Method for providing DNA fragments derived from an archived sample

• US 8,679,745 B2
• Filed: 09/30/2005
• Issued: 03/25/2014
• Est. Priority Date: 09/30/2004
• Status: Active Grant

• Current Assignee: Epigenomics AG
• Original Assignee: Epigenomics AG
• Inventors: Ballhause, Matthias, Berlin, Kurt, Dietrich, Dimo, Lukas, Antje Kluth, Schuster, Matthias, Wagner, Ute, Wasserkort, Reinhold, Ziebarth, Heike
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US11/664,367
• Publication Number:
  US 20080220418A1
• Time in Patent Office: 3,098 Days
• Field of Search: 435/6.1, 435/91.1, 435/91.2, 422/430
• US Class Current: 435/6.1
• CPC Class Codes: C12N 15/1003 Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2523/125 Bisulfite(s)
• CPC Class Codes: C12Q 2527/137 Concentration of a component of medium
• CPC Class Codes: C12Q 2527/149 Concentration of an enzyme

Abstract

Aspects of the present invention relate to compositions and methods for providing DNA fragments from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies, etc). Particular aspects provide methods whereby high yields of DNA are isolated as well as a substantial portion of the DNA consists of long DNA fragments, and where the isolated genomic DNA is free of associated or cross-linked contaminants like proteins, peptides, amino acids or RNA. The methods are facile, cost-effective, and are characterized by high reproducibility and reliability. Particular aspects provide methods for providing DNA fragments derived from an archived sample, wherein the yield of DNA before, for example, an amplification step is at least 20%, and amplicons up to a length of about 1,000 base pairs are amplifiable.

Claims

1. A method for providing DNA fragments derived from an archived sample, comprising:

contacting an archived sample comprising DNA with a protease to provide for an amount of protease-treated DNA;

extracting the protease-treated DNA;

reacting the extracted DNA with a bisulfite reagent, wherein the reaction is carried out in an organic solvent; and

purifying the bisulfite-treated DNA.

2. The method of claim 1, wherein the yield of the purified DNA is between about 30% and about 50% of that of the archived sample.

3. The method of claim 1, wherein 5% to about 60% of the purified DNA is amplifiable in a PCR reaction generating fragments of at least 110 bp in length.

4. The method of claim 1, wherein an average of about 10% of the purified DNA is amplifiable in a PCR reaction generating fragments of at least 110 bp in length.

5. The method of claim 1, wherein the archived sample is at least one selected from the group consisting of;

a paraffin-embedded tissue biopsy;

a fixed tissue biopsy;

a paraffin-embedded, fixed tissue biopsy;

a paraffin-embedded tissue section or portion thereof;

a fixed tissue section or portion thereof;

a paraffin-embedded, fixed tissue section or portion thereof.

6. The method of claim 5, further comprising at least one step selected from the group consisting of:

removing paraffin; and

amplifying the DNA.

7. The method of claim 6, wherein removing paraffin comprises dissolving the paraffin by an organic solvent, or comprises dissolving the paraffin by an organic solvent and washing by another organic solvent.

8. The method of claim 7, wherein the organic solvent for dissolving paraffin is a solvent selected from the group consisting of limonene, xylene and combinations of these solvents, and wherein the washing solvent is a solvent selected from the group consisting of ethanol, methanol, isopropanol and combinations of these solvents with each other or with water.

9. The method of claim 7, wherein the paraffin removal step comprises:

adding 0.1-3 ml of limonene to the archived sample;

incubating for at least 5 min at a temperature in the range of about 10°

C. to about 70°

C.;

centrifuging the incubated sample; and

removing of the limonene therefrom.

10. The method of claim 7, wherein the paraffin removal step comprises:

adding about 1 ml of limonene to the archived sample;

incubating for about 10 min to about 1 h at room temperature with mixing of the sample;

centrifuging the incubated sample at a force of at least 5,000×

g for about 5 min; and

removing the limonene therefrom.

11. The method of claim 8, wherein the washing solvent is ethanol, and wherein washing comprises:

adding about 0.1 to about 3 ml of ethanol;

centrifuging the ethanol containing sample;

removing the ethanol; and

drying.

12. The method of claim 11, further comprising, after addition of the ethanol, incubation for up to 10 min at a temperature in the range of about 15°

C. to about 30°

C.

13. The method of claim 7, comprising:

adding of about 1 ml ethanol;

incubating for about 10 min at room temperature with mixing the sample;

Centrifuging at a force of at least 5,000×

g for about 5 min;

removing the ethanol; and

incubating for a period of about 10 to about 30 min at about 50°

C.

14. The method of claim 6, wherein the protease is selected from the group consisting of a serine protease, a thiol protease, a carboxy protease, a metalloprotease, proteinase K and combinations of these proteases.

