US 2026/0308698 A1 · MULTIPLE-TIERED SCREENING AND SECOND ANALYSIS

Abstract

Disclosed herein are methods, non-transitory computer readable media, systems, and kits for performing a multiple tiered analysis for identifying individuals with a health condition for monitoring, treating, and/or enrolling the individuals in a clinical trial. Specifically, the multiple tiered analysis involves a first screen, which eliminates a large proportion of individuals who are identified as not at risk for a health condition, and a subsequent second analysis which detects presence of a health condition in the remaining individuals. The second analysis includes an intra-individual analysis, which involves combining sequence information from target nucleic acids and reference nucleic acids obtained from the individual. The target nucleic acids include signatures that may be informative for determining presence or absence of the health condition and the reference nucleic acids include baseline biological signatures of the individual. Altogether, the multiple tiered analysis achieves improved performance and accurate identification of individuals with the health condition.

Claims22

Dependent claims

A method for detecting circulating tumor DNA in a biological sample of a subject, the method comprising:

obtaining target nucleic acids from the biological sample obtained from the subject;
performing a targeted methylation assay on the sample, the assay comprising:
(i) performing bisulfite conversion of the target nucleic acids;
(ii) providing at least 1000 probes complementary to sequences within at least 1000 different CpG islands (CGIs) selected from Tables 1-4;
(iii) using the at least 1000 probes, selectively amplifying from the bisulfite converted target nucleic acids at least the sequences within at least 1000 different CpG islands (CGIs) selected from Tables 1-4;
and
(iv) generating a dataset comprising methylation information of at least the selectively amplified sequences within the at least 1000 different CGIs;
and
performing an analysis comprising analyzing, using a classifier, the methylation information of at least the sequences within the at least 1000 different CGIs to detect the presence of the circulating tumor DNA in the biological sample, wherein the analysis achieves at least a positive predictive value of 70% for detecting circulating tumor DNA.

6 more elements

A method for detecting circulating tumor DNA in a biological sample of a subject, the method comprising:

obtaining target nucleic acids from the biological sample obtained from the subject who is not asymptomatic and has previously undergone a first analysis that did not exclude cancer risk for the subject;
performing a targeted methylation assay on the sample, the assay comprising:
(i) performing bisulfite conversion of the target nucleic acids;
(ii) providing at least 1000 probes complementary to sequences within at least 1000 different CpG islands (CGIs), wherein differential methylation of the at least 1000 different CGIs were previously demonstrated to be associated with the initiation of or further development of an oncogenic state;
(iii) using the at least 1000 probes, selectively amplifying from the bisulfite converted target nucleic acids at least the sequences within the at least 1000 different CpG islands (CGIs);
and
(iv) generating a dataset comprising methylation information of at least the selectively amplified sequences within the at least 1000 different CGIs;
performing an analysis comprising analyzing, using a classifier, the methylation information of at least the sequences within the at least 1000 different CGIs to detect the presence of the circulating tumor DNA in the biological sample, wherein the analysis achieves at least a positive predictive value of 70% for detecting circulating tumor DNA;
and
comparing the results of the analysis to the results of a prior analysis comprising performing steps (i)-(iv) at a prior timepoint to determine whether or not a standard of care analysis should be applied to the subject.

7 more elements

Dependencies are inferred from the claim text.

Multiple-tiered screening and second analysis

Life of this patent

Multiple-tiered screening and second analysis

Life of this patent

Abstract

Claims22