US 12,410,482 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, INC., Menlo Park, CA (US)
Filed by GRAIL, INC., Menlo Park, CA (US)
Filed on Sep. 20, 2023, as Appl. No. 18/471,025.
Application 18/471,025 is a continuation of application No. 17/832,375, filed on Jun. 3, 2022, granted, now 11,795,513.
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.
Application PCT/US2019/053509 is a continuation in part of application No. PCT/US2019/025358, filed on Apr. 2, 2019.
Claims priority of provisional application 62/737,836, filed on Sep. 27, 2018.
Prior Publication US 2024/0084396 A1, Mar. 14, 2024
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); C12Q 1/6869 (2018.01); G16B 5/00 (2019.01); G16B 20/00 (2019.01); G16B 25/20 (2019.01); G16B 30/10 (2019.01); G16B 40/00 (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 comprising (a) an assay panel for enriching target polynucleotides for detecting cancer and/or a type of cancer in a subject, and (b) cell-free DNA (cfDNA) molecules or amplification products thereof;
wherein the assay panel comprises at least 1,000 polynucleotide probes that are biotinylated;
wherein the at least 1,000 polynucleotide probes comprise at least 500 different pairs of probes comprising a first probe and second probe, wherein the first probe differs from the second probe and overlaps with the second probe by an overlapping sequence of at least 30 contiguous bases;
wherein the polynucleotide probes of the at least 500 different pairs of probes are configured to collectively hybridize to target polynucleotides among cell-free DNA (cfDNA) molecules derived from at least 500 different target genomic regions of the subject, or amplification products thereof;
wherein the target genomic regions are human genomic regions;
wherein at least one probe for each of the at least 500 different target genomic regions (i) comprises a length of at least 45 bases complementary to a sequence of the target genomic region, and (ii) does not have at least 90% complementarity to at least 45 contiguous bases of 20 or more off-target regions in a GRCh37/hg19 genome;
wherein an off-target region does not comprise any of the at least 500 different target genomic regions; and
wherein each of the at least 500 different target genomic regions comprises at least five methylation sites and are differentially methylated in cancer samples relative to non-cancer samples.