Reagents and methods for the analysis of linked nucleic acids

• US 10,287,624 B2
• Filed: 12/19/2017
• Issued: 05/14/2019
• Est. Priority Date: 12/23/2016
• Status: Active Grant

• Current Assignee: CS Genetics Limited
• Original Assignee: CS Genetics Limited
• Inventors: Edelman, Lucas Brandon
• Primary Examiner(s): Zhang, Kaijiang
• Application Number:
  US15/750,824
• Publication Number:
  US 20180291427A1
• Time in Patent Office: 511 Days
• Field of Search: None
• 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 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• 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 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2537/159 Reduction of complexity, e.g. amplification of subsets, removing duplicated genomic regions
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

Abstract

Reagents and methods for the analysis of nucleic acids (e.g. genomic DNA) of circulating microparticles (i.e. microparticles originating from blood) are provided. The methods comprise linking at least two fragments of a target nucleic acid of a circulating microparticle to produce a set of at least two linked fragments of the target nucleic acid. In the methods, fragments of a target nucleic acid may be linked by techniques such as barcoding, partitioning, ligation and/or separate sequencing. The sequencing of a set of linked fragments provides a set of informatically linked sequence reads corresponding to the sequences of fragments from a single microparticle.

Claims

1. A method of analysing a sample comprising a cell-free circulating microparticle, wherein the cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises:

(a) preparing the sample for sequencing comprising linking at least two of the at least two fragments of genomic DNA to produce a set of at least two linked fragments of genomic DNA; and

(b) sequencing each of the linked fragments in the set to produce at least two linked sequence reads.

2. The method of claim 1, wherein at least 3, at least 4, at least 5, at least 10, at least 50, at least 100, at least 500, at least 1000, at least 5000, at least 10,000, at least 100,000, or at least 1,000,000 fragments of genomic DNA of the cell-free circulating microparticle are linked and then sequenced to produce at least 3, at least 4, at least 5, at least 10, at least 50, at least 100, at least 500, at least 1000, at least 5000, at least 10,000, at least 100,000, or at least 1,000,000 linked sequence reads.

3. The method of claim 1, wherein the sample comprises first and second cell-free circulating microparticles, wherein each cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises performing step (a) to produce a first set of linked fragments of genomic DNA for the first cell-free circulating microparticle and a second set of linked fragments of genomic DNA for the second cell-free circulating microparticle, and performing step (b) to produce a first set of linked sequence reads for the first cell-free circulating microparticle and a second set of linked sequence reads for the second cell-free circulating microparticle.

4. The method of claim 3, wherein prior to step (a), the method further comprises the step of partitioning the sample into at least two different reaction volumes.

5. The method of claim 1, wherein the sample comprises n cell-free circulating microparticles, wherein each cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises performing step (a) to produce n sets of linked fragments of genomic DNA, one set for each of the n cell-free circulating microparticles, and performing step (b) to produce n sets of linked sequence reads, one for each of the n cell-free circulating microparticles.

6. The method of claim 5, wherein n is at least 3, at least 5, at least 10, at least 50, at least 100, at least 1000, at least 10,000, at least 100,000, at least 1,000,000, at least 10,000,000, or at least 100,000,000 cell-free circulating microparticles.

7. The method of claim 1, wherein the method comprises:

(a) preparing the sample for sequencing comprising appending the at least two fragments of genomic DNA of the cell-free circulating microparticle to a barcode sequence to produce a set of linked fragments of genomic DNA; and

(b) sequencing each of the linked fragments in the set to produce at least two linked sequence reads, wherein the at least two linked sequence reads are linked by the barcode sequence.

8. The method of claim 7, wherein prior to the step of appending the at least two fragments of genomic DNA of the cell-free circulating microparticle to a barcode sequence, the method comprises appending a coupling sequence to each of the fragments of genomic DNA of the cell-free circulating microparticle, wherein the coupling sequences are then appended to the barcode sequence to produce the set of linked fragments of genomic DNA.

9. The method of claim 7, wherein the sample comprises first and second cell-free circulating microparticles, wherein each cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises performing step (a) to produce a first set of linked fragments of genomic DNA for the first cell-free circulating microparticle and a second set of linked fragments of genomic DNA for the second cell-free circulating microparticle, and performing step (b) to produce a first set of linked sequence reads for the first cell-free circulating microparticle and a second set of linked sequence reads for the second cell-free circulating microparticle, wherein the at least two linked sequence reads for the first cell-free circulating microparticle are linked by a different barcode sequence to the at least two linked sequence reads of the second cell-free circulating microparticle.

