CN112501282A - Method for obtaining BsmI and PvuII site base sequences by extracting DNA from whole blood and performing qPCR amplification detection - Google Patents

Method for obtaining BsmI and PvuII site base sequences by extracting DNA from whole blood and performing qPCR amplification detection Download PDF

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CN112501282A
CN112501282A CN202011596447.1A CN202011596447A CN112501282A CN 112501282 A CN112501282 A CN 112501282A CN 202011596447 A CN202011596447 A CN 202011596447A CN 112501282 A CN112501282 A CN 112501282A
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dna
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bsmi
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侯明飞
朱月艳
孙子奎
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Shanghai Personal Medicine Laboratory Co ltd
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Abstract

The invention discloses a method for obtaining BsmI and PvuII site base sequences by extracting DNA from whole blood and carrying out qPCR amplification detection, 1) sequencing data processing, 2) Seurat data filtering, 3) cell clustering and 4) cell population marker gene analysis.

Description

Method for obtaining BsmI and PvuII site base sequences by extracting DNA from whole blood and performing qPCR amplification detection
Technical Field
The invention relates to the technical field of gene detection, in particular to a method for obtaining base sequences of BsmI and PvuII sites by extracting DNA from whole blood and performing qPCR amplification detection.
Background
Osteoporosis is a metabolic disease of the whole body bone, and is mainly characterized by a decrease in bone mass and a change in bone microstructure accompanied by a decrease in bone strength, an increase in bone fragility, an increase in fracture risk, and the like. According to epidemiological statistics, the prevalence rate of osteoporosis in people over 50 years old in China is 20.7% for women and 14.4% for men. And according to global epidemiological investigation, the prevalence of osteoporosis is high in all countries. The onset of osteoporosis is associated with a variety of factors, of which sex factors and age factors are the most relevant to the onset of osteoporosis. The pain and the fracture caused by the osteoporosis seriously affect the life quality of the patient and endanger the survival of the patient, and the existing treatment means has relatively limited effect on the osteoporosis. In the elderly women, after the pathological fracture is mostly followed by osteoporosis, the residual fatality rate caused by osteoporosis fracture is high, and the fatality rate of the osteoporosis fracture exceeds the sum of the fatality rates of the elderly women suffering from breast cancer, cervical cancer and uterine body cancer at present.
The current clinical methods for diagnosing osteoporosis mainly comprise: 1. the physician consults a past medical history which provides a high risk factor for osteoporosis, such as alcohol abuse, heavy smoking, pre-menopausal bilateral ovariectomy, etc., and then needs further examination. 2. Bone mass is measured based on the measurement of bone mineral content and bone density, but the occurrence of fractures and osteoporosis does not depend solely on bone mass. 3. Ultrasound bone determination measures the speed of ultrasound through bone tissue, amplitude attenuation and stiffness index reflecting bone structure and bone mass.
The existing methods for diagnosing osteoporosis mainly have the following defects: 1. the physician can only provide reference for inquiring the past medical history and can not accurately judge whether osteoporosis exists. 2. Bone mass measurement is a commonly used means at present, but whether fracture occurs or not is mainly determined by bone strength, and the bone strength is composed of various aspects such as bone mass, bone quality, bone composition and bone shape, so that the judgment by the bone mass alone is not accurate. 3. The result of ultrasonic measurement is not the bone density or the bone mineral content, and can not compare with the true value, needs more observation data, and the huge inconvenience of moving of ultrasonic equipment in addition is higher shortcoming such as the cost of each measurement. Therefore, an improved product for diagnosing osteoporosis is needed in the market.
Disclosure of Invention
The invention provides a method for obtaining base sequences of BsmI and PvuII sites by extracting DNA from whole blood and performing qPCR amplification detection.
The scheme of the invention is as follows:
a method for extracting DNA from whole blood to carry out qPCR amplification detection to obtain base sequences of BsmI and PvuII sites comprises the following steps:
1) preparing a required DNA sample, extracting the DNA of the sample from whole blood, and storing the obtained DNA of the sample at the temperature of between 20 ℃ below zero and 4 ℃ for later use;
2) qPCR amplification of sample DNA, namely diluting the sample DNA in the step 1) to 5-30 ng/mu L, constructing a reaction system in a PCR tube, sending the reaction system into a PCR amplification instrument, setting a reaction program for reaction, and obtaining a target gene after the reaction is finished;
3) and (3) detecting the locus, namely detecting the target gene in the step 2) to obtain a detection report.
And (3) judging the risk of osteoporosis by detecting the base sequences of the BsmI site and the PvuII site.
As a preferred technical scheme, the DNA of the whole blood extracted sample is as follows:
cutting a Tip of a 1-mL Tip, inserting a pipette, extending into a blood collection tube, repeatedly blowing and beating whole blood for 3-4 times, fully suspending precipitated white blood cells, transferring the whole blood to an EP tube, adding MGS lysate, adding proteinase K, uniformly mixing, heating in a water bath kettle at 60 ℃ for 10-15 min, wherein the uniformly mixing time is more than 2 times;
taking out the EP pipe from the water bath kettle, pouring all solution in the EP pipe into a centrifugal adsorption column, putting the adsorption column into a collecting pipe, centrifuging at 8000rpm for 1min, taking out the adsorption column, and pouring out waste liquid in the collecting pipe;
