CN105274090A - Method of purifying paraffin DNA and application of paraffin DNA to genomics - Google Patents

Method of purifying paraffin DNA and application of paraffin DNA to genomics Download PDF

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CN105274090A
CN105274090A CN201510818823.XA CN201510818823A CN105274090A CN 105274090 A CN105274090 A CN 105274090A CN 201510818823 A CN201510818823 A CN 201510818823A CN 105274090 A CN105274090 A CN 105274090A
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dna
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CN105274090B (en
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陈科
慈维敏
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Beijing Institute of Genomics of CAS
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Abstract

The invention provides a method of purifying DNA in a paraffin embedding sample. The method comprises the steps that (1) the sample is dewaxed; (2) formaldehyde in the sample is removed; (3) cell lysis is conducted; (4) the DNA is extracted; (5) the DNA and protein are disconnected; (6) the DNA is purified; in the step (1), xylene is used for dewaxing the sample. The purity of the DNA obtained through the method is high, and the sequencing quality is approximate to that of a DNA sample of fresh tissue.

Description

A kind of paraffin DNA purification process and the application in genomics thereof
Technical field
The present invention relates to a kind of paraffin DNA purification process, and the application of the method in genomics, especially relate to the method for purify DNA from paraffin-embedded human tissue sample, belong to field of genetic engineering.
Background technology
The fast development of genomics is that accurate medical science brings opportunity.For tumor individual therapy, the tumour paraffin specimen that hospital pathology department is preserved finds drug target, realizes the prerequisite that cancer patients is precisely medical.But the treating processes (as dipped into formalin, paraffin embedding etc.) that paraffin specimen experiences in making processes is the major cause causing paraffin DNA highly to degrade.Paraffin DNA after degraded limitedly can only be applied to cancer genomics research---and-DNA is of poor quality, and (260/280 ratio is higher or on the low side, impurity is many), DNA requirement large (3-10 microgram), PCR cycle index large (12-18), ratio low (20-50%) (W.N is accepted after the order-checking of two generations, Deng, High-throughputdetectionofactionablegenomicalterationsin clinicaltumor, CancerDiscov2 (2012) 82-93. and G.H, Deng, Genome-scaleDNAmethylationmappingofclinicalsamplesatsing le-nucleotideresolution, NatMethods7 (2010) 133-136.).These factors hinder the development of the accurate medical science of tumour greatly.Therefore, be necessary very much for paraffin sample DNA extract flow process and purifying be optimized, provide abundant material foundation for realizing the accurate medical science of genomics power-assisted.
The treatment step of hospital pathology department paraffin embedding tumor tissues is as follows: 1, fixing; 2, wash; 3, dewater; 4, transparent; 5, waxdip; 6, embed; 7, cut into slices.Pathology Deparment doctor finally judges the nature and extent of disease according to HE dyeing, immunohistochemical methods, immunofluorescence etc. that paraffin section is originated.In this series for the treatment of processes, the tumor tissues DNA be embedded in paraffin mass inevitably experienced by multiple damages; This is also the basic reason why paraffin DNA highly degrades.
Now having the scheme that some bibliographical informations paraffin sample DNA extracts, is generally the extraction flow process based on silicon absorption.In the stage of fumbling in our early stage, find that the paraffin DNA existence that these schemes are extracted yields poorly, ropy popular feature (Fassunke, J., etal., Utilityofdifferentmassiveparallelsequencingplatformsform utationprofilinginclinicalsamplesandidentificationofpitf allsusingFFPEtissue.IntJMolMed, 2015).At present, not yet have and make full-range specific aim scheme to improve the seed output and quality of DNA extraction for paraffin section.Thus, we consider emphatically the film-making process that tumour paraffin sample experiences on follow-up layout strategy comprehensively, remove targetedly or reduce the degraded of these processes to DNA, thus reaching the final purpose improving paraffin sample DNA seed output and quality.
Summary of the invention
The object of this invention is to provide the DNA purification scheme in a kind of paraffin embedding sample, make it be applicable to extensive genomics research, for the accurate medical science realizing tumour patient establishes material foundation.
For this reason, the invention provides following technical scheme:
A DNA method of purification in paraffin embedding sample, described method comprises (1) and dewaxes to sample; (2) formaldehyde in sample is removed; (3) lysis; (4) DNA is extracted; (5) adhesion of DNA and protein is removed; (6) purify DNA, wherein, described step (1) comprises and dewaxing to sample with dimethylbenzene.
