Compositions containing identifier sequences on solid supports for nucleic acid sequence analysis

• US 10,731,213 B2
• Filed: 12/17/2015
• Issued: 08/04/2020
• Est. Priority Date: 01/17/2008
• Status: Active Grant

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Cantor, Charles R.
• Primary Examiner(s): Forman, Betty J
• Application Number:
  US14/973,467
• Publication Number:
  US 20160102352A1
• Time in Patent Office: 1,692 Days
• 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 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2531/101 Linear amplification, i.e. non exponential
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer

Abstract

Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

Claims

1. A collection of solid supports comprising single-stranded nucleic acid species,

(a) wherein each solid support in the collection comprises more than one single-stranded nucleic acid species covalently linked to the solid support,

wherein each single-stranded nucleic acid species linked to a common solid support comprises an identifier sequence and a probe sequence, and

wherein the identifier sequence is oriented 5′

to the probe sequence;

(b) wherein all the single-stranded nucleic acid species linked to the common solid support share the same identifier sequence, and

wherein the identifier sequence from the more than one single-stranded nucleic acid species linked to the common solid support in the collection is different from the identifier sequences of the single-stranded nucleic acid species linked to the other solid supports in the collection, whereby each solid support in the collection is associated with a unique identifier sequence; and

(c) wherein the probe sequence of each of the more than one single-stranded nucleic acid species linked to the solid support allows the more than one single-stranded nucleic acid to hybridize a subsequence in a sample nucleic acid, and

(d) wherein the probe sequences of the more than one single-stranded nucleic acid species on each solid support comprise at least 10 different species.

2. The solid support collection of claim 1, wherein the single-stranded nucleic acid species of each solid support in the collection further comprises a primer sequence.

3. The solid support collection of claim 2, wherein the primer sequence, the identifier sequence and the probe sequence are oriented 5′

-(primer sequence)-(identifier sequence)-(probe sequence)-3′

.

4. The solid support collection of claim 2, wherein single-stranded nucleic acid species linked to a common solid support in the collection share a common primer sequence.

5. The solid support collection of claim 4, wherein the primer sequence is a universal primer sequence.

6. The solid support collection of claim 2, wherein the single-stranded nucleic acid species of all the solid supports in the collection share a common primer sequence.

7. The solid support collection of claim 6, wherein the primer sequence is a universal primer sequence.

8. The solid support collection of claim 1, wherein the solid support is a bead or particle.

9. The solid support collection of claim 8, wherein the solid support is a microbead, a nanobead, a microparticle or a nanoparticle.

10. The solid support collection of claim 8, wherein the bead or particle is a gel.

11. The solid support collection of claim 8, wherein the bead or particle comprises a magnetic material.

12. The solid support collection of claim 1, wherein the more than one probe sequences are complementary to a DNA sequence.

13. The solid support collection of claim 1, wherein the more than one probe sequences are complementary to a fragmented DNA sequence.

14. The solid support collection of claim 1, wherein the more than one probe sequences are complementary to a single-stranded nucleic acid.

15. The solid support collection of claim 1, wherein the solid support collection is comprised in an emulsion.

16. A substrate comprising a solid support collection of claim 8, wherein:

(a) the solid supports are beads; and

(b) the beads are oriented in an array.

17. The substrate of claim 16, wherein the single-stranded nucleic acid species of each bead in the collection further comprises a primer sequence.

18. The substrate of claim 17, wherein the primer sequence, the identifier sequence and the probe sequence are oriented 5′

-(primer sequence)-(identifier sequence)-(probe sequence)-3′

.

19. The substrate of claim 17, wherein the single-stranded nucleic acid species linked to a common bead in the collection share a common primer sequence.

20. The substrate of claim 17, wherein the primer sequence is a universal primer sequence.

21. The substrate of claim 17, wherein the single-stranded nucleic acid species of all the beads in the collection share a common primer sequence.

22. The substrate of claim 21, wherein the primer sequence is a universal primer sequence.

23. The substrate of claim 16, wherein the solid support is a microbead or a nanobead.

24. The substrate of claim 16, wherein the bead comprises a gel.

25. The substrate of claim 16, wherein the bead comprises a magnetic material.

26. The substrate of claim 16, wherein the more than one probe sequences are complementary to a DNA sequence.

27. The substrate of claim 16, wherein the more than one probe sequences are complementary to a fragmented DNA sequence.