US 12,404,537 B2
Generation of phased read-sets for genome assembly and haplotype phasing
Richard E. Green, Jr., Santa Cruz, CA (US); Daniel S. Rokhsar, Kensington, CA (US); Paul Hartley, San Jose, CA (US); and Marco Blanchette, Santa Cruz, CA (US)
Assigned to DOVETAIL GENOMICS, LLC, Scotts Valley, CA (US)
Filed by Dovetail Genomics, LLC, Scotts Valley, CA (US)
Filed on Mar. 10, 2021, as Appl. No. 17/197,551.
Application 17/197,551 is a continuation of application No. 16/078,741, granted, now 10,975,417, previously published as PCT/US2017/019099, filed on Feb. 23, 2017.
Claims priority of provisional application 62/305,957, filed on Mar. 9, 2016.
Claims priority of provisional application 62/298,966, filed on Feb. 23, 2016.
Claims priority of provisional application 62/298,906, filed on Feb. 23, 2016.
Prior Publication US 2022/0064701 A1, Mar. 3, 2022
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6806 (2018.01); C12Q 1/68 (2018.01); C12Q 1/6869 (2018.01); C40B 40/06 (2006.01); C40B 40/08 (2006.01); G01N 33/53 (2006.01)
CPC C12Q 1/6806 (2013.01) [C12Q 1/68 (2013.01); C12Q 1/6869 (2013.01); C40B 40/06 (2013.01); C40B 40/08 (2013.01); G01N 33/5308 (2013.01)] 19 Claims
 
1. A method of sequencing a DNA molecule, comprising:
(a) providing a first DNA molecule having a first segment, a second segment, and a third segment, wherein the first segment and the second segment are not adjacent on the first DNA molecule, and wherein the third segment is not adjacent to the first segment or the second segment on the first DNA molecule;
(b) contacting the first DNA molecule to a DNA binding moiety such that the first segment, the second segment, and the third segment are held together independent of a common phosphodiester backbone of the first DNA molecule;
(c) cleaving the first DNA molecule such that the first segment, the second segment, and the third segment are not joined by a common phosphodiester backbone and comprise at least one exposed end;
(d) attaching the first segment to the second segment via a phosphodiester bond and attaching the third segment to the second segment via a phosphodiester bond to form a reassembled first DNA molecule; and
(e) sequencing at least a portion of the reassembled first DNA molecule comprising a junction between the first segment and the second segment and a junction between the second segment and the third segment in a single sequencing read.