adding cleaning solution into the adsorption column
Figure BDA0002870373130000022
8000rpm, centrifuging for 30s, taking out the adsorption column, and pouring off the waste liquid in the collection tube;
rinsing twice, taking out the adsorption column after the completion, pouring off the waste liquid in the collection tube, putting the adsorption column back into the collection tube again, centrifuging at 12000rpm for 1min, and removing the residual ethanol;
placing the adsorption column in a new 1.5ml centrifuge tube, and drying at room temperature for 2-3 min; dripping 60 deg.C eluent ET into the adsorption column near the center of the adsorption membrane, centrifuging at 12000rpm for 1-2min, collecting the liquid in the tube as sample DNA solution, covering with a cover, and lightly pulling the liquid in the tube to mix well.
As a preferable technical scheme, the rinsing treatment is to add a rinsing liquid Wash into the adsorption column at 8000rpm, centrifuge for 30s, take out the adsorption column and pour the waste liquid in the collection tube.
As a preferable technical scheme, the reaction system in the step 2) is as follows:
Figure BDA0002870373130000021
Figure BDA0002870373130000031
as a preferred technical scheme, MGB-TaqMan-FAM adopts FAM6 at the Apa I site, and the rest is FAM.
As a preferable technical scheme, the reaction procedure in the step 2) is as follows:
Figure BDA0002870373130000032
S3-S4 were cycled 45 times.
The method for obtaining the base sequences of BsmI and PvuII sites by extracting DNA from whole blood and performing qPCR amplification detection is adopted in the technical scheme, 1) the required DNA sample is prepared, the sample DNA is extracted from the whole blood, and the obtained sample DNA is stored at the temperature of-20-4 ℃ for later use; 2) qPCR amplification of sample DNA, namely diluting the sample DNA in the step 1) to 5-30 ng/mu L, constructing a reaction system in a PCR tube, sending the reaction system into a PCR amplification instrument, setting a reaction program for reaction, and obtaining a target gene after the reaction is finished; 3) and (3) detecting the locus, namely detecting the target gene in the step 2) to obtain a detection report.
The invention has the advantages that: the method has the advantages that the operation steps are simple, the graph result is visual, the interpretation is easy, the detection time is shortened, the detection efficiency is improved, and the detection accuracy is improved;
provides effective information, thereby improving the prediction accuracy of the osteoporosis risk.
Drawings
FIG. 1 is a graph of the amplification of the VDR BsmI detection site GG in accordance with the present invention;
FIG. 2 is a graph showing the AG amplification of VDR BsmI detection sites in accordance with one embodiment of the present invention;
FIG. 3 is a graph showing the AA amplification of the VDR BsmI detection site in the embodiment of the present invention;
FIG. 4 is a graph showing the amplification of the ESR PvuII detection site AA in the example of the present invention;
FIG. 5 is a graph showing the amplification of AG at the detection site of ESR PvuII in the example of the present invention;
FIG. 6 is a graph showing the amplification of the ESR PvuII detection site GG in the example of the present invention.
FIG. 7 is an analytical flow chart according to the present invention;
FIG. 8 is an interface diagram of the Roche 480 analysis software analysis site selection analysis according to an embodiment of the present invention;
FIG. 9 is an interface diagram of a Roche 480 analysis software selection analysis sample according to an embodiment of the present invention;
FIG. 10 is a graphical illustration of a Roche 480 analysis software analysis parameters selection interface according to an embodiment of the present invention;
FIG. 11 is a FAM interface diagram of the Roche 480 analysis software selection channel according to an embodiment of the present invention;
FIG. 12 is an interface diagram of FAM analysis results of Roche 480 analysis software according to an embodiment of the present invention;
FIG. 13 is an interface diagram of a Roche 480 analysis software exchange analysis channel according to an embodiment of the present invention;
FIG. 14 is a VIC channel interface diagram of Roche 480 analysis software according to an embodiment of the present invention;
FIG. 15 is an interface diagram of Roche 480 analysis software for importing analysis channels into the reading software separately according to an embodiment of the present invention;
FIG. 16 is an interface diagram of Roche 480 analysis software showing the amplification map of the FAM channel in accordance with an embodiment of the present invention;
FIG. 17 is an interface diagram of the Roche 480 analysis software showing the amplification map of the VIC channel in accordance with one embodiment of the present invention;
FIG. 18 is an interface diagram of the Roche 480 analysis software showing FAM and VIC dual channel amplification maps in accordance with the present invention.
Detailed Description
In order to make up for the above deficiencies, the present invention provides a method for obtaining base sequences of BsmI and PvuII sites by extracting DNA from whole blood and performing qPCR amplification detection to solve the above problems in the background art.
A method for extracting DNA from whole blood to carry out qPCR amplification detection to obtain base sequences of BsmI and PvuII sites comprises the following steps:
1) preparing a required DNA sample, extracting the DNA of the sample from whole blood, and storing the obtained DNA of the sample at the temperature of between 20 ℃ below zero and 4 ℃ for later use;
2) qPCR amplification of sample DNA, namely diluting the sample DNA in the step 1) to 5-30 ng/mu L, constructing a reaction system in a PCR tube, sending the reaction system into a PCR amplification instrument, setting a reaction program for reaction, and obtaining a target gene after the reaction is finished;