Preferably, in described step (1), repeatedly with dimethylbenzene, sample is dewaxed.
Preferred, dimethylbenzene carries out 2-3 dewaxing to sample.
Preferably, described step (2) comprise use sodium borohydride formaldehyde is reduced to methyl alcohol.
Preferred, the concentration of described sodium borohydride is 0.1-1.0M.
Preferably, described step (5) comprises and makes to spend linking agent to remove the adhesion of DNA and protein.
Preferred, described in go linking agent to include but are not limited to: SDS and NaHCO3.
Preferably, conbined usage Proteinase K is also comprised in described method steps (5) to remove the adhesion of DNA and protein.
Preferred, described Proteinase K addition is 20-40 μ l.Be more preferably, Proteinase K is 60-65 ° of lower water-bath.
The present invention also provides the application of a kind of above-mentioned either method in genomics.
The constraint using method of the present invention may suffer for paraffin-embedded DNA and damage, carried out corresponding improvement.Our strategy: based on DNA damaged points in paraffin specimen Making programme, design corresponding scheme pointedly.The DNA sample utilizing method of the present invention to prepare shows close to the genome of fresh sample.Specifically, technique effect of the present invention is: 1, by increasing the number of times of dimethylbenzene dewaxing, reduce the content of paraffin, thus reduces paraffin to the damage of DNA and constraint; 2, with sodium borohydride, formaldehyde is reduced to methyl alcohol, and evaporates, relieve formaldehyde to cyto-architectural fixing, reduce formaldehyde to the constraint of cell, thus improve the output of paraffin DNA; 3, in preferred scheme, make to spend crosslinker solution, reduce and just carry the crosslinked of DNA and albumen, thorough released dna, raising paraffin DNA quality; 4, combine increasing Proteinase K consumption, improve bath temperature, promote proteolytic degradation, reduce the pollution to DNA.By multi-scheme, for a long time optimization and improvement, the genomics performance of the paraffin specimen DNA that we extract obviously is better than existing program, has been in close proximity to the genomics performance of fresh sample.In equal initial olefin material with under extracting flow process simultaneously, our scheme can extract quantity more greatly, the paraffin DNA that quality is higher.What is more important, the application of subsequent gene group further demonstrate that the sequencing quality of these paraffin DNA equals to fresh sample.For carrying out the accurate medical science place mat of tumour patient material foundation stone on a large scale.
Accompanying drawing explanation
The DNA electrophoresis result figure of Fig. 1 embodiment 1;
Fig. 2: the DNA electrophoresis result figure of embodiment 2;
Fig. 3: the DNA electrophoresis result figure of embodiment 3;
Fig. 4: the gene order-checking Quality Map of embodiment 4.
Embodiment
Below in conjunction with specific embodiment, technical scheme of the present invention is further described.Be understandable that, particular implementation described here represents by way of example, and it is not as limitation of the present invention.When not deviating from the scope of the invention, principal character of the present invention may be used for various embodiment.One skilled in the art will appreciate that and maybe can confirm, only use normal experiment, many equivalents can be applied in particular step described herein.These equivalent places of being considered within the scope of the present invention, and cover by claim.
Embodiments of the invention relate to the test kit shown in table 1
Table 1: kit information
Embodiment 1
1. kidney paraffin sample (paraffin bits) room temperature (20-25 °) is placed 2 hours.
2. weighing≤25mg paraffin bits tissue, puts into 2mlEP pipe.
3. add 1200ul dimethylbenzene; Concussion mixing 10 seconds; Put gyroscope 10 minutes, room temperature.
4. centrifugal, 10000G, 70 seconds, room temperature.
5. abandon supernatant.
6. repeating step 3-5 once.
7. add 1200ul100% ethanol, concussion mixing 15 seconds.
8. centrifugal, 11000G, 70 seconds, room temperature.
9. abandon supernatant (not removing any precipitation).
10. repeating step 7-9 once.
11.37 ° of water-bath 2mlEP pipes 30 minutes.
12. add 100ul0.1M, 0.2M, 0.5M or 1.0M sodium borohydride solution (being set to the 2nd respectively, 3,4,5 groups).
13.50 ° of water-bath 2mlEP pipes 30 minutes.(control group does not add sodium borohydride, without step 12 and 13, is set as the 1st group)
14. add 180ulATL, 40ul Proteinase K; Concussion mixing 20 seconds.