10. The method of claim 1, wherein the method comprises:

(a) preparing the sample for sequencing comprising appending each of the at least two fragments of genomic DNA of the cell-free circulating microparticle to a different barcode sequence of a set of barcode sequences to produce a set of linked fragments of genomic DNA; and

(b) sequencing each of the linked fragments in the set to produce at least two linked sequence reads, wherein the at least two linked sequence reads are linked by the set of barcode sequences.

11. The method of claim 10, wherein prior to the step of appending each of the at least two fragments of genomic DNA of the cell-free circulating microparticle to a different barcode sequence, the method comprises appending a coupling sequence to each of the fragments of genomic DNA of the cell-free circulating microparticle, wherein each of the at least two fragments of genomic DNA of the cell-free circulating microparticle is appended to a different barcode sequence of the set of barcode sequences by its coupling sequence.

12. The method of claim 10, wherein the sample comprises first and second cell-free circulating microparticles, wherein each cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises performing step (a) to produce a first set of linked fragments of genomic DNA for the first cell-free circulating microparticle and a second set of linked fragments of genomic DNA for the second cell-free circulating microparticle, and performing step (b) to produce a first set of linked sequence reads for the first cell-free circulating microparticle and a second set of linked sequence reads for the second cell-free circulating microparticle, wherein the first set of linked sequence reads are linked by a different set of barcode sequences to the second set of linked sequence reads.

13. The method of claim 12, wherein prior to the step of appending, the method further comprises the step of partitioning the sample into at least two different reaction volumes.

14. The method of claim 1, wherein the method comprises:

(a) preparing the sample for sequencing comprising;

(i) contacting the sample with a multimeric barcoding reagent comprising first and second barcode regions linked together, wherein each barcode region comprises a nucleic acid sequence, and

(ii) appending barcode sequences to each of the at least two fragments of genomic DNA of the cell-free circulating microparticle to produce first and second different barcoded target nucleic acid molecules, wherein the first barcoded target nucleic acid molecule comprises the nucleic acid sequence of the first barcode region and the second barcoded target nucleic acid molecule comprises the nucleic acid sequence of the second barcode region; and

(b) sequencing each of the barcoded target nucleic acid molecules to produce at least two linked sequence reads;

and optionally wherein prior to the step of appending barcode sequences to each of the at least two fragments of genomic DNA of the cell-free circulating microparticle, the method comprises appending a coupling sequence to each of the fragments of genomic DNA of the cell-free circulating microparticle, wherein a barcode sequence is then appended to the coupling sequence of each of the at least two fragments of genomic DNA of the cell-free circulating microparticle to produce the first and second different barcoded target nucleic acid molecules.

15. The method of claim 14, wherein the method comprises analysing a sample comprising at least two cell-free circulating microparticles, wherein each cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises the steps of:

(a) preparing the sample for sequencing comprising;

(i) contacting the sample with a library of multimeric barcoding reagents comprising a multimeric barcoding reagent for each of the two or more cell-free circulating microparticles, wherein each multimeric barcoding reagent is as defined in claim 14; and

(ii) appending barcode sequences to each of the at least two fragments of genomic DNA of each cell-free circulating microparticle, wherein at least two barcoded target nucleic acid molecules are produced from each of the at least two cell-free circulating microparticles, and wherein the at least two barcoded target nucleic acid molecules produced from a single cell-free circulating microparticle each comprise the nucleic acid sequence of a barcode region from the same multimeric barcoding reagent; and

(b) sequencing each of the barcoded target nucleic acid molecules to produce at least two linked sequence reads for each cell-free circulating microparticle.

16. The method of claim 15, wherein prior to the step of appending, the method further comprises the step of partitioning the sample into at least two different reaction volumes.

17. The method of claim 1, wherein the cell-free circulating microparticle is selected from the group consisting of:

an exosome, an apoptotic body, and an extracellular microvesicle.

18. A method of preparing a sample for sequencing, wherein the sample comprises a cell-free circulating microparticle, wherein the cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises appending the at least two fragments of genomic DNA of the cell-free circulating microparticle to a barcode sequence, or to different barcode sequences of a set of barcode sequences, to produce a set of linked fragments of genomic DNA.

19. The method of claim 18, wherein prior to the step of appending the at least two fragments of genomic DNA of the cell-free circulating microparticle to a barcode sequence, or to different barcode sequences of a set of barcode sequences, the method comprises appending a coupling sequence to each of the fragments of genomic DNA of the cell-free circulating microparticle, wherein the coupling sequences are then appended to the barcode sequence, or to the different barcode sequences of a set of barcode sequences, to produce the set of linked fragments of genomic DNA.