3) and (3) detecting the locus, namely detecting the target gene in the step 2) to obtain a detection report.
And (3) judging the risk of osteoporosis by detecting the base sequences of the BsmI site and the PvuII site.
The whole blood extracted sample DNA is as follows:
cutting a Tip of a 1-mL Tip, inserting a pipette, extending into a blood collection tube, repeatedly blowing and beating whole blood for 3-4 times, fully suspending precipitated white blood cells, transferring the whole blood to an EP tube, adding MGS lysate, adding proteinase K, uniformly mixing, heating in a water bath kettle at 60 ℃ for 10-15 min, wherein the uniformly mixing time is more than 2 times;
taking out the EP pipe from the water bath kettle, pouring all solution in the EP pipe into a centrifugal adsorption column, putting the adsorption column into a collecting pipe, centrifuging at 8000rpm for 1min, taking out the adsorption column, and pouring out waste liquid in the collecting pipe;
adding cleaning solution into the adsorption column
Figure BDA0002870373130000053
8000rpm, centrifuging for 30s, taking out the adsorption column, and pouring off the waste liquid in the collection tube;
rinsing twice, taking out the adsorption column after the completion, pouring off the waste liquid in the collection tube, putting the adsorption column back into the collection tube again, centrifuging at 12000rpm for 1min, and removing the residual ethanol;
placing the adsorption column in a new 1.5ml centrifuge tube, and drying at room temperature for 2-3 min; dripping 60 deg.C eluent ET into the adsorption column near the center of the adsorption membrane, centrifuging at 12000rpm for 1-2min, collecting the liquid in the tube as sample DNA solution, covering with a cover, and lightly pulling the liquid in the tube to mix well.
And the rinsing treatment comprises the steps of adding a rinsing liquid Wash into the adsorption column at 8000rpm, centrifuging for 30s, taking out the adsorption column, and pouring out waste liquid in the collecting pipe.
The reaction system in the step 2) is as follows:
Figure BDA0002870373130000051
the MGB-TaqMan-FAM adopts FAM6 at the Apa I site, and the balance is FAM.
As a preferable technical scheme, the reaction procedure in the step 2) is as follows:
Figure BDA0002870373130000052
S3-S4 were cycled 45 times.
In order to make the technical means, the creation characteristics, the achievement purposes and the effects of the invention easy to understand, the invention is further described with the specific embodiments.
Example (b):
extraction of DNA from whole blood
1. Cutting off a Tip of a 1-mL Tip head, inserting a pipette, extending into a blood collection tube, repeatedly blowing and beating whole blood for 3-4 times to fully suspend precipitated white blood cells, transferring 200 mul of whole blood into a 2mL EP tube, adding 200 mul of MGS lysate and 20 mul of proteinase K, uniformly mixing, heating in a 60 ℃ water bath kettle for 10min (no more than 15min), uniformly mixing at least for 2-3 times, otherwise, enabling hemoglobin to cohere and agglomerate.
2. Taking out the sample from the water bath, pouring the solution into a centrifugal adsorption column, placing the adsorption column into a collecting tube, centrifuging at 8000rpm for 1min, taking out the adsorption column, and pouring off the waste liquid in the collecting tube.
3. Adding 500 μ l of cleaning solution into the adsorption column
Figure BDA0002870373130000062
8000rpm, centrifuging for 30s, taking out the adsorption column, and pouring the waste liquid in the collecting pipe.
4. Adding 500 μ l of rinsing liquid Wash to the adsorption column at 8000rpm, centrifuging for 30s, taking out the adsorption column, and pouring off waste liquid in the collection tube.
5. Repeat 4 times.
6. Taking out the adsorption column, pouring off waste liquid in the collection tube, putting the adsorption column back into the collection tube again, and centrifuging at 12000rpm for 1min to remove residual ethanol as much as possible.
7. The adsorption column was placed in a new 1.5ml centrifuge tube and dried for 2-3min at room temperature.
8. And (3) suspending and dropwise adding 50-100 μ l of eluent ET (preheating the eluent ET at 65 ℃ in advance to improve the elution efficiency) into the adsorption column close to the center of the adsorption film. 12000rpm, centrifuging for 1-2min, and collecting liquid in the centrifugal tube to obtain the DNA solution. And lightly stirring the liquid in the centrifugal tube after covering the cover to uniformly mix. The sample DNA is stored at 4 ℃ or-20 ℃ for a long period of time according to the application.
9. Can be directly used for PCR, enzyme digestion, library construction, sequencing reaction and the like.
qPCR amplification
Diluting the qualified DNA sample to 5-30 ng/muL;
qPCR reaction system
Reagent Volume of
2 × qPCR Mix (New sea NuHi SNP Mix) 5μL
Primer F/R 0.4μL
MGB-TaqMan-FAM (FAM 6 is adopted as Apa I locus, and FAM is adopted as the rest) 0.2μL
MGB-TaqMan-VIC 0.2μL
ddH2O 3.2μl
Template DNA 1μL
Roche 480 reaction procedure
Figure BDA0002870373130000061
Figure BDA0002870373130000071
Interpreting the result according to the result interpretation standard and issuing a detection report; the Roche 480 analysis software operates as in FIGS. 8-18 to analyze the amplification curves;
the risk of osteoporosis is judged by detecting the base sequences of BsmI site and PvuII site, which are shown in figure 1 to figure 6;
osteoporosis risk interpretation
Figure BDA0002870373130000072
The foregoing shows and describes the general principles, essential features, and advantages of the invention. It will be understood by those skilled in the art that the present invention is not limited to the embodiments described above, which are described in the specification and illustrated only to illustrate the principle of the present invention, but that various changes and modifications may be made therein without departing from the spirit and scope of the present invention, which fall within the scope of the invention as claimed. The scope of the invention is defined by the appended claims and equivalents thereof.

