KR102084965B1 - Qualitative or quantitative mutant genotyping methods and real-time PCR kits for performing the methods - Google Patents

Abstract

The present invention distinguishes the homozygous type and the heterozygous type of a mutation by using an internal control (IC) together with a probe or a primer capable of distinguishing a mutant trait, and a specific mutant genotype. The present invention relates to an efficient SNP quantification and quantitative analysis method based on real-time PCR capable of quantitative analysis of DNA. More specifically, irrespective of the mutant genotype, a PCR reaction of a target gene using a FenDEL probe or an ARMS primer capable of selecting and amplifying a specific mutant trait by PCR can be performed simultaneously. The present invention relates to a method for determining a mutant genotype by analyzing a relative change in the amount of amplified product of a target gene based on the amount of amplified product. In addition, the present invention relates to a method for quantitatively analyzing the incorporation rate of a mixed sample of a heterogeneous individual by using a simultaneous real-time polymerase chain reaction of a FenDEL probe and an internal control for a species-sensitive mutation marker.

Description

Qualitative or quantitative mutant genotyping methods and real-time PCR kits for performing the methods

The present invention distinguishes between a homozygous type and a heterozygous type of a mutation using an internal control (IC) together with probes and primers capable of distinguishing mutant traits, and identifies specific mutant genotypes. The present invention relates to an efficient mutant genotyping method and a heterogeneous quantitative analysis method based on real-time PCR that can be quantitatively analyzed. More specifically, the present invention simultaneously performs a target gene PCR reaction capable of selectively amplifying a specific mutant trait and an internal control that is amplified by PCR irrespective of the mutant genotype, and based on the amount of amplification products of the internal control that are PCR results. The present invention relates to a method for determining a mutant genotype by analyzing a relative change in the amount of amplification product of a target gene. In addition, the present invention relates to a method for quantitatively analyzing the mixing ratio of heterologous individual mixed samples by simultaneously performing PCR and internal control PCR on a mutant marker capable of species identification.

Real-time polymerase chain reaction (real-time PCR), also called quantitative polymerase chain reaction (qPCR), is an analytical technology based on polymerase chain reaction.

Polymerase chain reaction is one of the most powerful techniques in molecular biology experiments, and can be used to replicate or amplify specific sequences in DNA or cDNA thousands to tens of thousands of times.

Traditional PCR methods, also called end point PCR, require electrophoresis after the completion of the PCR reaction in order to detect or quantify the amount of DNA amplified, and then image the results. On the other hand, real-time PCR or qPCR can simultaneously perform amplification and quantification of target DNA molecules.

Since PCR theoretically doubles the amount of target DNA, the initial DNA amount can be determined by the amount of PCR product that has been completed. However, due to various factors affecting the PCR reaction, the actual accurate analysis is not easy. Indeed, in the initial cycle of PCR, there is an exponential phase in which the amount of PCR product increases rapidly, but a plateau appears due to the decrease of enzyme activity, dNTP and Mg ^+, etc. during the PCR reaction. Therefore, in order to measure the exact amount of DNA, it should be measured in the section where the amount of DNA increases exponentially, that is, exponential phase. Therefore, it is difficult to measure the exact amount of DNA by the traditional method of analyzing the reaction result after the PCR reaction is completed. The technology developed to overcome the limitations of this analytical method is real-time polymerase chain reaction. In the real-time polymerase chain reaction, the amount of PCR product is measured every cycle, thereby distinguishing the change pattern of PCR product amount, that is, exponent and stagnation phase.

In real-time polymerase chain reaction, a fluorescent reporter is used to measure the amount of DNA changed every cycle. As a fluorescent reporter, it is possible to use a substance capable of binding to double-stranded DNA (dsDNA) such as 'SYBR Green', or a specific base sequence such as 'TaqMan probe' or 'Molecular Beacons'. Fluorescent materials bound to primers or probes that can specifically bind are used. In each cycle, the intensity of the fluorescence signal is measured by a fluorescence measurement device connected to the PCR equipment, and the change in the fluorescence signal intensity is displayed as a curve graph according to the reaction, so that it is possible to check how much PCR products are produced in real time.

The advantages of real-time polymerase chain reaction are: first, real-time monitoring of the PCR reaction, second, accurate measurement of the amount of PCR product amplified each cycle, and third, the reaction and analysis is completed in one tube PCR There is no need for a separate experiment.

The basic use of real-time polymerase chain reaction is quantitative analysis such as gene expression analysis and copy number analysis of transgenes, but it is also used for qualitative analysis such as SNP genotyping, genetically engineered food test and virus pathogen detection. This is because there is no need to confirm the amplification products after the chain reaction by separate electrophoresis, so that the result can be easily and quickly obtained, and the risk of obtaining false PCR results due to contamination of other unwanted templates or amplification products can be reduced. .

Nucleic acid quantification using real-time polymerase chain reaction has two methods (absolute quantification and relative quantification) (Dhannasekaran, S. et al. 2010. Immunol Methods, 354 (1-2) : 34-9). Absolute quantification is a method of preparing a calibration curve using standard DNA and measuring the amount of target DNA using this method. This method essentially requires the same PCR efficiency of the sample and the standard DNA (Bar, T. et al. 2012 Nucleic Acids Research., 40 (4): 1395-1406). Relative quantification is a method of determining the difference in the relative expression level of the target gene based on the expression level of the reference gene. Therefore, in relative quantitative experiments, the reference gene should be measured in addition to the target gene whose expression level is desired. The reference gene is for template template standardization (correction) between samples, and a housekeeping gene is commonly used as a reference gene. To compare the expression levels, first, the template amount between samples is standardized using the quantitative value of the reference gene, and the standardized value is compared with the control sample to investigate the change in expression level.

Relative quantification is a method of quantifying using a calibration curve, and there is a comparative quantification method that measures relative quantitative values by mathematical calculations without using a calibration curve. In order to analyze the expression level by comparative quantitative method, all samples used for analysis should be prepared in the same way, and the PCR amplification efficiency should be nearly constant for all the genes measured, and the calibration sample may be used as a reference material. Should be used.