15.61.5 ° water-bath 48-72 hour, to liquid-transparent (period takes out EP and manages and shake 3-5 time).
16. add 200ulAL, concussion mixing 20 seconds.
17.70 ° of water-baths 10 minutes.
18. add 200ul dehydrated alcohol, concussion mixing 20 seconds, slightly centrifugal.
All mixtures in EP pipe are transferred to QIAampMinispincolumn (being enclosed within 2ml collection tube) by 19..
20. is centrifugal, 6000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
21. add 500ulAW1; Centrifugal, 7000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
22. add 500ulAW2; Centrifugal, 8000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
23. is centrifugal, 9000g, 1 minute; Abandoned stream fluid.
24. pillars are uncapped, and room temperature places 10 minutes; Pillar is put into new 1.5mlEP and is managed afterwards.
The 25. 60 ° of preheating nuclease free water adding 50ul, room temperature 1 minute.
26. is centrifugal, 12000g, 1 minute.
27. repeat step to play 25-26 once; Obtain the elutriant of 100ul containing DNA.
28. is quantitatively preliminary: with NanoDrop and 1% gel electrophoresis figure (see Fig. 1).As shown in Figure 1, the DNA band of experimental group 2-5 is obviously more than control group 1, and concentration is also higher than control group.DNA quantitative result is in table 2.As shown in table 2, the DNA concentration that the experimental group (comprising 2-5 group) of adding NaBH4 obtains, apparently higher than control group, have significant significant difference, and the DNA quality that each experimental group obtains also obviously is better than control group.
Table 2: control group and experimental group DNA quantitative result
Electrophoresis sequence+sample names Concentration (ng/ul) Volume A260/280
1. control group 8.3 100 2.26
2. add 0.1M NaBH4 17.3 100 1.96
3. add 0.2M NaBH4 35.1 100 1.78
4. add 0.5M NaBH4 31.5 100 2.05
5. add 1.0M NaBH4 12.4 100 2.11
Embodiment 2
1. kidney paraffin sample (paraffin bits) room temperature (20-25 °) is placed 2 hours.
2. weighing≤25mg paraffin bits tissue, puts into 2mlEP pipe.
3. add 1200ul dimethylbenzene; Concussion mixing 15 seconds; Put gyroscope 10 minutes, room temperature.
4. centrifugal, 10000G, 70 seconds, room temperature.
5. abandon supernatant.
6. repeating step 3-5 bis-times.
7. add 1200ul100% ethanol, concussion mixing 15 seconds.
8. centrifugal, 11000G, 70 seconds, room temperature.
9. abandon supernatant (not removing any precipitation).
10. repeating step 7-9 once.
11.37 ° of water-bath 2mlEP pipes 30 minutes.
12. add 100ul0.2M sodium borohydride solution.
13.50 ° of water-bath 2mlEP pipes 30 minutes.
14. add 180ulATL, 40ul Proteinase K; Concussion mixing 20 seconds.
15.61.5 ° water-bath 48-72 hour, to liquid-transparent (period takes out EP and manages and shake 3-5 time).
16. add 200ulAL, concussion mixing 20 seconds.
17.70 ° of water-baths 10 minutes.
18. add 200ul dehydrated alcohol, concussion mixing 20 seconds, slightly centrifugal.
All mixtures in EP pipe are transferred to QIAampMinispincolumn (being enclosed within 2ml collection tube) by 19..
20. is centrifugal, 6000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
21. add 500ulAW1; Centrifugal, 7000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
22. add 500ulAW2; Centrifugal, 8000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
23. is centrifugal, 9000g, 1 minute; Abandoned stream fluid.
24. pillars are uncapped, and room temperature places 10 minutes; Pillar is put into new 1.5mlEP and is managed afterwards.
The 25. 60 ° of preheating nuclease free water adding 50ul, room temperature 1 minute.
26. is centrifugal, 12000g, 1 minute.
27. repeat step to play 25-26 once; Obtain the elutriant of 100ul containing DNA.
28. is quantitatively preliminary: with NanoDrop and Qubit.
29. add 10ul5M sodium chloride solution, concussion mixing 20 seconds.
30. add 90ul composite solution (1%SDS, 100mMNaHCO3), concussion mixing 20 seconds
31. water-baths 80 °, 1 hour.
32. add Proteinase K 40ul or 20ul (be set as respectively the 2nd and 3 groups).
