing is sequencing by synthesis.

10. The method according to claim 9 , wherein the sequencing by synthesis is single molecule sequencing by synthesis.

11. The method according to claim 1 , wherein sequencing comprises:

hybridizing a primer to the template to form a template/primer duplex;

contacting the duplex with a polymerase enzyme in the presence of at least one detectably labeled nucleotide under conditions that permit the polymerase to add nucleotides to the primer in a template-dependent manner;

detecting a signal from the incorporated labeled nucleotide; and

sequentially repeating the contacting and detecting steps at least once, wherein sequential detection of incorporated labeled nucleotide determines the sequence of the nucleic acid.

12. The method according to claim 11 , wherein the detectably labeled nucleotide is an optically labeled nucleotide.

13. The method according to claim 12 , wherein the optically labeled nucleotide is a fluorescently labeled nucleotides.

14. The method according to claim 1 , wherein the pair of identifiers are first and second barcode sequences that are attached to the template.

15. The method according to claim 14 , wherein a first barcode sequence is attached to a 5′ end of the template and a second barcode sequence is attached to a 3′ end of the template.

16. A method for analyzing a nucleic acid, the method comprising:

obtaining a nucleic acid template;

attaching a pair of the same barcode sequences to the template, wherein the barcodes comprise four or more nucleotides;

sequencing the template to generate sequence reads, and

analyzing the sequence reads to determine if the pair of attached barcode sequences remain associated with the template.

17. The method according to claim 16 , wherein a first barcode sequence is incorporated into a 5′ portion of the template and a second barcode sequence is incorporated into a 3′ portion of the template.

18. The method according to claim 17 , wherein after attaching of the pair of barcode sequences, the template has the following configuration from 5′ to 3′: a first known sequence; a first barcode sequence; a second known sequence; a target polynucleotide sequence;

a third known sequence; a second barcode sequence; and a fourth known sequence.

19. The method according to claim 16 , wherein a first identifier is incorporated into a 5′ end of the template and a second identifier is incorporated into a 3′ end of the template.

20. The method according to claim 16 , wherein prior to sequencing, the template is attached to a substrate.

21. The method according to claim 20 , wherein the template is directly attached to the substrate.

22. The method according to claim 20 , wherein the template is indirectly attached to the substrate.

23. The method according to claim 20 , further comprising, amplifying the template.

24. The method according to claim 16 , wherein sequencing is sequencing by synthesis.

25. The method according to claim 24 , wherein the sequencing by synthesis is single molecule sequencing by synthesis.

26. The method according to claim 16 , wherein sequencing comprises:

hybridizing a primer to the template to form a template/primer duplex;

contacting the duplex with a polymerase enzyme in the presence of at least one detectably labeled nucleotide under conditions that permit the polymerase to add nucleotides to the primer in a template-dependent manner;

detecting a signal from the incorporated labeled nucleotide; and

sequentially repeating the contacting and detecting steps at least once, wherein sequential detection of incorporated labeled nucleotide determines the sequence of the nucleic acid.

27. The method according to claim 26 , wherein the labeled nucleotide is an optically labeled nucleotide.

28. The method according to claim 27 , wherein the optically labeled nucleotide is a fluorescently labeled nucleotides.

29. A method for analyzing a nucleic acid, the method comprising:

obtaining a nucleic acid template;

attaching a first barcode sequence to a 5′ portion of the template and a second barcode sequence to a 3′ portion of the template, wherein the first and second barcode sequences are the same, and wherein the barcode sequences comprise four or more nucleotides;

amplifying the template;

sequencing the template to generate sequence reads, and

analyzing the sequence reads to determine if the pair of attached barcode sequences remain associated with the template.

30. The method according to claim 29 , wherein after attaching of the first and second barcode sequences, the template has the following configuration from 5′ to 3′: a first known sequence; a first barcode sequence; a second known sequence; a target polynucleotide sequence; a third known sequence; a second barcode sequence; and a fourth known sequence.

31. The method according to claim 29 , wherein a first identifier is incorporated into a 5′ end of the template and a second identifier is incorporated into a 3′ end of the template.

32. The method according to claim 29 , wherein prior to amplifying, the template is immobilized to a solid support.

33. The method according to claim 29 , wherein sequencing comprises:

hybridizing a primer to the template to form a template/primer duplex;

contacting the duplex with a polymerase enzyme in the presence of at least one detectably labeled nucleotide under conditions that permit the polymerase to add nucleotides to the primer in a template-dependent manner;

detecting a signal from the incorporated labeled nucleotide; and

sequentially repeating the contacting and detecting steps at least once, wherein sequential detection of incorporated labeled nucleotide determines the sequence of the nucleic acid.