IP Library › Granted Patent US 12,486,542
Granted Patent B2
US 12,486,542 · App. 18/733,681 · Granted Dec 2, 2025

Detecting mutations and ploidy in chromosomal segments

Inventors: Joshua Babiarz (Castro Valley, CA); Tudor Pompiliu Constantin (Berkeley, CA); Lane A. Eubank (San Carlos, CA); George Gemelos (Portland, OR); Matthew Micah Hill (Belmont, CA); Huseyin Eser Kirkizlar (Los Angeles, CA); Matthew Rabinowitz (San Francisco, CA); Onur Sakarya (Redwood City, CA); Styrmir Sigurjonsson (San Jose, CA); Bernhard Zimmermann (Manteca, CA)
Assignee: Natera, Inc.
C12Q1/6886C12Q1/6869G06N7/01G06N20/00G16B15/00G16B20/00G16B20/10G16B20/20G16B25/00G16B40/00G16B40/20G16H10/40G16H50/20G16Z99/00C12Q2539/10C12Q2600/156C12Q2600/158C12Q2600/16C12Q2600/172G16B25/20
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Quick Facts
Patent No.
US 12,486,542
App. No.
18/733,681
Granted
Dec 2, 2025
Kind
B2
Abstract

The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

Claims (18)

1 . A method for preparing a DNA fraction from a biological sample of a subject useful for analyzing methylation patterns involved with cancer, comprising:

(a) extracting cell-free DNA from the biological sample;

(b) producing an enriched DNA fraction by: (i) treating the extracted cell-free DNA or DNA derived therefrom with an agent that discriminates between methylated and unmethylated cytosines, wherein the extracted DNA or its derivative or the treated DNA or its derivative is further tagged with at least one adaptor containing a universal priming sequence, thereby producing adapted treated DNA, (ii) performing universal amplification on at least some of the adapted treated DNA using the universal priming sequence and producing amplified adapted treated DNA, and (iii) selectively enriching for a subset of the amplified adapted treated DNA or its derivative that contain one or more preselected loci and producing enriched DNA that contain one or more preselected loci, wherein the enrichment comprises selectively enriching for at least 1,000 preselected loci in a single reaction volume using at least 1,000 target-specific oligonucleotides; and

(c) performing massively parallel sequencing on the enriched DNA or its derivative and obtaining sequence reads in a sequencer and obtaining an identification of one or more methylation patterns involved with cancer.

2 . The method of claim 1 , wherein the biological sample is a blood, plasma, serum, or urine sample.

3 . The method of claim 1 , wherein the one or more methylation patterns involved with cancer comprise methylation of at least a portion of one or more CpG islands in promoter region of one or more tumor-suppressor genes.

4 . The method of claim 3 , wherein the tumor-suppressor genes comprise p16, APC, RASSFIA, GSTP1, DAPK, or a combination thereof.

5 . The method of claim 1 , wherein step (b) comprises selectively enriching for 1,000-500,000 preselected loci.

6 . The method of claim 1 , wherein step (b) comprises selectively enriching for 10,000-200,000 preselected loci.

7 . The method of claim 1 , wherein the selectively enriching comprises targeted multiplex amplification.

8 . The method of claim 1 , wherein the selectively enriching comprises capturing at least some of the amplified adapted DNA comprising one or more preselected loci using hybrid capture probes.

9 . The method of claim 1 , wherein the universal amplification introduces a sample-specific barcode, and wherein the enriched DNA of multiple samples are pooled together and sequenced in the same sequencing run.

10 . The method of claim 1 , wherein the cell-free DNA comprises a mixture of cancer DNA and host DNA, and wherein the method further comprises estimating the fraction of cancer DNA in the cell-free DNA based on the sequence reads.

11 . The method of claim 1 , wherein the agent is bisulfite.

12 . The method of claim 1 , wherein the agent is an enzyme.

13 . The method of claim 12 , wherein the enzyme is one or more methylation sensitive restriction enzymes.

14 . The method of claim 1 , wherein the extracted DNA or its derivative is tagged with the at least one adaptor before being treated with the agent.

15 . The method of claim 1 , wherein the extracted DNA or its derivative is treated with the agent before being tagged with the at least one adaptor.

Continuity (11)
Continuation 17692469 · Mar 11, 2022
Continuation 15898145 · Feb 15, 2018
Continuation 14692703 · Apr 21, 2015
Provisional Application 62148173 · Apr 15, 2015
Provisional Application 62147377 · Apr 14, 2015
Provisional Application 62146188 · Apr 10, 2015
Provisional Application 62066514 · Oct 21, 2014
Provisional Application 61994791 · May 16, 2014
Provisional Application 61987407 · May 1, 2014
Provisional Application 61982245 · Apr 21, 2014
Related Publication 20240318263A1 · Sep 26, 2024
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