Granted Patent
B2
US 12,444,480 · App. 18/436,754 · Granted Oct 14, 2025
Methods for genome assembly and haplotype phasing
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Abstract
The disclosure provides methods to assemble genomes of eukaryotic or prokaryotic organisms. The disclosure further provides methods for haplotype phasing and meta-genomics assemblies.
Claims (23)
1. A method for haplotype phasing, the method comprising:
(a) crosslinking deoxyribonucleic acid (DNA) within chromosomes to form crosslinked DNA;
(b) fragmenting the crosslinked DNA to form fragmented crosslinked DNA;
(c) ligating regions of the fragmented crosslinked DNA to create a plurality of ligation products, wherein at least two of the regions comprise an intra-chromosomal pair;
(d) sequencing the plurality of ligation products or a derivative thereof to generate sequencing reads; and
(e) using the sequencing reads to determine haplotype phasing.
2. The method of claim 1 , further comprising isolating the chromosomes before the crosslinking.
3. The method of claim 1 , further comprising purifying the plurality of ligation products prior to (d).
4. The method of claim 3 , wherein the purifying comprises pulling down the plurality of ligation products.
5. The method of claim 1 , further comprising, after (b), marking ends of the fragmented crosslinked DNA.
6. The method of claim 5 , wherein the marking comprises filling in ends of the fragmented crosslinked DNA with nucleotides comprising one or more markers.
7. The method of claim 6 , wherein the one or more markers comprise biotin.
8. The method of claim 1 , wherein (b) comprises digesting the crosslinked DNA with a restriction enzyme.
9. The method of claim 1 , wherein (b) comprises shearing the crosslinked DNA.
10. The method of claim 1 , wherein (a) comprises contacting DNA with a chemical fixative.
11. The method of claim 10 , wherein the chemical fixative comprises formaldehyde.
12. The method of claim 10 , wherein the chemical fixative comprises psoralen.
13. The method of claim 1 , wherein (a) comprises contacting DNA with ultraviolet light.
14. The method of claim 1 , wherein (c) comprises contacting the fragmented crosslinked DNA with a ligase.
15. The method of claim 1 , wherein (d) comprises paired-end sequencing.
16. The method of claim 1 , further comprising, prior to (a), obtaining the chromosomes from a cell.
17. The method of claim 16 , wherein the cell is a human cell.
18. The method of claim 16 , wherein the cell is diploid.
Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Apr 1, 2025
From: GREEN, RICHARD E., JR.; LAREAU, LIANA F.
To: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
Reel/Frame 070698/0887 →
Continuity (6)
Provisional Application
61759941
· Feb 1, 2013
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