IP Library › Granted Patent US 12,428,669
Granted Patent B2
US 12,428,669 · App. 18/310,266 · Granted Sep 30, 2025

Isolation of nucleic acids

Inventors: Janelle J. Bruinsma (Madison, WI); Michael J. Domanico (Middleton, WI); Graham P. Lidgard (Madison, WI); Hongzhi Zou (Middleton, WI); William G. Weisburg (San Diego, CA); Hemanth D. Shenoi (Verona, WI); James P. Light, II (Middleton, WI); Keith Kopitzke (Fallbrook, CA); John Zeis (San Marcos, CA)
Assignee: Exact Sciences Corporation
C12Q1/6806B01D33/15B01D33/155B01L3/00B01L3/5021B03C1/30B04B3/00C12N15/1006C12N15/1013C12N15/1017C12Q1/6886C12Q2600/158C12Q2600/16Y10T436/143333
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Quick Facts
Patent No.
US 12,428,669
App. No.
18/310,266
Granted
Sep 30, 2025
Kind
B2
Abstract

Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting nucleic acids from problematic samples such as stool.

Claims (19)

1. A method for amplifying a human target nucleic acid from a fluid fraction prepared from human stool homogenate, the method comprising:

i) treating a fluid fraction from a human stool homogenate with insoluble polyvinylpyrrolidone to bind inhibitor, if present, in an insoluble inhibitor complex, to produce a treated stool fluid;

ii) exposing the treated stool fluid to a target sequence-specific capture reagent comprising particles attached to oligonucleotides complementary to at least a portion of human target nucleic acid, under conditions wherein the target sequence-specific capture reagent forms target sequence-specific capture reagent/human target nucleic acid capture complexes;

iii) separating the capture complexes from the treated stool fluid;

iv) recovering human target nucleic acid from the separated capture complexes of step iii) in a human target nucleic acid solution; and

v) treating a portion of the human target nucleic acid solution in an amplification reaction mixture comprising DNA polymerase, wherein the amplification reaction mixture comprises primers for amplifying a region of a human target nucleic acid captured by the target sequence-specific capture reagent.

2. The method of claim 1 , wherein the portion of human target nucleic acid solution has a volume and the amplification reaction mixture has a total volume, and wherein the volume of the human target nucleic acid solution is at least 1/25 th of the total volume of the amplification reaction mixture.

3. The method of claim 1 , wherein the portion of human target nucleic acid solution has a volume and the amplification reaction mixture has a total volume, and wherein the volume of the human target nucleic acid solution is at least ⅕ th of the total volume of the amplification reaction mixture.

4. The method of claim 1 , wherein the portion of human target nucleic acid solution has a volume and the amplification reaction mixture has a total volume, and wherein the volume of the human target nucleic acid solution is at least ⅓rd of the total volume of the amplification reaction mixture.

5. The method of claim 1 , wherein the amplification reaction mixture further comprises a detection probe complementary to at least a portion of DNA amplified from the region of human target nucleic acid captured by the target sequence-specific capture reagent.

6. The method of claim 5 , wherein the amplification reaction mixture further comprises a flap endonuclease.

7. The method of claim 1 , wherein treating the fluid fraction from a human stool homogenate with insoluble polyvinylpyrrolidone to produce the treated stool fluid comprises passing treated stool fluid through porous filtering material, wherein the insoluble inhibitor complex is retained by the porous filtering material.

8. The method of claim 1 , wherein particles are magnetic particles and wherein separating the capture complexes comprises exposing the capture complexes to a magnetic field.

9. The method of claim 1 , wherein recovering the human target nucleic acid comprises eluting the human target nucleic acid from the separated capture complexes.

10. The method of claim 1 , wherein the human target nucleic acid captured by the target sequence-specific capture reagent comprises DNA from a gene associated with colorectal cancer and/or colorectal adenoma.

11. The method of claim 1 , wherein the human target nucleic acid captured by the target sequence-specific capture reagent comprises at least one of NDRG4, BMP3, and KRAS DNA.

12. The method of claim 1 , wherein the human target nucleic acid comprises a human reference gene.

13. The method of claim 12 , wherein the human reference gene is β-actin.

14. The method of claim 1 , wherein the human target nucleic acid is DNA.

Assignments (3)
TERMINATION AND RELEASE OF SECURITY INTEREST IN PATENT RIGHTS (REEL/FRAME 69898/0249) Recorded Mar 27, 2026
From: JPMORGAN CHASE BANK, N.A.
To: EXACT SCIENCES CORPORATION
Reel/Frame 075288/0393 →
PATENT SECURITY AGREEMENT Recorded Jan 14, 2025
From: EXACT SCIENCES CORPORATION
To: JPMORGAN CHASE BANK, N.A.
Reel/Frame 069898/0249 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded May 1, 2023
From: BRUINSMA, JANELLE J.; DOMANICO, MICHAEL J.; LIDGARD, GRAHAM P.; ZOU, HONGZHI; WEISBURG, WILLIAM G.; SHENOI, HEMANTH D.; LIGHT, JAMES P., II; KOPITZKE, KEITH; ZEIS, JOHN
To: EXACT SCIENCES CORPORATION
Reel/Frame 063497/0160 →
Continuity (13)
Continuation 17035822 · Sep 29, 2020
Continuation 16212143 · Dec 6, 2018
Continuation 16046669 · Jul 26, 2018
Continuation 15807970 · Nov 9, 2017
Continuation 14939925 · Nov 12, 2015
Continuation 14713289 · May 15, 2015
Continuation 14145082 · Dec 31, 2013
Continuation PCTUS2012037581 · May 11, 2012
Provisional Application 61485386 · May 12, 2011
Provisional Application 61485338 · May 12, 2011
Provisional Application 61485448 · May 12, 2011
Provisional Application 61485214 · May 12, 2011
Related Publication 20240026422A1 · Jan 25, 2024
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