US 11,725,251 B2
Methylation markers and targeted methylation probe panel
Samuel S. Gross, Menlo Park, CA (US); Oliver Claude Venn, Menlo Park, CA (US); Seyedmehdi Shojaee, Menlo Park, CA (US); John Beausang, Menlo Park, CA (US); and Arash Jamshidi, Menlo Park, CA (US)
Assigned to GRAIL, LLC, Menlo Park, CA (US)
Filed by GRAIL, LLC, Menlo Park, CA (US)
Filed on Dec. 21, 2022, as Appl. No. 18/69,502.
Application 18/069,502 is a continuation of application No. 17/832,375, filed on Jun. 3, 2022.
Application 17/832,375 is a continuation of application No. 17/214,190, filed on Mar. 26, 2021, granted, now 11,410,750, issued on Aug. 9, 2022.
Application 17/214,190 is a continuation of application No. PCT/US2019/053509, filed on Sep. 27, 2019.
Claims priority of provisional application 62/737,836, filed on Sep. 27, 2018.
Prior Publication US 2023/0140937 A1, May 11, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); C12Q 1/6869 (2018.01); G16B 30/10 (2019.01); G16B 5/00 (2019.01); G16B 40/00 (2019.01); G16B 25/20 (2019.01); G16B 20/00 (2019.01); G16B 40/20 (2019.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6869 (2013.01); C12Q 2600/154 (2013.01); G16B 5/00 (2019.02); G16B 20/00 (2019.02); G16B 25/20 (2019.02); G16B 30/10 (2019.02); G16B 40/00 (2019.02); G16B 40/20 (2019.02)] 19 Claims
OG exemplary drawing
 
1. A mixture for processing cell-free DNA fragments, the mixture comprising (a) converted cell-free DNA (cfDNA) molecules or amplification products thereof; and (b) a panel of different oligonucleotide probes configured to hybridize to converted cell-free DNA fragments derived from at least 500 target genomic regions;
wherein the converted cfDNA molecules comprise deaminated nucleotides obtained by treating cfDNA molecules with a deaminating agent;
wherein each target genomic region of the at least 500 target genomic regions has an anomalous methylation pattern in cancerous samples; and
wherein each of the at least 500 target genomic regions comprises a sequence with complementarity to at least a pair of probes in the panel, wherein each probe of a pair has a first portion and a second portion, wherein the first portions of a probe pair are complementary to the same sequence of at least 25 nucleotides in length, and wherein the second portions of a probe pair are complementary to different sequences at different ends of the sequence complementary to the respective first portions.