The calibration curve used for quantitative analysis is obtained by stepwise dilution of standard DNA or standard sample, and the quality of calibration curve is very important because it is the standard for absolute or relative quantification of unknown sample. The quality of the calibration curve is assessed by the slope and linearity (correlation coefficient, R ² value) used to calculate the amplification efficiency of PCR.

The equation for calculating the PCR amplification efficiency through the slope of the calibration curve varies depending on the method of taking the X and Y axes of the calibration curve and converting the initial template amount to algebra, but the X axis is substituted for the initial template concentration (Log10) and the Y axis as the Ct value. In this case, the equation 'Efficiency (E) = -1 +10 ^{(-1 / slope)} ' is applied. In this case, if the slope is between -3.1 and -3.6, the amplification efficiency is 90 to 110%. Usually, the amplification efficiency is acceptable at an appropriate level of 80 ~ 120%, if the amplification efficiency is low, redesign the primer or suspected the presence of PCR inhibitors, and review the preparation method of the sample.

The linearity of the calibration curve is represented by the correlation coefficient (R ² ) and the closer to 1, the closer to the straight line. The linearity generally accepted in real time polymerase chain reaction is above 0.98.

Single nucleotide polymorphism (SNP) is a single-substituted DNA polymorphism that occurs more than 1% of the population. Depending on the SNP trait that an individual has, individual differences may arise that are important for metabolic processes such as disease susceptibility and therapeutic response. In particular, SNP is useful when examining the distribution of individual genes for diseases with complex multiple gene bias.

SNP genotyping refers to determining the sequencing of SNPs, which is performed using various molecular biological analysis techniques that can distinguish DNA variations. Most SNP discrimination methods are based on the use of hybridization, enzymes such as nucleases or polymerases, and SNPs can be determined through direct sequencing.

Representative SNP identification methods utilizing polymerase chain reaction or real-time polymerase chain reaction include Tetra-primer amplification refractory mutation system PCR (ARMS-PCR) (Newton, CR et al. 1989. Nucleic Acids Research, 17 (7): 25032516), Allele-specific PCR (AS-PCR) (Gaudet, MI et al. 2009. Methods Mol Biol., 578: 415-424), Single-strand conformational polymorphism (SSCP) assay (Masato, O. et al. 1989. Proc. Natl. Acad. Sci. USA., 86 (8): 2766-2770), Denaturing high performance liquid chromatography (DHPLC) (Oefner, PJ et al. 1995. Am J Hum Genet. , 57: 10310), and high-resolution melting of the entire amplicon (Pasay C. et al. 2008. Med. Vet. Entomol., 22 (1): 8288).

SNP genotyping methods based on real-time polymerase chain reaction have many advantages over other SNP discrimination techniques, such as large-scale analysis, reduced risk of false PCR results due to contamination of other unwanted templates or amplification products, and labor savings. It is actively used in basic research and diagnostics.

In order to distinguish SNP traits using real-time polymerase chain reaction, it is common to use two kinds of hydrolysis probes simultaneously (Wittwe, C. T. et al., 1997. BioTechniques, 22: 176-181). TaqMan probe, a typical hydrolysis probe, is an oligonucleotide consisting of several to several tens of bases having complementary sequences to SNPs and its surrounding sequences, and reporter dyes and quenchers at the 5 'and 3' ends, respectively. Modified polymers. Depending on the mutant trait, different kinds of phosphors are used as reporters, for example, using the TaqMan probe modified with mutant trait 1 as 'VIC' and mutant trait 2 as 'FAM'. In addition, the length of the nucleotide sequence of the TaqMan probe should be as short as possible in order to give specificity for each SNP trait, which inevitably lowers the Tm value, making it difficult to maintain a stable annealing state. Groove Binder) is also used to combine the MGB-TaqMan probe (Kutyavin, IV et al. 2000. Nucleic Acids Res., 28: 655-661). The MGB-TaqMan probe is similar to the general TaqMan probe, but by adding a minor groove coupling portion at the 3 'end, it maintains stable annealing under PCR conditions because the Tm is high even if the probe is short.

SNPs can be analyzed by applying the AMRS (amplification refractory mutation system) PCR principle with TaqMan probes without the use of a separate modified probe such as MGB (Ellison, G. et al. 2010. J. Exp. Clin. Cancer Res) , 29: 132). ARMS PCR, however, is very difficult to find the optimal PCR conditions to distinguish SNPs (Punia, P. et al., Http://www.horizonpress.com/pcrbooks).

FenDEL ( FEN 1 activity de creasing The ed by a probe system is a new SNP detection technology that can analyze mutations by real-time polymerase chain reaction using the flap endonuclease ("FEN") specificity of DNA polymerase. Korean Patent No. 10-1598398), more specifically, the 3 'terminal sequence of the probe and the 3' terminal sequence of the sense primer is complementary, the probe 5 'terminal is positioned to correspond to the SNP point of the PCR product, When a part of the 5 'end of the probe meets the mutation of the SNP point, the flap structure of two or more bases is formed, and the polymerization reaction is stopped. Real-time polymerase chain reaction and hydrolysis probes such as hybridization probes or TaqMan probes distinguish SNPs by simply using the difference in the complementary binding force of the probes over temperature, whereas the FenDEL system uses The specificity of the test is excellent because it uses the characteristics of the enzyme rather than the classification, and it is advantageous in multi-analysis. Real-time polymerase chain reaction using FenDEL probe is a rapid, sensitive, specific, and economical means for detecting genetic mutations, and is one of the applicable methods for detecting tumor-specific mutations requiring high specificity and sensitivity.

SNP genotyping using fluorescent probes such as MGB-TaqMan and real-time polymerase chain reaction uses the fluorescent signal of the reporter dye at the end of the PCR reaction. In other words, at the end of the PCR reaction, the fluorescence signal of the reporter dyes representing the two SNP traits is measured, and the SNP genotype of the sample is determined by analyzing the type and ratio of the measured fluorescence signal. In general, the signal of the reporter dye is visualized in the form of a plot and used for transfection.

