CN113151448A - KCNH2 gene detection kit and detection method - Google Patents
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Abstract
The invention discloses a KCNH2 gene detection kit and a detection method, wherein the detection method comprises the following steps: A. extracting DNA; B. performing quality inspection on the genome DNA; C. constructing an amplicon targeted capture library; D. performing on-machine sequencing on the prepared library; E. carrying out standard analysis on the data result; F. controlling the quality of data; G. the detection method has simple operation and low cost, and covers the full coding region of the KCNH2 gene, 50bp around the coding region, and sites such as chr7:150652688, chr7:150652610, chr7:150646655, chr7:150646928 and the like; meanwhile, the method can amplify 19 pairs of specific primers, reduces the complexity of operation compared with the traditional first-generation sequencing technology, and reduces the cost while keeping the same sequencing depth as the second-generation sequencing technology.
Description
Technical Field
The invention relates to the technical field of gene detection, in particular to a KCNH2 gene detection kit and a detection method.
Background
Sudden cardiac death refers to the natural death caused by cardiac causes characterized by sudden loss of consciousness occurring within 1 hour after the onset of acute symptoms, and accounts for the majority of sudden death, and whether the dead is born with or without cardiovascular disease. Sudden cardiac death has the characteristics of acute onset, rapid progress, high fatality rate and the like. Every year, 1700 thousands of people die globally due to cardiovascular diseases, and sudden cardiac death accounts for about 25 percent. The incidence of sudden cardiac death in women is 1.40/1000/year and in men 6.68/1000/year. About 50% of cardiac arrest occurs in individuals without known cardiac disease, but most patients have undiagnosed ischemic heart disease. It is estimated that more than 50 million people with sudden cardiac death in our country are getting younger. The vast majority of sudden cardiac deaths suffer from organic heart diseases, mainly including coronary heart disease, hypertrophic and dilated cardiomyopathies, valvular heart disease, myocarditis, non-atherosclerotic coronary artery abnormalities, invasive lesions, conduction abnormalities (QT interval prolongation syndrome, heart block), severe ventricular arrhythmias, etc. In addition, drug intoxication such as digitalis and quinidine can also be caused. Most sudden cardiac death is caused by ventricular tachyarrhythmia. Transient functional factors, such as cardiac instability, platelet aggregation, coronary spasm, myocardial ischemia, and reperfusion, destabilize the original stable cardiac structure. Sudden cardiac death may be triggered by factors such as autonomic nervous system instability, electrolyte imbalance, excessive exertion, emotional depression, and the use of ventricular arrhythmias. Home screening of first degree relatives of sudden cardiac death victims is a very important intervention that not only identifies at-risk families, advises on available treatments, but also adequately prevents sudden death. In relatives of up to 50% of victims of sudden arrhythmic syndrome, a diagnosis of inherited arrhythmogenic diseases can be made.
Long QT syndrome (LQTS) is a familial hereditary electrical activity disorder heart disease. The QT interval is the total time period from the beginning of the QRS complex to the end of the T wave on the electrocardiogram, representing the total time for ventricular depolarization and repolarization, which is a reflection of the conduction of electrical excitation in the ventricle. The clinical manifestations of LQTS are mainly repeated syncope and sudden death caused by torsade de pointes ventricular tachycardia. The symptoms of most patients occur during exercise, emotional stress, agitation, syncope generally lasts for 1-2min, and sudden death of a small percentage of patients occurs during sleep. The electrocardiogram is an important basis for diagnosing LQTS, QT intervals on the electrocardiogram of most patients are prolonged (male is more than or equal to 470ms, female is more than or equal to 480ms), but the QT intervals of a small part of patients can be normal, and the patient is called as 'normal QT interval' or 'hidden type' LQTS. LQTS is the earliest discovered ion channel disease, and has relatively more pathogenic genes and mutation sites, and relates to Na + channels, K + channels, Ca2+ channels, certain subunits and even proteins with a regulation function on the ion channels. Experts recommend the detection of genes associated with LQTS for the following cases: patients who are highly suspected of LQTS by cardiologists based on medical history, family history, and electrocardiogram phenotype; asymptomatic prolongation of the QT interval which is characteristic of this disease; patients with secondary QT interval prolonging factors were excluded.