33. water-baths 60 °, 48 hours.(control group does not have step 30-33, is set as the 1st group).
34. add 3-4 times of volume ChIPDNABindingBuffer, concussion mixing 20 seconds.
EP pipe content is transferred to Zymo-Spin by 35. tMiC-XLColumn (ZymoResearch).
36. is centrifugal, 6000g, 30 seconds; Abandoned stream effluent.
37. to add 200ulDNAWashBuffer. centrifugal, 7000g, 30 seconds; Abandoned stream effluent.Repeat 2 times.
38. pillars are uncapped, room temperature 5 minutes; Pillar is put into new 1.5mlEP and is managed afterwards.
The 39. 60 ° of preheating nuclease free water adding 25ul, room temperature 1 minute.
40. is centrifugal, 12000g, 1 minute.
41. repeating step 39-40 once; Obtain the DNA of the final purifying of 50ul.
42. is quantitative: with Qubit and 1% gel electrophoresis figure (see Fig. 2); As shown in Figure 2, the DNA band of experimental group 2-3 is obviously more than control group 1, and concentration is also higher than control group.Standby subsequent gene group application.DNA quantitative result is in table 3.As shown in table 3, each experimental group compares the DNA concentration obtained with control group obviously high, and both have statistical significant difference.
Table 3: control group and experimental group DNA quantitative result
Embodiment 3
1. liver cancer, lymphoglandula, prostate cancer, hyperplasia of prostate sample (paraffin bits) (being set as experimental group 1-4 respectively) room temperature (20-25 °) are placed 2 hours.
2. weighing≤25mg paraffin bits tissue, puts into 2mlEP pipe.
3. add 1200ul dimethylbenzene; Concussion mixing 15 seconds; Put gyroscope 10 minutes, room temperature.
4. centrifugal, 10000G, 70 seconds, room temperature.
5. abandon supernatant.
6. repeating step 3-5 once.
7. add 1200ul100% ethanol, concussion mixing 15 seconds.
8. centrifugal, 11000G, 70 seconds, room temperature.
9. abandon supernatant (not removing any precipitation).
10. repeating step 7-9 once.
11.37 ° of water-bath 2mlEP pipes 30 minutes.
12. add 100ul0.2M sodium borohydride solution.
13.50 ° of water-bath 2mlEP pipes 30 minutes.
14. add 180ulATL, 40ul Proteinase K; Concussion mixing 20 seconds.
15.61.5 ° water-bath 48-72 hour, to liquid-transparent (period takes out EP and manages and shake 3-5 time).
16. add 200ulAL, concussion mixing 20 seconds.
17.70 ° of water-baths 10 minutes.
18. add 200ul dehydrated alcohol, concussion mixing 20 seconds, slightly centrifugal.
All mixtures in EP pipe are transferred to QIAampMinispincolumn (being enclosed within 2ml collection tube) by 19..
20. is centrifugal, 6000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
21. add 500ulAW1; Centrifugal, 7000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
22. add 500ulAW2; Centrifugal, 8000g, 1 minute; Abandoned stream fluid, changes 2ml collection tube.
23. is centrifugal, 9000g, 1 minute; Abandoned stream fluid.
24. pillars are uncapped, and room temperature places 10 minutes; Pillar is put into new 1.5mlEP and is managed afterwards.
The 25. 60 ° of preheating nuclease free water adding 50ul, room temperature 1 minute.
26. is centrifugal, 12000g, 1 minute.
27. repeat step to play 25-26 once; Obtain the elutriant of 100ul containing DNA.
28. is quantitatively preliminary: with NanoDrop and Qubit.
29. add 10ul5M sodium chloride solution, concussion mixing 20 seconds.
30. add 90ul composite solution (1%SDS, 100mMNaHCO3), concussion mixing 20 seconds.
31. water-baths 80 °, 1 hour.
32. add 3-4 times of volume ChIPDNABindingBuffer, concussion mixing 20 seconds.
EP pipe content is transferred to Zymo-Spin by 33. tMiC-XLColumn (ZymoResearch).
34. is centrifugal, 6000g, 30 seconds; Abandoned stream effluent.
35. to add 200ulDNAWashBuffer. centrifugal, 7000g, 30 seconds; Abandoned stream effluent.Repeat 2 times.
36. pillars are uncapped, room temperature 5 minutes; Pillar is put into new 1.5mlEP and is managed afterwards.