A series of analytical procedures, such as SNP calling, genotyping and visualization of the measured fluorescence signal, is performed by an automated analysis program. However, attention should be paid to characterization when analyzing rare alleles or when signal distinction of SNP genotypes is unclear. That is, accurate SNP calls require the manual work of experts to assess data quality, set fluorescence signal thresholds, and determine the genotype of SNPs. To avoid this problem, all genotyping assays may include a positive control assay or a statistical analysis called K-mer (Ranade, K. et al. 2001. Genome Res. , 11: 1262-1268).

In order to measure the absolute or relative amount of the sample by using real-time polymerase chain reaction, the PCR cycle, which is the exponential increase in PCR products, is used as basic information, and the SNP genotyping is used. In the case of analysis, it is common to use the type of fluorescence and the magnitude value of the fluorescence signal (Rn or RFU) as basic information at the end of PCR reaction.

Threshold cycle (Ct) refers to the period at which the fluorescence signal crosses a threshold and may be used as a term Cp (cross point cycle) or Cq (quantification cycle) depending on the real-time polymerase chain reaction device used. The change in Ct value is related to the amount of target DNA used in the PCR, and the magnitude of the Ct value is inversely proportional to the concentration of the initial template to be applied in the reaction. In other words, if the Ct value is high, the concentration of the initial template used for PCR is low. If the Ct value is low, the concentration of the initial template is high.

According to the analyzer, the magnitude value of the fluorescence signal is expressed differently as Rn or RFU. Rn (Relative normalized fluorescence) is a value used to correct the deviation of the fluorescence signal generated between PCR wells, and normalized by dividing the magnitude value of the fluorescence signal emitted from the reporter dye by the magnitude value of the fluorescence signal emitted from the reference sample. Say the value. ABI's 7300/7500 Real Time PCR System is a representative analyzer that uses Rn. Another measurement unit used for fluorescence detection assay, RFU (Relative fluorescent units) is a unit of fluorescence signal used in analyzers that do not need to compensate for deviations between PCR wells. The RFU value increases as the amount of amplified DNA increases. The value can range from 0 to thousands. Bio-Rad's CFX-96 Real Time System is a representative analyzer that uses RFU.

In general, it is known that stagnant phases in which PCR product increase no longer occurs due to binding competition between primers and PCR products during PCR reactions (Kainz, P. et al. 2000. Biochim Biophys Acta , 1494 (1-2): 23-27). In other words, the more PCR products bind to the target, the less likely the primer is to bind to the target, so that no new synthesis can occur. Thus, increasing the PCR cycle does not necessarily increase the total amount of PCR product and consequently there is no correlation between the total PCR product identified at the plateau and the amount of starting target. In addition, depending on the type of analyzer used for the real-time polymerase chain reaction, the magnitude of the final detected fluorescence signal may be different even under the same analysis conditions. In addition, even if the same analyzer is used, the fluorescence value may be different depending on the state of the instrument at the time of measurement, for example, the intensity of the light emission and the state of the detector, and the position of the well that determines the distance from the light source. For this reason, in the real-time polymerase chain reaction analysis, the Rn or RFU value at the end of the PCR reaction could not be used for the quantitative analysis of the sample.

As described above, various genotyping and genetic quantitative methods using real-time polymerase chain reaction have been developed, but there is still a need for more economical and efficient improved technology.

An object of the present invention is to perform a PCR reaction capable of selectively amplifying a specific mutant trait and an internal control which is amplified by a PCR reaction regardless of the mutant genotype in a real-time polymerase chain reaction simultaneously in one well, and the internal generated by PCR By comparing and analyzing the relative changes in the amount of amplified products of the mutant traits selectively amplified based on the amount of amplified products of the control group, a qualitative analysis method for determining the mutant genotype of the target genes more clearly and economically than conventional methods is provided. will be.

It is also an object of the present invention to provide a method capable of quantitatively analyzing the incorporation rate of mixed samples of heterogeneous individuals using dual PCR using a FenDEL probe and an internal control for a mutant marker capable of species identification.

To this end, the present inventors PCR amplified a common internal control with a specific mutation test sample to determine the mutant genotype based on real-time polymerase chain reaction, and as a result, the Ct value of the internal control and the Ct of the specific mutation test sample were measured. The relative change of the values, and the relative change of the fluorescence intensity of the stagnant or exponential phase on the amplification curve of the internal control and the exponential fluorescence intensity on the amplification curve of the specific mutant test sample were calculated. And the present invention was completed by deriving a formula that can clearly determine the mutant genotype and quantitatively analyze the incorporation rate of specific mutant traits by applying various relations based on the calculated values.

In the present invention, the term 'amplification plot (plot)' refers to a curve expressed by connecting the magnitude value of the fluorescent signal measured every cycle in the real-time polymerase chain reaction. The greater the initial number of copies of the target nucleic acid to be amplified, the faster the onset period in which an increase in fluorescence value is observed.

In the present invention, the term 'passive reference dye' refers to a reference dye used to correct a deviation of a fluorescence signal generated between PCR wells. If the reference dye does not affect the reaction, there is no particular limitation, but ROX Dyes are most commonly used.

In the present invention, the term 'Rn (Relative normalized fluorescence)' refers to a normalized value by dividing the magnitude value of the fluorescence signal emitted from the reporter dye by the magnitude value of the fluorescence signal emitted from the passive reference dye.

In the present invention, the term 'delta Rn (ΔRn)' means a magnitude value of a fluorescent signal obtained by subtracting a baseline from Rn.

As used herein, the term 'threshold' refers to the delta Rn used to determine the Ct value in a real time polymerase chain reaction. The threshold is typically the position above the baseline where the amplification starts exponentially and is set automatically or manually.

