Reagents and methods for the analysis of linked nucleic acids

• US 10,640,811 B2
• Filed: 02/15/2019
• Issued: 05/05/2020
• 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, Kaijang
• Application Number:
  US16/277,794
• Publication Number:
  US 20190169678A1
• Time in Patent Office: 445 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) 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) measuring 5-methylcytosine in each of the linked fragments in the set to produce at least two linked measurements of 5-methylcytosine.

2. The method of claim 1, wherein step (b) comprises an enrichment process to enrich for fragments of genomic DNA containing 5-methylcytosine.

3. The method of claim 1, wherein step (b) comprises a bisulfite conversion process.

4. The method of claim 1, wherein step (b) comprises a nucleic acid sequencing process.

5. 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 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 measurements of 5-methylcytosine.

6. 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 measurements of 5-methylcytosine for the first cell-free circulating microparticle and a second set of linked measurements of 5-methylcytosine for the second cell-free circulating microparticle.

7. 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 measurements of 5-methylcytosine, one for each of the n cell-free circulating microparticles.

8. The method of claim 7, 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.

9. The method of claim 6, wherein prior to step (a), the method further comprises the step of partitioning the sample into at least two different reaction volumes.

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

(a) 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) measuring 5-methylcytosine in each of the linked fragments in the set to produce at least two linked measurements of 5-methylcytosine, wherein the at least two linked measurements of 5-methylcytosine are linked by the barcode sequence.

11. The method of claim 10, 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.

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 measurements of 5-methylcytosine for the first cell-free circulating microparticle and a second set of linked measurements of 5-methylcytosine for the second cell-free circulating microparticle, wherein the at least two linked measurements of 5-methylcytosine for the first cell-free circulating microparticle are linked by a different barcode sequence to the at least two linked measurements of 5-methylcytosine of the second cell-free circulating microparticle.

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) 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) measuring 5-methylcytosine in each of the linked fragments in the set to produce at least two linked measurements of 5-methylcytosine, wherein the at least two linked measurements of 5-methylcytosine are linked by the set of barcode sequences.

15. The method of claim 14, 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.

16. The method of claim 14, 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 measurements of 5-methylcytosine for the first cell-free circulating microparticle and a second set of linked measurements of 5-methylcytosine for the second cell-free circulating microparticle, wherein the first set of linked measurements of 5-methylcytosine are linked by a different set of barcode sequences to the second set of linked measurements of 5-methylcytosine.

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