Claims (6)

1. A method for extracting DNA from whole blood to carry out qPCR amplification detection to obtain base sequences of BsmI and PvuII sites is characterized by comprising the following steps:
1) preparing a required DNA sample, extracting the DNA of the sample from whole blood, and storing the obtained DNA of the sample at the temperature of between 20 ℃ below zero and 4 ℃ for later use;
2) qPCR amplification of sample DNA, namely diluting the sample DNA in the step 1) to 5-30 ng/mu L, constructing a reaction system in a PCR tube, sending the reaction system into a PCR amplification instrument, setting a reaction program for reaction, and obtaining a target gene after the reaction is finished;
3) and (3) detecting the locus, namely detecting the target gene in the step 2) to obtain a detection report.
2. The method for obtaining the base sequences of BsmI and PvuII sites by qPCR amplification assay of whole blood extracted DNA as claimed in claim 1, wherein the DNA of the whole blood extracted sample is as follows:
cutting a Tip of a 1-mL Tip, inserting a pipette, extending into a blood collection tube, repeatedly blowing and beating whole blood for 3-4 times, fully suspending precipitated white blood cells, transferring the whole blood to an EP tube, adding MGS lysate, adding proteinase K, uniformly mixing, heating in a water bath kettle at 60 ℃ for 10-15 min, wherein the uniformly mixing time is more than 2 times;
taking out the EP pipe from the water bath kettle, pouring all solution in the EP pipe into a centrifugal adsorption column, putting the adsorption column into a collecting pipe, centrifuging at 8000rpm for 1min, taking out the adsorption column, and pouring out waste liquid in the collecting pipe;
adding cleaning solution into the adsorption column
Figure FDA0002870373120000012
8000rpm, centrifuging for 30s, taking out the adsorption column, and pouring off the waste liquid in the collection tube;
rinsing twice, taking out the adsorption column after the completion, pouring off the waste liquid in the collection tube, putting the adsorption column back into the collection tube again, centrifuging at 12000rpm for 1min, and removing the residual ethanol;
placing the adsorption column in a new 1.5ml centrifuge tube, and drying at room temperature for 2-3 min; dripping 60 deg.C eluent ET into the adsorption column near the center of the adsorption membrane, centrifuging at 12000rpm for 1-2min, collecting the liquid in the tube as sample DNA solution, covering with a cover, and lightly pulling the liquid in the tube to mix well.
3. The method of claim 1 for obtaining base sequences of BsmI and PvuII sites by qPCR amplification detection of DNA extracted from whole blood, wherein: and the rinsing treatment comprises the steps of adding a rinsing liquid Wash into the adsorption column at 8000rpm, centrifuging for 30s, taking out the adsorption column, and pouring out waste liquid in the collecting pipe.
4. The method for obtaining base sequences of BsmI and PvuII sites by qPCR amplification detection of DNA extracted from whole blood as claimed in claim 1, wherein the reaction system in step 2) is as follows:
Figure FDA0002870373120000011
Figure FDA0002870373120000021
5. the method of claim 4 for obtaining base sequences of BsmI and PvuII sites by qPCR amplification detection of DNA extracted from whole blood, wherein: the MGB-TaqMan-FAM adopts FAM6 at the Apa I site, and the balance is FAM.
6. The method for obtaining base sequences of BsmI and PvuII sites by qPCR amplification assay of DNA extracted from whole blood as claimed in claim 5, wherein the reaction procedure in step 2) is as follows:
Figure FDA0002870373120000022
S3-S4 were cycled 45 times.
CN202011596447.1A 2020-12-29 2020-12-29 Method for obtaining BsmI and PvuII site base sequences by extracting DNA from whole blood and performing qPCR amplification detection Pending CN112501282A (en)