In the present invention, the term 'Relative fluorescent unit (RFU)' is a unit of measurement used for fluorescence detection analysis. As the amount of DNA amplified increases, the RFU value increases and the RFU value may range from 0 to thousands.

In the present invention, 'Raf (Relative Amplification efficiency)' refers to amplification efficiency relative to an internal control of a specific mutant trait.

In the present invention, the term 'RCt (relative Ct)' is a value obtained by dividing the Ct value of a specific mutant trait by the Ct value of an internal control.

In the present invention, the term 'ΔCt' is obtained by subtracting the Ct value of the internal control from the Ct value of a specific mutant trait.

In the present invention, the term 'RΔRn1 (relative ΔRn1)' refers to the fluorescence value of the internal control when the fluorescence value of the real-time polymerase chain reaction is expressed as ΔRn and the fluorescence value of the internal control is greater than that of a specific mutant trait. It is divided by the fluorescence value of the mutant trait.

In the present invention, the term 'RRFU1 (relative RFU1)' refers to the fluorescence value of the internal control when the fluorescence value of the real-time polymerase chain reaction is expressed as RFU and the fluorescence value of the internal control is greater than that of a specific mutant trait. It is divided by the fluorescence value of the mutant trait.

In the present invention, the term 'RΔRn2 (relative ΔRn2)' refers to the fluorescence value of a specific mutant trait when the fluorescence value of a real-time polymerase chain reaction is expressed as ΔRn and the fluorescence value of a specific mutant is greater than that of an internal control. It is divided by the fluorescence value of the internal control.

In the present invention, the term 'RRFU2 (relative RFU2)' refers to the fluorescence value of a specific mutant trait when the fluorescence value of a real-time polymerase chain reaction is expressed as RFU and the fluorescence value of a specific mutant is greater than that of an internal control. It is divided by the fluorescence value of the internal control.

In the present invention, the term 'ΔΔRn1' is a case where the fluorescence value of the real-time polymerase chain reaction is expressed as ΔRn and the fluorescence value of the internal control is greater than the fluorescence value of the specific mutant. Minus value.

In the present invention, the term 'ΔRFU1' refers to the fluorescence value of a specific mutant trait at the fluorescence value of the internal control when the fluorescence value of the real-time polymerase chain reaction is expressed as RFU and the fluorescence value of the internal control is greater than that of the specific mutant trait. Minus value.

In the present invention, the term 'ΔΔRn2' refers to the fluorescence value of the internal control at the fluorescence value of a specific mutant trait when the fluorescence value of the real-time polymerase chain reaction is expressed as ΔRn and the fluorescence value of a specific mutant is greater than that of the internal control. Minus value.

In the present invention, 'ΔRFU2' refers to the fluorescence value of the internal control at the fluorescence value of the specific mutant trait when the fluorescence value of the real-time polymerase chain reaction is expressed as RFU and the fluorescence value of the specific mutant is greater than the fluorescence value of the internal control. Minus value.

In the present invention, the term 'c-value' is a value calculated for each experimental condition to clarify the classification of mutant genotypes, including SNPs, and results of real-time polymerase chain reaction of DNAs of the same number of standard heterozygotes and standard homozygotes. Different relative values (ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU) or various correlation values (multiplied or divided relative Ct and relative fluorescence values) that can be calculated based on the identifiable Ct and fluorescence values Is the average value.

The present invention is intended to economically and accurately determine one or more mutant alleles using real-time polymerase chain reaction and / or to effectively analyze the incorporation rate of a particular mutant trait.

The present invention is characterized by performing internal control amplification simultaneously with amplification for analysis of specific mutant traits.

In the present invention, the internal control is characterized in that the gene is amplified in common irrespective of the mutant trait. It is preferable to select a housekeeping gene as the internal control.

The present invention is characterized by using a primer or probe that can distinguish and amplify the mutant trait. Mutant traits can be distinguished by using a mutant-specific primer (hereinafter referred to as ARMS) capable of selectively amplifying mutant traits (hereinafter referred to as ARMS) or by using FEN (Flap endonuclease) specificity of DNA polymerase. By using the FenDEL system that can detect a mutation such as SNP.

The present invention is characterized by using a fluorescence modified probe, such as a TaqMan probe that can be confirmed whether amplification and the amount of amplification.

The present invention is characterized by using the Ct value measured in real time polymerase chain reaction and the fluorescence value of the exponent or stagnant phase of the amplification curve.

In the present invention, the fluorescence value of the internal control measured in the real-time polymerase chain reaction is the fluorescence value of the exponent or stagnant phase of the amplification curve, and the fluorescence value of a specific mutant trait is characterized by the fluorescence value of the exponent phase of the amplification curve. .

In the present invention, the Ct value of a specific mutant is always greater than the Ct value of an internal control, and the fluorescence value of a specific mutant is characterized by being smaller or greater than the fluorescence value of an internal control.

The present invention relates to the internal control and the relative Ct value (combined with "Rct" or "ΔCt (delta Ct)" in the specification and drawings) and the internal control measured in the real control polymerase chain reaction. Relative fluorescence values (relative fluorescence values, interchangeable with "RΔRn", "RRFU", "ΔΔRn" or "ΔRFU" in the following description and drawings) of particular mutant traits are used.

In the present invention, the method of calculating the relative Ct value or the relative fluorescence value of the internal control and the specific mutant trait is characterized by subtracting a small value from a large value or dividing a large value by a small value.

In addition, the present invention is characterized by using a correlation value multiplied or divided by the relative Ct value and the relative fluorescence value of the internal control and the specific mutant trait.

The present invention calculates coefficients of various relative and correlation values based on the Ct and fluorescence values measured in real time polymerase chain reaction (hereinafter referred to as "C-value"), respectively. It is characterized by determining the mutant genotype using this.

In the present invention, the 'C-value' is calculated based on the Ct value and the fluorescence value confirmed as a result of the real-time polymerase chain reaction of the standard heterozygotes and the standard homozygous DNA of the same quantity under the same analysis conditions. It is done.

