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US 2026/0226536 A1Published application
Markers of disease
AssigneeNucleix Ltd.
InventorsDanny FRUMKIN, Revital KNIRSH, Orna SAVIN, Adam WASSERSTROM, Nimrod AXELRAD
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Abstract
The invention relates to methods for identifying and using markers of disease, in particular based on methylation levels in cfDNA CpG loci.
Claims32
A method of preparing a database comprising cfDNA CpG loci, the method comprising:
- (a) Providing DNA extracted from:
- (i) a sample of disease tissue from one or more first subjects with a disease;
- (ii) a sample comprising cfDNA from the one or more first subjects;
- and
- (iii) a sample comprising cfDNA from one or more second subjects without the disease,
- (b) Digesting at least a portion of the DNA with one or more methylation-sensitive restriction enzymes (MSREs) and/or one or more methylation-dependent restriction enzymes (MDREs), producing digested DNA;
- (c) Sequencing the digested DNA with high-throughput sequencing, thereby identifying cfDNA CpG loci;
- (d) Determining methylation levels of the cfDNA CpG loci in the samples of (i), the samples of (ii), and the samples of (iii);
- and
- (e) Preparing the database by recording:
- the cfDNA CpG loci identified by the sequencing in (c);
- the methylation levels determined in (d) for the cfDNA CpG loci;
- a sample identifier;
- and
- a subject identifier.
12 more elements
A method of preparing a database comprising cfDNA CpG loci, the method comprising:
- (a) providing DNA extracted from:
- (i) a sample of disease tissue from a plurality of first subjects with a disease;
- and
- (ii) a sample comprising cfDNA from the plurality of first subjects,
- (b) digesting at least a portion of the DNA with one or more methylation-sensitive restriction enzymes (MSREs) and/or one or more methylation-dependent restriction enzymes (MDREs), producing digested DNA;
- (c) sequencing the digested DNA with high-throughput sequencing, thereby identifying cfDNA CpG loci;
- (d) determining methylation levels of the cfDNA CpG loci in the samples of (i) and the samples of (ii);
- and
- (e) preparing the database by recording:
- the cfDNA CpG loci identified by the sequencing in (c);
- the methylation levels determined in (d) for the cfDNA CpG loci;—a sample identifier;
- and
- a subject identifier,
- wherein the plurality of first subjects comprises one or more primary first subjects with a disease classification, and one or more other first subjects without the disease classification.
11 more elements
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Dependencies are inferred from the claim text.