20. The method of claim 18, wherein the sample comprises first and second cell-free circulating microparticles, wherein each cell-free circulating microparticle contains at least two fragments of genomic DNA, and wherein the method comprises appending the at least two fragments of genomic DNA of the first cell-free circulating microparticle to a first barcode sequence, or to different barcode sequences of a first set of barcode sequences, to produce a first set of linked fragments of genomic DNA and appending the at least two fragments of genomic DNA of the second cell-free circulating microparticle to a second barcode sequence, or to different barcode sequences of a second set of barcode sequences, to produce a second set of linked fragments of genomic DNA.

21. The method of claim 20, wherein prior to the step of appending, the method further comprises the step of partitioning the sample into at least two different reaction volumes.

22. The method of claim 18, wherein the cell-free circulating microparticle is selected from the group consisting of:

an exosome, an apoptotic body, and an extracellular microvesicle.

23. A method of preparing a sample for sequencing, wherein the sample comprises first and second cell-free circulating microparticles, and wherein each cell-free circulating microparticle contains at least two fragments of a target nucleic acid, and wherein the method comprises the steps of:

(a) contacting the sample with a library comprising at least two multimeric barcoding reagents, wherein each multimeric barcoding reagent comprises first and second barcode regions linked together, wherein each barcode region comprises a nucleic acid sequence and wherein the first and second barcode regions of a first multimeric barcoding reagent are different to the first and second barcode regions of a second multimeric barcoding reagent of the library; and

(b) appending barcode sequences to each of first and second fragments of the target nucleic acid of the first cell-free circulating microparticle to produce first and second barcoded target nucleic acid molecules for the first cell-free circulating microparticle, wherein the first barcoded target nucleic acid molecule comprises the nucleic acid sequence of the first barcode region of the first multimeric barcoding reagent and the second barcoded target nucleic acid molecule comprises the nucleic acid sequence of the second barcode region of the first multimeric barcoding reagent, and appending barcode sequences to each of first and second fragments of the target nucleic acid of the second cell-free circulating microparticle to produce first and second barcoded target nucleic acid molecules for the second cell-free circulating microparticle, wherein the first barcoded target nucleic acid molecule comprises the nucleic acid sequence of the first barcode region of the second multimeric barcoding reagent and the second barcoded target nucleic acid molecule comprises the nucleic acid sequence of the second barcode region of the second multimeric barcoding reagent.

24. The method of claim 23, wherein the method comprises the steps of:

(a) contacting the sample with a library comprising at least two multimeric barcoding reagents, wherein each multimeric barcoding reagent comprises first and second barcoded oligonucleotides linked together, wherein the barcoded oligonucleotides each comprise a barcode region and wherein the barcode regions of the first and second barcoded oligonucleotides of a first multimeric barcoding reagent of the library are different to the barcode regions of the first and second barcoded oligonucleotides of a second multimeric barcoding reagent of the library; and

(b) annealing or ligating the first and second barcoded oligonucleotides of the first multimeric barcoding reagent to first and second fragments of the target nucleic acid of the first cell-free circulating microparticle to produce first and second barcoded target nucleic acid molecules, and annealing or ligating the first and second barcoded oligonucleotides of the second multimeric barcoding reagent to first and second fragments of the target nucleic acid of the second cell-free circulating microparticle to produce first and second barcoded target nucleic acid molecules;

and optionally wherein prior to the step of annealing or ligating the first and second barcoded oligonucleotides to first and second fragments of genomic DNA, the method comprises appending a coupling sequence to each of the fragments of genomic DNA, wherein the first and second barcoded oligonucleotides are then annealed or ligated to the coupling sequences of the first and second fragments of genomic DNA.

25. The method of claim 24, wherein step (b) comprises:

(i) annealing the first and second barcoded oligonucleotides of the first multimeric barcoding reagent to first and second fragments of genomic DNA of the first cell-free circulating microparticle, and annealing the first and second barcoded oligonucleotides of the second multimeric barcoding reagent to first and second fragments of genomic DNA of the second cell-free circulating microparticle; and

(ii) extending the first and second barcoded oligonucleotides of the first multimeric barcoding reagent to produce first and second different barcoded target nucleic acid molecules and extending the first and second barcoded oligonucleotides of the second multimeric barcoding reagent to produce first and second different barcoded target nucleic acid molecules, wherein each of the barcoded target nucleic acid molecules comprises at least one nucleotide synthesised from the fragments of genomic DNA as a template.

26. The method of claim 23, wherein prior to step (b), the method further comprises the step of partitioning the sample into at least two different reaction volumes.

27. The method of claim 23, wherein the cell-free circulating microparticle is selected from the group consisting of:

an exosome, an apoptotic body, and an extracellular microvesicle.