US 11,935,626 B2
Methods for genome assembly and haplotype phasing
Richard E. Green, Jr., Santa Cruz, CA (US); and Liana F. Lareau, San Francisco, CA (US)
Assigned to The Regents of the University of California, Oakland, CA (US)
Filed by The Regents of the University of California, Oakland, CA (US)
Filed on Oct. 9, 2020, as Appl. No. 17/066,868.
Application 17/066,868 is a continuation of application No. 15/900,723, filed on Feb. 20, 2018, granted, now 10,825,553.
Application 15/900,723 is a continuation of application No. 15/167,880, filed on May 27, 2016, granted, now 9,910,955, issued on Mar. 6, 2018.
Application 15/167,880 is a continuation of application No. 14/170,339, filed on Jan. 31, 2014, granted, now 9,411,930, issued on Aug. 9, 2016.
Claims priority of provisional application 61/759,941, filed on Feb. 1, 2013.
Prior Publication US 2021/0125687 A1, Apr. 29, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6874 (2018.01); G16B 30/00 (2019.01); G16B 30/20 (2019.01)
CPC G16B 30/20 (2019.02) [C12Q 1/6874 (2013.01); G16B 30/00 (2019.02)] 14 Claims
OG exemplary drawing
 
1. A method for haplotype phasing, the method comprising:
providing a cell comprising chromosomes;
crosslinking DNA within the chromosomes to form crosslinked DNA;
fragmenting the crosslinked DNA to form fragmented crosslinked DNA;
ligating two regions of the fragmented crosslinked DNA that are in close physical proximity to create ligated DNA comprising a ligation product, wherein the two regions comprise an intra-chromosomal pair;
shearing the ligated DNA to generate a plurality of smaller genomic fragments;
sequencing the plurality of smaller genomic fragments to generate sequencing reads;
identifying at least one heterozygous site in the sequencing reads; and
using the sequencing reads to determine haplotype phasing of the at least one heterozygous site.