The 37. 60 ° of preheating nuclease free water adding 25ul, room temperature 1 minute.
38. is centrifugal, 12000g, 1 minute.
39. repeating step 37-38 once; Obtain the DNA of the final purifying of 50ul.
40. is quantitative: with Qubit and 1% gel electrophoresis figure (see Fig. 3); As shown in Figure 3, use method of the present invention, after adding sodium borohydride and removing linking agent, be equally applicable to other tissue samples, the DNA band of extraction is all very many, and concentration is also high.Standby subsequent gene group application.DNA quantitative result is in table 4.As shown in table 4, the DNA concentration of each sample is all very high.
Table 4: each tissue samples DNA quantitative result
Electrophoresis sequence+sample names Concentration (ng/ul) Volume
1. liver cancer 51.2 50
2. lymphoglandula 194.5 50
3. prostate cancer 176.1 50
4. hyperplasia of prostate 45.6 50
Simultaneously, invent also independent for liver cancer tissue, relatively (namely there is no the step 30-31 of the present embodiment not making to spend linking agent, be set to control group, 1st group) and use linking agent (namely the aforesaid method of the present embodiment, is set to experimental group, the 2nd group) when DNA purification effect, result is as shown in table 5: the DNA concentration of experimental group is apparently higher than control group, and both have statistical significant difference.
Table 5: control group and experimental group DNA quantitative result
Electrophoresis sequence+sample names Concentration (ng/ul) Volume
1. control group 24.8 50
2. remove linking agent 51.2 50
Embodiment 4 paraffin DNA full genome sets up storehouse
According to the paraffin DNA of embodiment 2 purification, we start full genome and set up storehouse (according to NEB ultra tMdNALibraryPrepKitfor #E7370L).The Hiseq-2000 platform of Illunima company checks order.Crucial sequencing quality parameter is shown in Fig. 4: as shown in Figure 4, and A schemes: after fresh sample DNA order-checking, the reads base quality of >90% is higher than 30 (base mass range 0-40; More high better).B schemes: after paraffin sample DNA (method that we improve) order-checking, the reads base quality of >80% is higher than 30.C scheme: paraffin sample DNA order-checking after only 40% reads base quality higher than 30.As shown in table 6, the MappingB ratio of the paraffin sample B group that our method obtains up to 70-85%, close to the fresh sample of A group.
Table 6: the Mapping ratio of various sample
Sample source Mapping ratio
A. fresh sample 85-95%
B. paraffin sample (our improved plan) 70-85%
C. paraffin sample (Qiagene scheme) 20-50%
Above result shows, greatly can improve the sequencing quality of paraffin DNA by our improved plan, close to fresh sample, makes it the accurate medical science needs being adapted to tumour patient completely.

Claims (7)

1. the DNA method of purification in paraffin embedding sample, described method comprises (1) and dewaxes to sample; (2) formaldehyde in sample is removed; (3) lysis; (4) DNA is extracted; (5) adhesion of DNA and protein is removed; (6) purify DNA, is characterized in that, described step (1) comprises and dewaxing to sample with dimethylbenzene.
2. the method for claim 1, is characterized in that, in described step (1), repeatedly dewaxes to sample with dimethylbenzene.
3. method as arbitrary in claim 1-2, is characterized in that, described step (2) comprises use sodium borohydride and formaldehyde is reduced to methyl alcohol.
4. method as claimed in claim 3, it is characterized in that, the concentration of described sodium borohydride is 0.1-1.0M.
5. method as arbitrary in claim 1-4, is characterized in that, described step (5) comprises to be made to spend linking agent to remove the adhesion of DNA and protein.
6. method as claimed in claim 5, is characterized in that, also comprise conbined usage Proteinase K to remove the adhesion of DNA and protein in described step (5).
7. the application of method in genomics that claim 1-6 is arbitrary.
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CN105779438A (en) * 2016-03-22 2016-07-20 北京交通大学 Method for quickly separating and detecting crosslinking DNA in paraffin-embedded tissue sample
CN108998445A (en) * 2018-08-15 2018-12-14 益善生物技术股份有限公司 A kind of kit and its method extracting nucleic acid from paraffin section sample

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Publication number Priority date Publication date Assignee Title
CN105779438A (en) * 2016-03-22 2016-07-20 北京交通大学 Method for quickly separating and detecting crosslinking DNA in paraffin-embedded tissue sample
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