Recovering long-range linkage information from preserved samples
AssigneeDovetail Genomics, LLC
InventorsChristopher John Troll, Martin P. Powers, Nicholas H. Putnam, Marco Blanchette, Paul Hartley
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Abstract
The disclosure provides methods to isolate genome or chromosome level structural information from preserved samples. In some cases, samples preserved under conditions where long-range nucleic acid information is believed to be irreparably lost, such as FFPE samples, are treated to recover nucleic acid-protein complexes stabilized as part of the sample preservation process. The complexes are processed so as to recover information regarding which nucleic acids are bound to a common complex, and the information is used to recover genomic structural information.
Claims16
A method, comprising
- obtaining a preserved sample from a subject, the sample comprising protein-DNA complexes;
- treating the preserved sample with a proteinase at a temperature not greater than 40° C. to isolate nucleic acids such that 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 sample, wherein the preserved sample is a formalin fixed paraffin-embedded (FFPE) sample.
Dependencies are inferred from the claim text.