In the present invention, the analysis conditions for calculating the 'C-value' are the same as the unknown test sample analysis conditions, and the types of analyzers used in the analysis and the preparation conditions of the kit are the same.

The present invention divides various relative or correlation values calculated based on the Ct value and the fluorescence value into respective C-values to determine the conjugate form of the mutant trait when the value is greater than or less than one. It is characterized by.

Correlation for mutant genotyping in the present invention is Ct value-based calculated value and fluorescence than ΔΔRn, ΔRFU, RΔRn, RRFU calculated by using only the Ct value divided by each C-value Genetic traits can be more clearly distinguished by multiplying or dividing the value-based output and dividing by the C-value.

In the present invention, the correlation is characterized in that when the fluorescence value of the specific mutant trait is less than the fluorescence value of the internal control, the calculated value based on the Ct value and the calculated value based on the fluorescence value. For example, Raf1 = (RCt x RΔRn1) / C-value.

In the present invention, the correlation is characterized in that when the fluorescence value of a specific mutant trait is greater than the fluorescence value of the internal control, the calculated value based on the Ct value and the calculated value based on the fluorescence value. For example, Raf2 = (RCt ÷ RRFU2) / C-value.

In addition, the present invention is characterized by providing a method for preparing a calibration curve using a standard sample knowing the incorporation rate of a specific mutant trait and measuring the mixing ratio of a specific mutant trait of an unknown test sample using the prepared calibration line.

In the present invention, the standard sample used for preparing the calibration curve is characterized by using two or more standard samples having different incorporation rates of specific mutant traits.

In the present invention, the calibration curve is characterized by using a correlation value obtained by multiplying or dividing a relative Ct value or a relative fluorescence value or a relative Ct value and a relative fluorescence value measured in a real-time polymerase chain reaction.

In the present invention, an unknown test is performed using a calibration curve having a larger slope than a calibration curve having a small slope among calibration curves prepared by using a correlation value multiplied or divided by a relative Ct value, a relative fluorescence value, or a relative Ct value and a relative fluorescence value. Analysis of a specific mutational incorporation rate of a sample is characterized by a more accurate value.

The present invention is a method for detecting mutations using real-time PCR,

(A) real-time PCR for screening and amplifying a specific mutant trait of the test sphere in one tube and performing a real-time PCR for the internal control by designating one of the genes in the genome containing the specific mutation as an internal control;

(B) performing real-time PCR on a standard sample in which a homozygote sample and a heterozygote sample for a specific mutant trait are present in a specific molar ratio under the same conditions and the same type as in the above (a);

(C) obtaining at least one of the Ct value measured in the internal control PCR and the test PCR, and ΔRn and RFU, which are fluorescence values at the end of PCR;

(D) RCt (relative Ct), which is the larger value divided by the smaller of the Ct value measured by the internal control PCR and the Ct value measured by the test PCR, and ΔCt (delta Ct, which is the value obtained by subtracting the small value from the larger value of the Ct value. ), Obtaining RΔRn, RRFU, which is a large value divided by a small value of fluorescence values, ΔΔRn, ΔRFU, which is a value obtained by subtracting a small value from a large value of fluorescence values, and multiplying these values or dividing these values by one or more ;

(E) obtaining one or more of each Ct value and each fluorescence value ΔRn and RFU for the homozygous sample and the heterozygous sample from the PCR result for the standard sample;

(F) Ct value, homofluorescence value ΔRn value or RFU value of homozygous sample and heterozygous sample in the standard sample, ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU and their relative values Or obtaining a C-value which is a value obtained by dividing a relative value and an average value of these values;

(G) Ct value, ΔRn value, RFU value, their relative values ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU, and their relative values obtained from (D) and the control group, or their relative values. Dividing the value by C-values, which are average values of the corresponding step (f), respectively; And

(H) dividing the value obtained in step (g) into a heterozygote if greater than 1 and homozygous if less than 1; and a method for identifying a mutation using real-time PCR.

In addition, the present invention is a mutation using a real-time PCR, characterized in that the mutation is any one or more of the insertion, deletion, substitution and single nucleotide polymorphism (SNP) of the base (nucleotide) It is about how to check.

The present invention also relates to a method for identifying a mutation using real-time PCR, characterized in that the mutation is present in plants, animals, microorganisms, human body, agricultural products and processed products thereof.

In addition, the present invention uses a real-time PCR, characterized in that the real-time PCR method for screening and amplifying the specific mutant trait selected from one of FenDEL-PCR, ARMS-PCR, TaqMan-PCR, MGB-TaqMan-PCR and PNA-PCR To identify a mutation.

The present invention also relates to a method for identifying mutations using real-time PCR, characterized by selecting a house keeping gene as the internal control.

In addition, in the present invention, the steps (b), (e), and (b) are performed separately from the other steps, so that each Ct value and each fluorescence value ΔRn and RFU for the homozygous standard sample and the heterozygous standard sample are different. Ct value, fluorescence value of ΔRn value or RFU value or relative value of ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU, and relative values of homozygous and heterozygous samples C-value, which is the average value of the divided by, is provided as a protocol, and a method for identifying a mutation using real-time PCR.

In addition, the present invention provides a primer and probe for the internal control to perform the method; Standard sample including homozygous sample and heterozygous sample; Primers and probes for the standard sample; And a primer and a probe capable of distinguishing mutant traits of a test sample.

In addition, the present invention provides a method for carrying out the above method.

Each Ct value and each fluorescence value for homozygous and heterozygous standard samples or at least one of ΔRn and RFU, or Ct values for homozygous and heterozygous samples in standard samples, ΔRn or RFU values for fluorescence, and these values Protocols in which relative values ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU and their relative values are multiplied or divided by relative values and the average of these values are recorded as C-values;

Primers and probes for internal controls; And

It relates to a real-time PCR kit comprising a; and a primer and a probe that can distinguish the mutant trait of the test sample.