KCNH2(human ether-a-go-go-related gene) is a gene of a rapid activation delayed rectifier potassium ion channel and codes a rapid activation delayed rectifier (cardiac rapid activation delayed rectifier K)+current, IKr) potassium channel, plays an important role in repolarization of cardiac myocyte action potential. The gene polymorphism enables the IKr channel function to be gained, namely the channel function is enhanced at each period of action potential, the outflow of potassium ions is increased, the repolarization is accelerated, the action potential time course is shortened, and the dispersion of the repolarization of atrial and ventricular muscles is increased, so that reentry arrhythmia is easy to occur, and the susceptibility of sudden cardiac death is increased.
The mutation of KCNH2 gene is one of the causes of sudden cardiac death, and gene diagnosis is also an important means for determining sudden cardiac death. However, the currently accepted sudden cardiac death causing gene variation only aims at the discovered hot spot mutation, and part of the variation is not used as a target for preventing and controlling or treating sudden cardiac death. (however, the mutation of any site of the gene is not related to sudden cardiac death; and the detection result of false negative caused by the fact that sudden cardiac death is inevitable by detecting the existing few gene mutation sites.) the invention firstly clarifies the feasibility of early diagnosis or prognosis prediction of sudden cardiac death by taking the whole coding region and part of the non-coding region of the human KCNH2 gene as new screening targets.
Disclosure of Invention
The invention aims to provide a KCNH2 gene detection kit and a detection method, so as to solve the problems in the background technology.
In order to achieve the purpose, the invention provides the following technical scheme: a KCNH2 gene detection method comprises the following steps:
A. extracting DNA;
B. performing quality inspection on the genome DNA;
C. constructing an amplicon targeted capture library;
D. performing on-machine sequencing on the prepared library;
E. carrying out standard analysis on the data result;
F. controlling the quality of data;
G. and (5) detecting variation.
Preferably, the step a specifically operates as follows: taking 200 microliters of a whole blood sample, extracting whole genome DNA by an extraction method, and detecting the quality and concentration of the DNA type by using Nanodrop 2000; wherein, the ratio of A260/280 is 1.8-2.0, the ratio of A260/230 is 1.7-1.9, the DNA sample is judged to be qualified, and finally the qualified DNA sample is uniformly diluted to 100 ng/microliter.
Preferably, the Qubit in the step B accurately quantifies the DNA concentration, the OD value is generally 1.8-2.0, the total amount of DNA is greater than 40ng, and DNA samples meeting the library building standard are used for subsequent library building sequencing.
Preferably, in the step C, a multiplex PCR technique and a KCNH2 gene multiplex PCR primer are used to simultaneously amplify a plurality of target regions on the genomic DNA to obtain an amplicon, then a second-generation sequencing linker is added to both sides of the amplicon by a PCR method to obtain an amplicon library, and a second-generation sequencing is performed to obtain sequence information of the target regions.
Preferably, in the step D, illumina nova is used for performing on-machine sequencing, PE150 is used, and the sample data size is not less than 1G.
Preferably, in the step G, based on the bam result of the alignment with the genome reference sequence, samtools and GATK software are used to search for the SNP and the InDel, and then ANNOVAR software is used to annotate the SNP and the InDel sites to determine the gene information, the functional information and the harmfulness corresponding to the mutation sites.
Preferably, the operation is performed according to a library construction process, which comprises the following steps:
1) taking 1 μ l of library, quantifying by using a Qubit dsDNA HS Assay Kit, and recording the concentration of the library, wherein the concentration of the library is about 10-50ng/μ l;
2) a1. mu.l sample was taken for library fragment length determination using an Agilent 2100Bioanalyzer system, with a library length of between about 300-450 bp.
Preferably, in the original data obtained by sequencing in step F, a small number of reads may include linker information, low-quality bases or undetected bases, in order to ensure the quality of information analysis, Raw reads need to be preliminarily filtered to obtain Clean reads, and subsequent analysis is performed based on Clean reads, and the content of data filtering is mainly as follows:
(1) cutting off sequences with the average base quality value less than 20 in an 8bp sliding window mode;
(2) removing the linker sequence at the tail of the sequence;
(3) if the first base or the tail base of the sequence is less than 20, the base is directly sheared off;
(4) and (4) downloading normally, and discarding the pair of sequences if the remaining sequence length is less than 40 after the removal.
Preferably, the KCNH2 gene detection kit comprises the detection method of any one of the above items.
