WO2018149264A1 - Kit de détection par pcr quantitative fluorescente et procédé de détection - Google Patents

Kit de détection par pcr quantitative fluorescente et procédé de détection Download PDF

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WO2018149264A1
WO2018149264A1 PCT/CN2018/073181 CN2018073181W WO2018149264A1 WO 2018149264 A1 WO2018149264 A1 WO 2018149264A1 CN 2018073181 W CN2018073181 W CN 2018073181W WO 2018149264 A1 WO2018149264 A1 WO 2018149264A1
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detection
risk
quantitative pcr
result
gene
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PCT/CN2018/073181
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English (en)
Chinese (zh)
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吴少鸿
肖晶晶
周文根
姜萍萍
李欣
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深圳美因医学检验实验室
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the invention relates to the field of biological detection, in particular to a genetic detection and evaluation system, in particular to a fluorescent quantitative PCR detection kit and a detection method.
  • DS direct sequencing
  • LDR ligase detection reaction
  • RFLP restriction fragment length polymorphism
  • DPLC denaturing high performance liquid chromotography
  • quantitative PCR in which direct sequencing using a DNA analyzer is a gold standard, but the above methods have problems such as high cost, low accuracy, cumbersome operation, and poor repeatability.
  • qPCR Real-time Quantitative PCR Detection System
  • qPCR also known as real-time quantitative gene amplification fluorescence detection system
  • real-time PCR detection of the addition of fluorophores in the PCR reaction system the use of Fluorescence signal accumulation monitors the whole PCR process in real time, and finally quantifies the unknown template through the standard curve.
  • the qPCR system is a three-generation PCR detection technology. qPCR has high detection sensitivity, wide detection linear range, good detection accuracy and repeatability. The advantage is therefore recognized as the most advanced nucleic acid molecular diagnostic technology used in clinical practice in the world today. Therefore, this technology can be used for motion gene detection efficiently and accurately.
  • SNPs Single Nucleotide Polymorphisms
  • SNPs refer to the variation of single nucleotides in the genome, including transformation, transversion, deletion and insertion, and the formation of genetic markers, which are numerous and polymorphic.
  • SNP is a third-generation genetic marker.
  • Many phenotypic differences in human body, susceptibility to drugs or diseases may be related to SNP.
  • SNP research is an important step in the application of human genome project. This is mainly because SNPs will provide a powerful tool for the discovery of high-risk groups, identification of disease-related genes, drug design and testing, and basic research in biology. SNPs are widely distributed in the genome, and studies have shown that every 300 base pairs appear in the human genome.
  • SNP loci A large number of SNP loci exist, which gives people the opportunity to discover genomic mutations related to various diseases, including tumors. From the experimental operation, it is easier to find disease-related gene mutations through SNPs than through families; some SNPs do not directly cause The expression of a disease gene, but because it is adjacent to certain disease genes, it becomes an important marker. SNP has also played a huge role in basic research. Through the analysis of Y chromosome SNPs, a series of important achievements have been made in the field of human evolution, human population evolution and migration. SNPs are widely found in the human genome, with an average of one in every 500 to 1000 base pairs, with an estimated total of 3 million or more.
  • Sudden cardiac death is a natural death caused by a cardiac condition characterized by a sudden loss of consciousness that occurs within 1 hour of the onset of acute symptoms.
  • the majority of patients with sudden cardiac death have organic heart disease, including coronary heart disease, hypertrophic and dilated cardiomyopathy, valvular heart disease, myocarditis, non-atherosclerotic coronary abnormalities, invasive lesions, and conduction abnormalities ( Sudden death-related hereditary arrhythmias may be asymptomatic before the onset of QT prolongation syndrome, cardiac arrest, and severe ventricular arrhythmias, and may be fatal if attacked. Most sudden cardiac death is caused by ventricular tachyarrhythmias.
  • ECG instability ECG instability
  • platelet aggregation coronary spasm
  • myocardial ischemia ischemic reperfusion
  • post-ischemic reperfusion Some temporary functional factors, such as ECG instability, platelet aggregation, coronary spasm, myocardial ischemia, and post-ischemic reperfusion, have caused instability of the original stable cardiac structure.
  • Some factors such as autonomic nervous system instability, electrolyte imbalance, overwork, emotional depression, and medications that cause ventricular arrhythmias can trigger sudden cardiac death.