In addition, the present invention is a method for detecting a mutation using real-time PCR,

(A) real-time PCR for screening and amplifying a specific mutant trait of the test sphere in one tube and performing a real-time PCR of the internal control with one of the genes in the genome containing the specific mutation as an internal control;

(B) real-time PCR of homohomygote standard and heterozygote standard samples and one or more standard samples where homozygotes and heterozygotes exist in a specific molar ratio for the specific mutant trait. Performing the same conditions and the same model;

(C) obtaining at least one of the Ct value measured in the internal control PCR and the test PCR, and ΔRn and RFU, which are fluorescence values at the end of PCR;

(D) RCt (relative Ct), which is the larger value divided by the smaller of the Ct value measured by the internal control PCR and the Ct value measured by the test PCR, and ΔCt (delta Ct, which is the value obtained by subtracting the small value from the larger value of the Ct value. ), Obtaining RΔRn, RRFU, which is a large value divided by a small value of fluorescence values, ΔΔRn, ΔRFU, which is a value obtained by subtracting a small value from a large value of fluorescence values, and multiplying these values or dividing these values by one or more ;

(E) obtaining one or more of each Ct value and each fluorescence value ΔRn and RFU for each standard sample after PCR on the standard sample;

(F) Ct, fluorescence, ΔRn, or RFU, relative values of ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU, and their relative values; Obtaining a C-value, which is an average of the relative value divided by the relative value;

(G) preparing a calibration curve for the standard sample using the values obtained in step (f);

(H) Ct value, ΔRn value, RFU value, their relative values ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU and their relative values obtained from (D), or the relative values of the internal control and test spheres; Dividing the value by C-values, which are average values of the corresponding step (f), respectively; And

(I) substituting the value obtained in step (h) into the calibration curve obtained in step (g) to calculate the homozygote / heterozygote mixing rate of the test zone; It is about how to check.

In addition, the present invention relates to a method characterized in that the mutation is any one or more of the insertion (insertion), deletion (deletion), substitution (substitution) and single nucleotide polymorphism (SNP) of the base.

The present invention also relates to a method characterized in that the mutation is present in plants, animals, microorganisms, human bodies, agricultural products and processed products thereof.

In addition, the present invention is characterized in that the real-time PCR method for screening and amplifying the specific mutant trait is one selected from FenDEL-PCR, ARMS-PCR, TaqMan-PCR, MGB-TaqMan-PCR and PNA-PCR.

In addition, the present invention is characterized by selecting a house keeping gene as the internal control.

In addition, the present invention (B), (E), (B) and (G) step is carried out separately from the other steps homozygotes standard sample, heterozygotes standard sample and homozygotes and heterozygotes exist in a specific molar ratio ΔCt, RCt, ΔΔRn, each Ct value and at least one of each fluorescence value ΔRn and RFU or at least one Ct value of homozygous and heterozygous samples in standard sample, ΔRn fluorescence value or relative value of RFU value , ΔRFU, RΔRn, RRFU, and C-values, which are averages of the product of these relative values, or the relative value divided by the relative value, and a calibration curve prepared for the standard sample.

In addition, the present invention provides a method for carrying out the above method.

Primers and probes for internal controls;

A standard sample comprising a homozygote sample, a heterozygote sample, and two or more mixed samples in which the homozygote and the heterozygote are mixed at a predetermined ratio;

Primers and probes for the standard sample; And

It relates to a real-time PCR kit comprising a; and a primer and a probe that can distinguish the mutant trait of the test sample.

In addition, the present invention provides a method for carrying out the above method.

One or more of each Ct value and each fluorescence value ΔRn and RFU, or a homozygous sample in a standard sample, for a homozygous standard sample, a heterozygous standard sample, and one or more standard samples where the homozygous and heterozygotes exist in a specific molar ratio Sample Ct value, ΔRn value of fluorescence value or ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU and relative value of RFU value, or C-value, which is the average value of the relative value divided by, or standard sample A protocol in which a calibration curve created for is recorded;

Primers and probes for internal controls; And

It relates to a real-time PCR kit comprising a; and a primer and a probe that can distinguish the mutant trait of the test sample.

In addition, the present invention is characterized in that the kit is used for discriminating the variety of the variety or breeding of any of agricultural products, livestock products, aquatic products and processed products thereof.

According to the present invention, homozygous and heterozygous forms of mutant alleles based on real-time polymerase chain reaction can be quickly and clearly distinguished.

In addition, according to the present invention, it is possible to quantitatively analyze the mixing ratio of a specific mutant trait in a sample.

According to the method of the present invention, the mutant genotype is more accurately determined by using the Ct value and the fluorescence signal value identified in the real-time polymerase chain reaction result for the determination and quantitative analysis of the mutant trait. The mixing ratio can be quantified efficiently.

In addition, according to the present invention, unlike the conventional method using two kinds of fluorescently labeled probes reflecting the mutant trait to determine the mutant trait based on real-time polymerase chain reaction, the internal control amplification product reflecting fluorescence The use of labeled probes and fluorescent label probes that reflect only one of the two mutant traits provides an economical means of analyzing multiple mutations simultaneously in one in vitro.