Compared with the prior art, the invention has the beneficial effects that: the detection method is simple to operate and low in cost, and covers the full coding region of the KCNH2 gene, 50bp around the coding region, chr7:150652688, chr7:150652610, chr7:150646655, chr7:150646928 and other sites; meanwhile, the method can amplify 19 pairs of specific primers, reduces the complexity of operation compared with the traditional first-generation sequencing technology, and reduces the cost while keeping the same sequencing depth as the second-generation sequencing technology.
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FIG. 1 is a flow chart of a standard assay of the present invention;
FIG. 2 is a flow chart of library construction according to the present invention.
Detailed Description
The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
Referring to fig. 1-2, the present invention provides a technical solution: a KCNH2 gene detection method comprises the following steps:
A. extracting DNA;
B. performing quality inspection on the genome DNA;
C. constructing an amplicon targeted capture library;
D. performing on-machine sequencing on the prepared library;
E. carrying out standard analysis on the data result;
F. controlling the quality of data;
G. and (5) detecting variation.
In the invention, the step A specifically comprises the following operations: taking 200 microliters of a whole blood sample, extracting whole genome DNA by an extraction method, and detecting the quality and concentration of the DNA type by using Nanodrop 2000; wherein, the ratio of A260/280 is 1.8-2.0, the ratio of A260/230 is 1.7-1.9, the DNA sample is judged to be qualified, and finally the qualified DNA sample is uniformly diluted to 100 ng/microliter.
In the invention, the Qubit in the step B accurately quantifies the DNA concentration, the OD value is generally between 1.8 and 2.0, the total amount of the DNA is more than 40ng, and the DNA sample meeting the library building standard is used for subsequent library building sequencing.
In the invention, in the step C, multiple PCR technology and KCNH2 gene multiple PCR primers are utilized to simultaneously amplify a plurality of target regions on the genome DNA to obtain an amplicon, then a second-generation sequencing joint is added to two sides of the amplicon in a PCR mode to obtain an amplicon library, and second-generation sequencing is carried out to obtain sequence information of the target regions.
In the invention, in the step D, illumina nova is adopted for upper machine sequencing, PE150 is adopted, and the sample data size is not less than 1G.
In the invention, in step G, based on the bam result compared with the genome reference sequence, samtools and GATK software are adopted to search SNP and InDel, and ANNOVAR software is used to annotate the SNP and InDel sites so as to determine the gene information, the functional information and the harmfulness corresponding to the mutation site.
In the invention, the operation is carried out according to a library construction process, and the specific process is as follows:
1) taking 1 μ l of library, quantifying by using a Qubit dsDNA HS Assay Kit, and recording the concentration of the library, wherein the concentration of the library is about 10-50ng/μ l;
2) a1. mu.l sample was taken for library fragment length determination using an Agilent 2100Bioanalyzer system, with a library length of between about 300-450 bp.
In the invention, a small amount of reads containing linker information, low-quality bases or undetected bases exist in the original data obtained by sequencing in the step F, Raw reads need to be preliminarily filtered to obtain Clean reads in order to ensure the information analysis quality, subsequent analysis is performed on the basis of the Clean reads, and the content of data filtering is mainly as follows:
(1) cutting off sequences with the average base quality value less than 20 in an 8bp sliding window mode;
(2) removing the linker sequence at the tail of the sequence;
(3) if the first base or the tail base of the sequence is less than 20, the base is directly sheared off;
(4) and (4) downloading normally, and discarding the pair of sequences if the remaining sequence length is less than 40 after the removal.
KCNH2 gene multiplex PCR primers from Table 1, Table 2 and Table 3
TABLE 1
TABLE 2
TABLE 3
In conclusion, the detection method is simple to operate and low in cost, and covers the full coding region of the KCNH2 gene, the front and back 50bp of the coding region, the chr7:150652688, the chr7:150652610, the chr7:150646655, the chr7:150646928 and other sites; meanwhile, the method can amplify 19 pairs of specific primers, reduces the complexity of operation compared with the traditional first-generation sequencing technology, and reduces the cost while keeping the same sequencing depth as the second-generation sequencing technology.
Although embodiments of the present invention have been shown and described, it will be appreciated by those skilled in the art that changes, modifications, substitutions and alterations can be made in these embodiments without departing from the principles and spirit of the invention, the scope of which is defined in the appended claims and their equivalents.
