US 12,065,691 B2
Recovering long-range linkage information from preserved samples
Christopher John Troll, Santa Cruz, CA (US); Martin P. Powers, San Francisco, CA (US); Nicholas H. Putnam, Waltham, MA (US); Marco Blanchette, Santa Cruz, CA (US); and Paul Hartley, San Jose, CA (US)
Assigned to DOVETAIL GENOMICS, LLC, Scotts Valley, CA (US)
Filed by Dovetail Genomics, LLC, Scotts Valley, CA (US)
Filed on Feb. 3, 2021, as Appl. No. 17/166,394.
Application 17/166,394 is a continuation of application No. 16/053,610, filed on Aug. 2, 2018, granted, now 10,947,579.
Application 16/053,610 is a continuation of application No. PCT/US2017/032466, filed on May 12, 2017.
Claims priority of provisional application 62/410,599, filed on Oct. 20, 2016.
Claims priority of provisional application 62/336,252, filed on May 13, 2016.
Prior Publication US 2021/0371904 A1, Dec. 2, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6806 (2018.01); C12Q 1/6816 (2018.01); C40B 40/06 (2006.01)
CPC C12Q 1/6806 (2013.01) [C12Q 1/6816 (2013.01); C40B 40/06 (2013.01)] 17 Claims
 
1. A method, comprising
obtaining a formalin fixed paraffin-embedded (FFPE) sample from a subject, the FFPE sample comprising protein-DNA complexes;
treating the FFPE sample with a proteinase to isolate nucleic acids such that the protein-DNA complexes are not destroyed, such that a first double-stranded segment and a second double-stranded segment are held together independent of a phosphodiester backbone, and such that the first double-stranded segment and the second double-stranded segment each have at least one exposed nucleic acid end; and
deriving genomic structural information by analyzing nucleic acids of the protein-DNA complexes in the FFPE sample,
wherein the treating the FFPE sample with the proteinase does not comprise overnight proteinase treatment.