1 is a method for determining the SNP genotype (A) and heteromorphism by real-time polymerase chain reaction using a FenDEL probe capable of selecting and amplifying only an internal control (IC) and one SNP trait (foreign SNP trait). This is a basic conceptual diagram that distinguishes between A / B heterozygote and B / B homozygote.
Figure 2 shows the amplification curve (A) and repeated analysis of the gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero) three times using a 7500 Real Time PCR System (ABI) and This is the result of applying the correlation (Raf1 = RCt x RΔRn1 / C-value) to determine the genotype based on the Ct value and the fluorescence value measured in each amplification curve (B).
Figure 3 gDNA of 100% domestic sesame (A / A Homo), 100% foreign sesame (B / B Homo), 50% mixed sesame (A / B Hetero) using CFX96 Real-Time System (Bio-Rad) The amplification curves were analyzed three times (set 1, 2, 3).
Figure 4 is a 100% foreign sesame (B / B Homo) and 50% mixed sesame (A / B Hetero) gDNA was measured in an amplification curve repeated three times using the CFX96 Real-Time System (Bio-Rad) The genotype is divided by the correlation between Ct and fluorescence.
5 is a gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero) was measured in an amplification curve repeated 10 times under the same conditions using a 7500 Real Time PCR System (ABI). The reproducibility was confirmed by applying the correlation Raf1 (RCt x RΔRn1 / C-value) using the Ct value and the fluorescence value.
6 shows three replicates (3 batches (set 1, set 2, set 3)) with different reagents (5x qPCRMix, 10x Primer Mix) and analytical dates and C-values calculated for each batch. Genotyping results were compared when the mean C-values of the three batches were applied to the correlation Raf1 (RCt x RΔRn1 / C-value).
Figure 7 shows the gDNA of 100% domestic sesame seeds (A / A Homo), 100% foreign sesame seeds (B / B Homo), 50% mixed sesame seeds (A / B Hetero) to determine the effect of DNA concentration on genotyping Real-time polymerase chain reaction amplification curves using 6.9 ng (set 1, 2) and 4.1 ng (set 3, 4), respectively.
FIG. 8 is repeated repeated analysis of gDNA of 100% domestic sesame seeds (A / A Homo), 100% foreign sesame seeds (B / B Homo), and 50% mixed sesame seeds (A / B Hetero) using ARMS PCR technique. set 1, 2) Amplification curve.
9 shows 100% domestic sesame seeds (A / A Homo), 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero) when the fluorescence value of a specific SNP trait is greater than the internal control fluorescence value. It is the result of applying the correlation Raf2 ((RCt ÷ RRFU2) / C-value) to determine the SNP genotype based on the amplification curve analyzed by gDNA and the Ct and fluorescence values measured in each amplification curve.
10A and 10B show amplification curves 10a and five 80% mixed samples of foreign samples for measuring the mixing ratio of foreign SNP traits (70% mixed with SNP traits and 80% mixed with SNP traits). Real time polymerase chain reaction amplification curve 10b.
FIG. 11 shows a calibration curve using relative Ct values (RCt), relative fluorescence values (ΔΔRn2) and correlation values (RCt / ΔΔRn2) calculated from real-time polymerase chain reaction amplification of standard samples. This calibration curve was used to calculate the incorporation rate of foreign SNP traits of five foreign 80% mixed samples. "DdRn" in the graph was used in the same meaning as "ΔΔRn".

Hereinafter, the structure of the present invention will be described in more detail with reference to Examples. These examples are only for illustrating the present invention, it is apparent to those skilled in the art that the scope of the present invention is not limited to the description of these examples.

[DNA Preparation]

Genomic DNA (gDNA) was extracted from domestic fresh sesame and foreign (Chinese) fresh sesame and used as a template for real-time polymerase chain reaction. Domestic and foreign sesame samples were taken 10g each and ground using a mortar and then, 20mg each of the ground sesame powder was taken and used for gDNA extraction and purification. DNA extraction and purification was performed using the NucleoSpin Plant II kit (MN), and the detailed method was in accordance with the manual provided in the extraction kit. Extracted and purified gDNA of domestic and foreign sesame seeds was quantified using Qubit dsDNA BR Assay kits (Thermo Fisher Scientific) and fluorescence detection system, and the detailed method was in accordance with the manual provided in the kit and fluorescence detection system. As a gDNA to be used as a template for PCR experiments, A / A homozygotes are 100% domestic, B / B homozygotes 100% domestic, A / B heterozygotes 50% domestic and foreign gDNA Each was prepared by mixing the same amount. In addition, a sample prepared by mixing 70% and 80% of the foreign sesame gDNA was prepared for the mixing rate measurement experiment. The gDNA thus prepared was cryopreserved until use in the experiment.

[ primer  And Probe  making]

A primer and TaqMan probe designed to PCR amplify a specific region of gDNA prepared from domestic and foreign sesame are designed for PCR amplification and amplification confirmation of internal control, and based on SNP marker that can distinguish domestic and foreign sesame. Primers and probes designed to PCR amplify only foreign sesame seeds were designed for PCR amplification and confirmation of specific SNP traits. The designed primers and probes were prepared using the oligonucleotide synthesis system of the present inventors Genotech. The primers or probes used in each example were prepared and used in the form of 10x primer mix or 10x probe mix to facilitate the preparation of PCR reaction compositions and to reduce the experimental error between repeated experiments.

Primer and Probe for Internal Control PCR Amplification

 Internal control front primer: 5'-GTCCAACTCGGAATTTGCATGGAAG-3 '

 Internal control posterior primer: 5'-TTTTCACCAATTTTCCAACACTGG-3 '

 Internal control TaqMan probe: 5'-FAM-TAGAGGCGTCTATATATGATGGCA-BHQ1-3 '

The base sequence and the surrounding sequence of sesame genomic DNA used as the internal control gene are shown in Table 1.

----------------------------------- TATATATATATCGGTAATAAATACTTATTTACAAAGGTAACGAAATAATCTTTATATAGTTCAATTAAATCAAATTAATTAGGCGTTATGTGTATGAAATTAATATGTATACATTGAATTGAGTTATTAATCATAAATTCCACAACGATGTTATGTATATAT GTCCAACTCGGAATTTGCATGGAAG CTACGCTCTGACATAAACTAACACATAGATATTGACCTCTTACACTACATGTAGAGGCGTCTATATATGATGGCAGGACCCAGCTACTTAACACCCTTTCCACATTATTTTTGCAGAATTT CCAGTGTTGGAAAATTGGTGAAAA TTACACTTTTAGTCTCTTCGGATAGAAAATTCGTCATTTTTAGACTTATACTTTATGAAACTTTTAAATGATCCCAAAGTTAGAAAAAGATCGACATATCTAGTCCCATAAATTGTGTAAAGCAAGAACTAAATATGTCAAAATTTCTCAATTTCATGACCA ---------- -------------