  • Most of the existing studies on cardiac death gene are based on the study of the upper locus of ion channel-related genes, which are based on the strong correlation sites of large sample GWAS studies in European population, and are applied to Asian populations, especially In China, the location of the population is weak, and it is difficult to obtain more accurate results through testing. Therefore, it is very necessary to establish an evaluation system for the Chinese population.
  • the inventors provide a fluorescence quantitative PCR detection kit, which includes a fluorescence quantitative PCR detection unit and a result processing evaluation unit, wherein the result processing evaluation unit includes a detection result processing system corresponding to a site and a reference.
  • the database; the reagents, the amount and the amplification detection method involved in the fluorescence quantitative PCR detection unit can be referred to the published prior art, and will not be described herein.
  • the detection kit comprises fluorescence quantitative PCR detection and result processing evaluation of at least two sites; that is, the detection kit is a multiplex quantitative PCR detection kit, and the plurality of sites are not limited to the same DNA fragment.
  • the reference database in the result processing evaluation department uses the East Asian population genomic data in the genome of thousands of people as the common population level, and the detection result is included in the database in real time; the reference database includes the allelic risk according to the test gene locus. Value and risk rating, frequency of occurrence of the gene, genetic risk and other statistical data, and related recommendations.
  • the genotypes of the points and the corresponding risk points are obtained, and the risk value P of the gene to be tested is calculated, and according to the average risk value Pa and the average variance S, the following five treatment results are obtained:
  • P a +0.6S ⁇ P is a high risk level; P a +0.2S ⁇ P ⁇ P a +0.6S is a slightly higher risk level; P a -0.2S ⁇ P ⁇ P a + 0.2S is a general risk level; a -0.6S ⁇ P ⁇ P a - 0.2S is a slightly lower risk level; P ⁇ P a - 0.6S is a low risk level.
  • the real-time PCR kit of the present invention is a cardiogenic sudden death site detection kit, and the kit detects two SNP sites, and the detection sites are rs4665058 and rs2824292, rs4665058
  • the OR values of the AA-AC-CC genotypes were 3.68-1.98-1, respectively; the OR values of the GG-GA-AA genotypes of the rs2824292 locus were 3.16-1.778-1, respectively; P values ⁇ 2.33 were high risk levels. 2.13 ⁇ P value ⁇ 2.33 is a high risk, 1.93 ⁇ P value ⁇ 2.13 is a general risk, 1.72 ⁇ P value ⁇ 1.93 is a low risk, P value ⁇ 1.72 is a low risk.
  • Another object of the present invention is to provide a fluorescence quantitative PCR detection method according to the above-described real-time PCR detection kit, wherein the detection method specifically includes:
  • the result is processed, and the risk points of each point are counted to obtain the risk value of the test gene, and the risk level in the database is corresponding;
  • the specific method is as follows:
  • the genotypes of each point and the corresponding risk points are obtained, and the risk value P of the gene to be tested is calculated, and according to the average risk value Pa and the average variance S, the following five treatment results are obtained:
  • P a +0.6S ⁇ P is a high risk level; P a +0.2S ⁇ P ⁇ P a +0.6S is a slightly higher risk level; P a -0.2S ⁇ P ⁇ P a + 0.2S is a general risk level; a -0.6S ⁇ P ⁇ P a - 0.2S is a slightly lower risk level; P ⁇ P a - 0.6S is a low risk level.
  • the mean variance S is calculated as follows:
  • i is the number of detection sites for the gene to be tested.
  • the average risk value passes the genomic data of the East Asian population, wherein the total number of people in the population is N, and the calculation formula of Pa is:
  • the above technical solution can evaluate the detection results of various genes by using a multiplex detection kit for real-time quantitative PCR, and based on the scientific and accurate result reference database, it can be obtained very accurately and personalizedly and strongly. Personalized results and recommendations for test samples have achieved more effective genetic testing and have a wider use and promotion value.
  • the detection kit and the detection method of the invention have high specificity, high detection rate, high efficiency and low cost. For example, in the field of gene diagnosis, comprehensive detection and analysis of whether the test population carries the test gene and evaluate the test The risk of the gene, screening the sample range, and follow-up guidance to the sample, to play a more in-depth guidance.
  • Figure 5 is a flow chart for evaluation based on the results of the test sample test.
  • a fluorescent quantitative PCR detection kit is used to detect a cardiac death-related gene, wherein two polymorphic sites on two genes related to sudden cardiac death (rs4665058) And rs2824292) to detect, using specific designed primers and probes, optimize the amplification system and conditions, and simultaneously complete the detection of two polymorphic sites on the two genes in the same system.