15. The method of claim 14, wherein contacting the archived sample with the protease comprises:

adding about 0.05 to about 1 ml of lysis buffer comprising about 50 mmol/l tris-hydroxymethyl-amino-methan pH 8.0, 1 mmol/l EDTA, 0.5% Tween 20 v/v to from 1 to about 10 deparaffinated formalin-fixed tissue sections, or to an equal amount of a deparaffinated formalin-fixed tissue biopsy;

adding about 10 to about 100μ

of a proteinase K solution comprising about 10 to about 30 g/l proteinase K, and subsequently agitating the sample; and

incubating for at least 2.5 h at a temperature of about 40 to about 70°

C.

16. The method of claim 15, further comprising, after incubating, inactivating the proteinase K by heating, by use of an inhibitor, or both.

17. The method of claim 14, wherein contacting the archived sample with the protease comprises:

adding about 190 μ

l of lysis buffer to 1 to about 6 deparaffinated formalin-fixed tissue sections, or to an equal amount of a deparaffinated formalin-fixed tissue biopsy;

adding about 20 μ

l of proteinase K solution comprising about 30 g/l proteinase K, with subsequent vortexing;

incubating for a period of about 3 to about 48 h at a temperature of about 50°

C. to about 60°

C. with mixing the sample; and

incubation for about 10 min at a temperature of at least 95°

C.

18. The method of claim 17, further comprising, after incubating at about 50°

C. to about 60°

C. with mixing for 24 h, adding of at least 20 μ

l proteinase K solution after the first 24 h incubation at 50°

C.-60°

C., and prior to incubation at the temperature of at least 95°

C.

19. The method according to claim 14, wherein contacting the archived sample with the protease comprises:

adding about 50 to about 1,000 μ

l of lysis buffer to 1 to about 10 deparaffinated formalin-fixed tissue sections, or to an equal amount of a deparaffinated formalin-fixed tissue biopsy, the lysis buffer pH 8.0 comprising about 50 mmol/l tris-hydroxymethyl-amino-methan, 1 mmol/l EDTA, 0.5% Tween 20 v/v;

incubating for about 5 to about 20 min at a temperature of about 40 to about 75°

C.

adding about 5 to about 40 μ

l of proteinase K solution, the proteinase K solution comprising about 30 mg/ml proteinase K; and

incubating for at least 2.5 h at a temperature of about 40 to about 70°

C.

20. The method of claim 19, wherein the lysis buffer further comprises about 5 ng/μ

l poly-dA DNA.

21. The method of claim 19, wherein the proteinase K is activated by heating, by use of an inhibitor, or both.

22. The method according to claim 19, wherein contacting the archived sample with the protease comprises:

adding about 100μ

lysis buffer to 1 to about 6 deparaffinated formalin-fixed tissue sections, or to an equal amount of a deparaffinated formalin-fixed tissue biopsy;

incubating for about 10 min at about 65°

C. in a thermo mixer at 1,000 rpm;

incubating at about 50°

C. in a thermo mixer at about 1,400 rpm adding about 10 μ

l of proteinase K solution;

incubating for about 3 to about 48 h at about 60°

C. in a thermo mixer at about 1,000 rpm; and

incubating for about 10 min at a temperature greater than 95°

C.

23. The method of claim 6, wherein extracting the DNA comprises binding of DNA to silica surfaces, or silica membranes.

24. The method according to claim 23, wherein binding of DNA to silica surfaces, or silica membranes comprises utilizing a DNA extraction step from at least one kit, wherein the at least one kit is selected from products containing silica surfaces or silica membranes appropriate for binding DNA sold under the trademarks DNEASY®

96 Tissue Kit, QIAAMP®

96 DNA Blood Kit, QIAAMP®

DSP 96 Virus MDX Kit, DNEASY®

Tissue Kit, QIAAMP®

DNA Mini Kit, or QIAAMP®

DNA Micro Kit, QIAAMP®

Viral RNA Mini, and QIAAMP®

DSP Virus Kit.

25. The method of claim 6, wherein treating the extracted DNA with a bisulfite reagent comprises:

mixing of about 10 to about 60 μ

l of the solution containing the genomic DNA with about 50 to about 120 μ

l of bisulfite solution, the bisulfite solution having a pH in the range of about 5.45 to about 5.50 comprising about 4.83 to about 4.93 mol/l hydrogensulfite;

adding about 8 to about 45 μ

l of an organic radical scavenger solution, the organic radical scavenger solution comprising an organic solvent and about 158 to about 500 mmol/l of 6-hydroxy-2,5,7,8-tetramethyl-chroman-2-carboxylic acid; and

applying a temperature protocol for about 3 to about 8 h, wherein the reaction is conducted in a temperature range of about 0 to about 80°

C. with about 2 to about 5 additional temperature increases, in each case for about 1 to about 10 min, to a temperature of about 85 to about 100°

C. including an initial temperature increase to a temperature of about 85 to about 100°

C.

