Isolation and detection of DNA from plasma

Patent metadata

Field	Value
Publication number	US-11674168-B2
Application number	US-202017031383-A
Country	US
Kind code	B2
Filing date	Sep 24, 2020
Priority date	Oct 30, 2015
Publication date	Jun 13, 2023
Grant date	Jun 13, 2023

Abstract

Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.

First claim

We claim:

1. A method of processing a plasma sample, the method comprising:
a) combining a plasma sample with
i) protease;
ii) a first portion of guanidine thiocyanate;
iii) a first portion of non-ionic detergent; and
iv) bulk fish DNA diluent,

to form a first mixture wherein proteins are digested by said protease;
b) to the first mixture adding
v) silica particles;
vi) isopropyl alcohol;
vii) a second portion of guanidine thiocyanate; and
viii) a second portion of non-ionic detergent,

to form a second mixture under conditions wherein DNA is bound to said silica particles;
c) separating silica particles with bound DNA from the second mixture;
d) to the separated silica particles with bound DNA adding a first wash solution, said first wash solution comprising guanidine hydrochloride or guanidine thiocyanate, and ethyl alcohol;
e) separating the silica particles with bound DNA from said first wash solution;
f) to the separated silica particles with bound DNA adding a second wash solution, said second wash solution comprising a buffer and ethyl alcohol;
g) separating the washed silica particles with bound DNA from said second wash solution;
h) eluting DNA from said washed silica particles with bound DNA to produce an isolated DNA sample.

2. The method of claim 1 , wherein steps f)-g) are repeated 1 to 3 additional times prior to step h).

3. The method of claim 1 , wherein the first portion and the second portion of non-ionic detergent are the same or different, and are selected from the group consisting of polyethylene glycol sorbitan monolaurate (Tween-20), octylphenoxypolyethoxyethanol (Nonidet P-40), and octylphenoxy poly(ethyleneoxy) ethanol, branched (IGEPAL CA-630).

4. The method of claim 1 , wherein said protease is Proteinase K protease.

5. The method of claim 1 , further comprising a step after step g) and prior to step h) of drying the washed silica particles with bound DNA.

6. The method of claim 1 , wherein in the mixture of step a), further the bulk fish DNA diluent comprises a synthetic methylated DNA comprising a zebrafish DNA nucleotide sequence.

7. The method of claim 6 , wherein said synthetic methylated DNA comprising a zebrafish DNA nucleotide sequence comprises a zebrafish Ras association domain (RalGDS/AF-6) family 1 (RASSF1) sequence.

8. The method of claim 1 , wherein said plasma sample has a volume of at least 2 mL.

9. The method of claim 1 , wherein said first portion of guanidine thiocyanate and said first portion of non-ionic detergent are added to the plasma sample together as a first lysis reagent comprising about 4.3 M guanidine thiocyanate and 10% w:v IGEPAL CA-630 and/or wherein said second portion of guanidine thiocyanate and said second portion of non-ionic detergent are added to the first mixture together as a second lysis reagent comprising 4.3 M guanidine thiocyanate and 10% w:v IGEPAL CA-630 combined with isopropyl alcohol.

10. The method of claim 1 , wherein said first wash solution comprises about 3 M guanidine hydrochloride or 3 M guanidine thiocyanate and about 57% ethyl alcohol and/or said second wash solution comprises about 80% ethyl alcohol and about 20% 10 mM Tris pH 8.0 buffer.

11. The method of claim 1 , further comprising analyzing said isolated DNA sample for multiple target nucleic acids, comprising:
a) treating said isolated DNA sample with bisulfite to produce a bisulfite treated DNA sample;
b) treating said bisulfite-treated DNA sample to an amplification reaction under conditions wherein a plurality of different target regions, if present in said sample, are amplified to form a pre-amplified mixture;
c) partitioning said pre-amplified mixture into a plurality of different detection assay reaction mixtures; and
d) conducting a plurality of detection assays with said detection assay reaction mixtures, wherein said plurality of different target regions, if present in said sample at step a), are detected in one or more of said plurality of different detection assay reaction mixtures.

Assignees

• Exact Sciences Corp

Inventors

• Allawi Hatim
• Lidgard Graham P
• Aizenstein Brian
• Sander Tamara J
• Giakoumopoulos Maria
• Kaiser Michael W
• Gray Melissa M
• Vaccaro Abram Michael

Classifications

• C12Q2600/166

  Oligonucleotides used as internal standards, controls or normalisation probes · CPC title

• C12Q1/686

  Polymerase chain reaction [PCR] · CPC title

• C12N15/1006

  by means of a solid support carrier, e.g. particles, polymers · CPC title

• C12Q1/6806 Primary

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• C12Q2600/154

  Methylation markers · CPC title