US 12,435,375 B2
Methylation markers and targeted methylation probe panel
Samuel S. Gross, Menlo Park, CA (US); Hamed Amini, Menlo Park, CA (US); Arash Jamshidi, Menlo Park, CA (US); Seyedmehdi Shojaee, Menlo Park, CA (US); Srinka Ghosh, Menlo Park, CA (US); Rongsu Qi, Menlo Park, CA (US); M. Cyrus Maher, Menlo Park, CA (US); Alexander P. Fields, Menlo Park, CA (US); and Oliver Claude Venn, Menlo Park, CA (US)
Assigned to GRAIL, Inc., Menlo Park, CA (US)
Filed by GRAIL, Inc., Menlo Park, CA (US)
Filed on Oct. 1, 2020, as Appl. No. 17/061,013.
Application 17/061,013 is a continuation of application No. PCT/US2019/025358, filed on Apr. 2, 2019.
Claims priority of provisional application 62/651,643, filed on Apr. 2, 2018.
Claims priority of provisional application 62/738,271, filed on Sep. 28, 2018.
Prior Publication US 2021/0017609 A1, Jan. 21, 2021
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/68 (2018.01); C12Q 1/6886 (2018.01); C12Q 1/70 (2006.01); C40B 40/06 (2006.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/70 (2013.01); C40B 40/06 (2013.01); C12Q 2600/154 (2013.01)] 26 Claims
 
1. An assay panel for enriching nucleic acids, wherein the assay panel comprises at least 1,000 different polynucleotide probes;
wherein each of the at least 1,000 different polynucleotide probes comprises a nucleic acid sequence that comprises:
(1) a first sequence that is identical to the sequence of at least 45 contiguous nucleotides within a target genomic region,
(2) a second sequence that varies with respect to the sequence of at least 45 contiguous nucleotides within the target genomic region by one or more transitions comprising one or more transitions that occur at a nucleotide corresponding to a CpG site in the target genomic region, or
(3) a third sequence that varies with respect to the sequence of at least 45 contiguous nucleotides within the target genomic region by comprising an adenine in place of a guanine;
wherein the at least 1,000 different polynucleotide probes comprise at least 500 different pairs of polynucleotide probes;
wherein each pair of the at least 500 different pairs of polynucleotide probes comprises two different polynucleotide probes tiled with respect to the same target genomic region;
wherein the two different polynucleotide probes of each pair of the at least 500 pairs of polynucleotide probes comprise (i) an identical overlapping sequence comprising 30 contiguous nucleotides of the first, second or third sequence, and (ii) a different non-overlapping sequence of 15 contiguous nucleotides of the first, second or third sequence; and
wherein each of the at least 1,000 different polynucleotide probes is conjugated to an affinity moiety.