26. The method of claim 25, wherein treating the extracted DNA with a bisulfite reagent comprises:

mixing of about 44 to about 50 μ

l of a solution containing the genomic DNA with about 83 to about 95 μ

l of the bisulfite solution;

adding about 13 to about 15 μ

l of DME solution, the DME solution comprising about 500 mmol/l of 6-hydroxy-2,5,7,8-tetramethyl-chroman-2-carboxylic acid dissolved in diethyleneglycoldimethylether; and

applying a temperature protocol for about 4 to about 7 h, wherein the reaction is conducted in a temperature range of about 57 to about 65°

C. with about 2 to about 5 additional temperature increases, in each case for about 3 to about 5 min, to a temperature of about 94 to about 100°

C. including an initial temperature increase to a temperature of about 94 to about 100°

C.

27. Method according to claim 25, wherein treating the extracted DNA with a bisulfite reagent comprises:

mixing about 15 to about 20 μ

l of solution containing the genomic DNA with about 60 to about 85 μ

l of the bisulfite solution;

adding about 25 to about 35 μ

l of dioxane solution, the dioxane solution comprising about 158 mmol/l of 6-hydroxy-2,5,7,8-tetramethyl-chroman-2-carboxylic acid dissolved in 1,4-dioxane; and

applying a temperature protocol for about 4 to about 7 h, wherein the reaction is conducted in a temperature range of about 57 to about 65°

C. with about 2 to about 5 additional temperature increases, in each case for about 3 to about 5 min, to a temperature of about 94 to about 100°

C. including an initial temperature increase to a temperature of about 94 to about 100°

C.

28. The method of claim 6, wherein purifying the bisulfite-treated DNA comprises use of a centrifugal filter device, and further comprises:

adjusting the sample after the bisulfite reaction with water to a volume of about 350 to about 500 μ

l;

binding of the DNA onto a centrifugal filter device;

treating with about 25 to about 1,000 μ

l of about 0.2 mol/l sodium hydroxide, wherein there is optional incubating for about 3 to about 25 min at a temperature of about 15 to about 26°

C.;

washing with about 200 to about 1,000 μ

l TE buffer, the TE buffer pH 8.0 comprising about 10 mmol/l tris-hydroxymethyl-amino-methan and about 0.1 mmol/l EDTA;

removing the DNA by means of about 30 to about 100 μ

l TE buffer preheated to a temperature of about 40 to about 65°

C. incubated for about 5 to about 25 min at a temperature of about 10 to about 60°

C.

29. The method of claim 28, wherein purifying the bisulfite treated DNA comprises:

adjusting the sample after the bisulfite reaction with water to a volume of about 400 μ

l;

applying the mixture onto a centrifugal filter device and subsequent centrifugation at about 14,000×

g for about 15 min, wherein there are 1 to 2 optional repetitions of the following washing step;

applying of about 400 μ

l TE buffer, the TE buffer pH 8 containing about 10 mmol/l tris-hydroxymethyl-amino-methan and about 0.1 mmol/l EDTA, subsequent centrifuging at about 14,000×

g for about 12 min;

applying about 100 to about 400 μ

l of about 0.2 mol/l sodium hydroxide, wherein there is optional incubating for about 10 min at room temperature, and subsequent centrifuging at about 14,000×

g for about 10 to about 12 min;

applying, in 1 to about 4 repetitions, the following;

applying of about 400 μ

l water or TE buffer and subsequent centrifuging at about 14,000×

g for about 12 min; and

eluting in one or two steps by application of about 37.5 to about 75 μ

l TE buffer preheated to about 50°

C., incubation for about 10 min at a temperature of about 15 to about 50°

C., and subsequent inversion of the centrifugal filter device and centrifugation at about 1,000×

g for about 5 min.

30. The method of claim 6, wherein amplifying of the DNA comprises use of at least one method selected from the group consisting of the PCR method;

the bisulfite sequencing method;

the Combined Bisulfite Restriction Analysis (COBRA) method;

the Methylation-sensitive Single Nucleotide Primer Extension (Ms-SNuPE) method;

the Methylation Specific PCR MSP method;

the nested MSP method;

the HEAVYMETHYL®

method;

the MethyLight method; and

the quantitative methylation (QM) assay.

31. The method of claim 1, wherein, with respect to purifying the bisulfite-treated DNA, the yield of the purified DNA is at least 20% of that of the archived sample, and wherein at least 5% of the purified DNA is amplifiable in a PCR reaction generating fragments of at least 110 bp in length.

32. The method of claim 1, wherein the organic solvent is of structural formula (I):