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Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN108220426A (en) * 2018-02-27 2018-06-29 北京岳昊科技发展有限公司 A kind of kit for being used to detect osteoporosis
CN110257507A (en) * 2019-07-11 2019-09-20 上海联吉医学检验所有限公司 A kind of pregnancy period folic acid metabolism, calcium metabolism and H-type hypertension associated detecting method
CN111019940A (en) * 2019-12-25 2020-04-17 上海派森诺生物科技股份有限公司 Extracting solution for directly extracting whole blood genome DNA and extracting method thereof
CN111534588A (en) * 2020-04-23 2020-08-14 南京实践医学检验有限公司 Kit and method for detecting gene mutation in acute lymphocytic leukemia based on fluorescent quantitative PCR
CN111996244A (en) * 2020-10-28 2020-11-27 上海鼎晶生物医药科技股份有限公司 Composition for detecting single nucleotide polymorphism and application thereof

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN108220426A (en) * 2018-02-27 2018-06-29 北京岳昊科技发展有限公司 A kind of kit for being used to detect osteoporosis
CN110257507A (en) * 2019-07-11 2019-09-20 上海联吉医学检验所有限公司 A kind of pregnancy period folic acid metabolism, calcium metabolism and H-type hypertension associated detecting method
CN111019940A (en) * 2019-12-25 2020-04-17 上海派森诺生物科技股份有限公司 Extracting solution for directly extracting whole blood genome DNA and extracting method thereof
CN111534588A (en) * 2020-04-23 2020-08-14 南京实践医学检验有限公司 Kit and method for detecting gene mutation in acute lymphocytic leukemia based on fluorescent quantitative PCR
CN111996244A (en) * 2020-10-28 2020-11-27 上海鼎晶生物医药科技股份有限公司 Composition for detecting single nucleotide polymorphism and application thereof

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