  • a single fluorescent labeled probe is used in this embodiment, Roche On the 480 platform, the rs4665058 and rs2824292 loci were detected by melting curve peak map.
  • the PCR amplification reaction is performed on the amplified sequence, and the specific reaction process (cycle) setting parameters are as follows:
  • test sample rs4665058 is G
  • test sample rs2824292 is the result of AG
  • the retest is performed by sequencing to prove the accuracy and reliability of the test method. .
  • the above two sites are respectively from the articles published by Bezzina et al. and Dr. Ar-king.
  • the article obtained two susceptible sites directly related to sudden cardiac death by GWAS study and calculated two The risk allele genotype risk value of the locus, ie the OR value.
  • the GWAS study found that common genetic variations in the CXADR and BAZ2B genes may be associated with ventricular fibrillation/SCD.
  • Bezzina et al found that the SNP locus on the CXADR gene (rs2824292) is a risk factor for ventricular fibrillation after acute myocardial infarction.
  • Rs2824292 can reduce the transcript abundance of CXADR, and the animal model of myocardial infarction carrying this mutation exhibits severe cardiac conduction disorder and arrhythmia susceptibility.
  • Dr. Ar-king compared the genes of 4402 patients with cardiac arrest with 30,000 normal people and found that cardiac arrest occurred when the BAZ2B gene was mutated (rs4665058). The probability is significantly higher, and often occurs in the absence of any warning, with a mortality rate of 95%.
  • studies have shown that the disease associated with the CXADR gene is myocarditis and dilated cardiomyopathy, and has a ventricular impulse.
  • the BAZ2B gene has no related function, but it is expressed in the heart.
  • the above two loci were evaluated.
  • the different genotypes and their risk values (OR) were: BAZ2B gene rs4665058, AA-AC-CC genotype had 0R values of 3.68-1.98-1, respectively; CXADR gene rs2824292, GG-GA-AA
  • the OR values of the genotypes ranged from 3.16 to 1.78-1. Since the incidence of sudden cardiac death is less than 10%, the OR value approximates the RR value, which is the risk value.
  • the risk value of each locus is calculated according to the genotype, that is, the risk value of the homozygous risk allele genotype is the square of the OR value, and the risk value of the heterozygous risk allele genotype is OR value, homozygous non-risk, etc.
  • each SNP site has a susceptibility value based on the detected genotype. We define this score as S, then the subject's individual cardiogenic death is easy.
  • the sense value is P, and the P value is the product of the OR values of the two genotypes:
  • the genomic data of the East Asian population in the thousand human genome is the level of the general population, and the total number is defined as N.
  • the average score of the genotypes of the East Asian population in the thousand human genome was set as the average score of the population:
  • the risk of sudden cardiac death in East Asian population is graded, and the risk value of sudden cardiac death of the subject is corresponding to the population classification.
  • the population is divided into five levels, which are high-slightly high. - General - slightly lower - lower five risk levels.
  • Pa+0.6S ⁇ P is a high risk level; Pa+0.2S ⁇ P ⁇ Pa+0.6S is a slightly higher risk level; Pa-0.2S ⁇ P ⁇ Pa+0.2SC is a general risk level; Pa-0.6S ⁇ P ⁇ Pa-0.2S is a slightly lower risk level; P ⁇ Pa-0.6S is a low risk level.
  • P value ⁇ 2.33 is high risk level
  • 2.13 ⁇ P value ⁇ 2.33 is high risk
  • 1.93 ⁇ P value ⁇ 2.13 is general risk
  • 1.72 ⁇ P value ⁇ 1.93 is partial Low risk
  • P value ⁇ 1.72 is low risk.
  • the two OR values are multiplied to obtain the susceptibility value of the sudden cardiac death, that is, the risk value.
  • the risk value corresponds to the risk level of sudden cardiac death of the individual obtained by the grading method, according to the level corresponding to the P value of the subject, the risk of sudden cardiac death of the subject is comprehensively obtained, thereby giving an individual health management plan.
  • the risk of sudden cardiac death risk is calculated according to the risk value of sudden cardiac death risk at each locus, and the population classification is performed according to the existing database, and the individual sudden cardiac death risk level is obtained through the individual score.
  • the risk of sudden death of the subject guide high-risk people to improve their lifestyle, avoid predisposing factors, and increase the frequency of physical examination.
  • a database of Chinese populations with two genetic polymorphism sites was established, which laid the foundation for the establishment of a unique cardiac death assessment in the Chinese population.
  • the present invention can assess the risk associated with sudden cardiac death in a subject.
  • the detection kit provided by the invention has high specificity, high detection rate, high efficiency and low cost, and can comprehensively detect and analyze whether the tested population carries the “heart-borne sudden death susceptibility gene” and evaluates the sudden cardiac death.