Claims (9)
1. A KCNH2 gene detection method is characterized in that: the detection method comprises the following steps:
A. extracting DNA;
B. performing quality inspection on the genome DNA;
C. constructing an amplicon targeted capture library;
D. performing on-machine sequencing on the prepared library;
E. carrying out standard analysis on the data result;
F. controlling the quality of data;
G. and (5) detecting variation.
2. The method for detecting the KCNH2 gene, according to claim 1, wherein the method comprises the following steps: the step A specifically comprises the following operations: taking 200 microliters of a whole blood sample, extracting whole genome DNA by an extraction method, and detecting the quality and concentration of the DNA type by using Nanodrop 2000; wherein, the ratio of A260/280 is 1.8-2.0, the ratio of A260/230 is 1.7-1.9, the DNA sample is judged to be qualified, and finally the qualified DNA sample is uniformly diluted to 100 ng/microliter.
3. The method for detecting the KCNH2 gene, according to claim 1, wherein the method comprises the following steps: and B, accurately quantifying the DNA concentration by the Qubit in the step B, wherein the OD value is generally between 1.8 and 2.0, the total amount of the DNA is more than 40ng, and the DNA sample meeting the library building standard is used for subsequent library building sequencing.
4. The method for detecting the KCNH2 gene, according to claim 1, wherein the method comprises the following steps: and C, amplifying a plurality of target regions on the genome DNA by using a multiplex PCR technology and KCNH2 gene multiplex PCR primers to obtain an amplicon, adding a second-generation sequencing joint to two sides of the amplicon in a PCR mode to obtain an amplicon library, and performing second-generation sequencing to obtain sequence information of the target regions.
5. The method for detecting the KCNH2 gene, according to claim 1, wherein the method comprises the following steps: and D, performing upper machine sequencing by using illumina nova, and performing PE150 on the sample data, wherein the sample data size is not less than 1G.
6. The method for detecting the KCNH2 gene, according to claim 1, wherein the method comprises the following steps: and G, searching SNP and InDel by adopting samtools and GATK software based on the bam result compared with the genome reference sequence, annotating SNP and InDel sites by using ANNOVAR software, and determining the gene information, functional information and harmfulness corresponding to the mutation sites.
7. The method for detecting the KCNH2 gene according to claim 4, wherein the method comprises the following steps: the operation is carried out according to a library construction process, and the specific process is as follows:
1) taking 1 μ l of library, quantifying by using a Qubit dsDNA HS Assay Kit, and recording the concentration of the library, wherein the concentration of the library is about 10-50ng/μ l;
2) a1. mu.l sample was taken for library fragment length determination using an Agilent 2100Bioanalyzer system, with a library length of between about 300-450 bp.
8. The method for detecting the KCNH2 gene, according to claim 1, wherein the method comprises the following steps: in the original data obtained by sequencing in the step F, a small number of reads including linker information, low-quality bases or undetected bases may exist, Raw reads need to be preliminarily filtered to obtain Clean reads in order to ensure the quality of information analysis, and subsequent analysis is performed based on the Clean reads, and the content of data filtering is mainly as follows:
(1) cutting off sequences with the average base quality value less than 20 in an 8bp sliding window mode;
(2) removing the linker sequence at the tail of the sequence;
(3) if the first base or the tail base of the sequence is less than 20, the base is directly sheared off;
(4) and (4) downloading normally, and discarding the pair of sequences if the remaining sequence length is less than 40 after the removal.
9. A KCNH2 gene detection kit is characterized in that: the KCNH2 gene detection kit comprises the detection method of any one of claims 1-8.
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WO2018036176A1 (en) * | 2016-08-26 | 2018-03-01 | 广州永诺生物科技有限公司 | Multiplex pcr primer for amplifying brca1/2 gene and design method for multiplex pcr primer |
CN109022559A (en) * | 2018-08-21 | 2018-12-18 | 华中农业大学 | A kind of molecular mark detection method based on two generation sequencing technologies |
CN109593828A (en) * | 2018-12-07 | 2019-04-09 | 北京安智因生物技术有限公司 | A kind of construction method and its kit in the genetic test library of heredity arrhythmia cordis |
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CN117487907B (en) * | 2023-12-29 | 2024-04-23 | 湖南家辉生物技术有限公司 | KCNH2 gene mutant, mutant protein, reagent, kit and application |
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