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Abstract

La présente invention concerne un kit de détection par PCR quantitative fluorescente, qui comprend une partie de détection par PCR quantitative fluorescente et une partie de traitement et d'évaluation de résultat, la partie de traitement et d'évaluation de résultat comprenant un système de traitement de résultat de détection correspondant à des loci et une base de données de référence. Un locus ayant été amplifié est détecté au moyen d'un diagramme de pic d'une courbe de dissociation, de façon à obtenir le résultat de détection du locus correspondant ; le résultat de détection est traité ; des statistiques relatives au point de risque de chaque locus sont collectées, pour obtenir la valeur de risque d'un gène à détecter ; puis le risque du gène et du résultat de traitement associé sont obtenus de manière globale, sur la base d'un niveau de risque correspondant dans la base de données. L'emploi d'un kit de détection multiple employant une PCR quantitative fluorescente permet d'évaluer les résultats de détection de multiples gènes ; le recours à une base de données de référence contenant des résultats scientifique et exacts permet d'obtenir un résultat de bonne exactitude et extrêmement individualisé ; un résultat individualisé et une suggestion peuvent être attribués à un échantillon détecté, de façon à atteindre l'objectif d'une détection plus efficace des gènes.
PCT/CN2018/073181 2017-02-20 2018-01-18 Kit de détection par pcr quantitative fluorescente et procédé de détection WO2018149264A1 (fr)

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WO2022073259A1 (fr) * 2020-10-10 2022-04-14 苏州大学 Kit pour détecter la susceptibilité d'une mort cardiaque subite sur la base de sites polymorphes d'insertion et de délétion de gène cox10

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CN107893107A (zh) * 2017-11-30 2018-04-10 深圳美因医学检验实验室 一种用于黑色素瘤基因筛查的荧光定量pcr检测系统及其应用
CN112862297B (zh) * 2021-02-02 2022-03-01 方舟生物安全科技(广州)有限公司 一种病原微生物物联网实时监测系统

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Publication number Priority date Publication date Assignee Title
WO2022073259A1 (fr) * 2020-10-10 2022-04-14 苏州大学 Kit pour détecter la susceptibilité d'une mort cardiaque subite sur la base de sites polymorphes d'insertion et de délétion de gène cox10

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