Primers and Probes for Target Gene PCR Amplification of Test Cells

 Primers and Probes for the FenDEL System

 Target gene front primer: 5'-TTCGGCAGAATTTCCTGCtGAAG-3 '

 Target gene posterior primer: 5'-CATGGACAACATAAACTCCCTACC-3 '

FenDEL probe: 5'- C gTGCTTtaGCAGGAAATTCTGCCG-P-3 '

 Target gene TaqMan probe: 5'-JOE-TGTGGACATAGAACAAAGCAGC-BHQ1-3 '

 Primers and Probes for ARMS

Target gene anterior ARMS primer: 5'-CAGAATTTCCTGCCGAAGCtA G -3 '

 Target gene rear primer: 5'-AAGACCTAGTTGTTGCCCCAAG-3 '

 Target gene TaqMan probe: 5'-JOE-TGTGGACATAGAACAAAGCAGC-BHQ1-3 '

Lowercase letters indicate the nucleotide and non-complementary sequences of the template. This is an artificially substituted base to improve SNP discrimination ability.

The dark base represents the SNP trait of the foreign sesame.

P means phosphate.

Sesame origin SNP markers (domestic T, G) and surrounding sequences used as target genes are shown in Table 2.

--------------------------------- AGGATCATTATGCTACTATATAAAGTTAAAATACGAAAACATCAAATGAACTAAGTTACGAGACTCTATGCTTCAATTCACATTACTATGTTTAATTTGAGTTGTGAAATATCCTAAAATCTTTCAAAGAAACTTCGTGTCGTATCGTCGTTTTTGTGTCAATGCATCATAAATAAATAACGATCTCTATTAATGTGCGGTCATTTTTGAATCTTTTCTTTTCGGCAGAATTTCCTGCCGAAGCAA [T / G] TTTGAATGCAGATACGTTAGCGGGATGTGGACATAGAACAAAGCAGCCATGTTTGCCCTTTTGGTAGGGAGTTTATGTTGTCCATGAATTTCTGGGAACAAAGACGGCTACAAACGACCTAGGAGTACTCGGACTTGTCTAGCTATATATCATTGATCAACCCCGGCAGGAGACAATCTCAAATTCCAAGCGCATAAAATTTTACTTGGGGCAACAACTAGGTCTTTGTGCATTTTTACTAGGAAT ---------- ------------

[ qPCR  Reaction and confirmation]

Using domestic and foreign sesame gDNA prepared as described above as a template, real-time polymerase chain reaction was performed using the prepared primers and probes. In this example, the polymerase and the reaction composition were prepared using 5x qPCRMix (50mM Tris, pH 9.0, 7.5mM MgCl ₂ , 300mM KCl, 50mM (NH ₄ ) ₂ SO ₄ , 5mM dNTPs, 0.05% Tween20, 3.5x α-E10 AFA solution. , 2.5x ROX dye, 5U Hot-Taq DNA polymerase, Genotech Co., Ltd., Korea) were used. Real-time polymerase chain reaction conditions were denatured at 95 ℃ for 10 minutes, repeated 40 times at 95 ℃ 30 seconds-60 seconds at 55 ℃ was set to measure the fluorescence at 55 ℃. The 7500 Real Time PCR System (ABI) or CFX96 Real-Time System (Bio-Rad) was used as the analyzer for real-time polymerase chain reaction. The Ct and ΔRn or RFU values for quantitative analysis of fluorescence signal change were The decision was made using the software provided with the analyzer.

Example  One

Domestic homozygotes (A / A homozygote, 100% domestic) and foreign homozygotes (B) by real-time polymerase chain reaction using FenDEL probe that can select and amplify only SNP traits of internal control (IC) and foreign sesame seeds. / B homozygote, 100% foreign) and mixed heterozygotes (A / B heterozygote, 50%) to determine the concept and method to test. The analyzer used a 7500 Real Time PCR System (ABI) or CFX96 Real-Time System (Bio-Rad), and the PCR reaction composition is as follows.

RT-PCR Reactant Composition

5 ul (1.38ng / ul) sesame gDNA and 2 ul 10x Primer Mix (10 uM internal control front primer, 10 uM internal control rear primer, 1.25 uM internal control TaqMan probe, 6 uM) into each reaction tube Target gene anterior primer, 6 uM target gene posterior primer, 2.25 uM FenDEL probe, 5 uM target gene TaqMan probe) and 4 ul of 5x qPCRMix and sterile water were mixed to a final total dose of 20 ul.

1 is a method for determining a mutant genotype by real-time polymerase chain reaction using a FenDEL probe capable of selectively amplifying an internal control and one SNP trait (foreign SNP trait) (A) and heterozygote (A / B heterozygote). This is a basic conceptual diagram that distinguishes between and B / B homozygote (B). If only the IC amplification curve is found in the results of real-time polymerase chain reaction, it is determined as A / A homozygotes (100% of domestic), and if the amplification curves of IC and foreign SNP traits are confirmed together, Ct and fluorescence values ( Various calculation values calculated on the basis of ΔRn or RFU) can be used to determine the B / B homozygotes (outside 100%) and the A / B heterozygotes (mix 50%).

(-△-): Amplification curve of internal control (IC), (-○-): Amplification curve of foreign SNP trait (B), (-×-): Amplification curve of domestic SNP trait (A), Ct _JOE : Ct value of foreign SNP trait (B), Ct _FAM : Ct value of internal control (IC), ΔRn _JOE : fluorescence value of foreign SNP trait (B), ΔRn _FAM : fluorescence value of internal control (IC).

Figure 2 shows the amplification curves of 100% foreign sesame (B / B Homo) and 50% mixed sesame (A / B Hetero) gDNA three times using 7500 Real Time PCR System (ABI) and each amplification curve It is the result of applying the correlation Raf1 (RCt x RΔRn1 / C-value) to determine the genotype based on the measured Ct value and fluorescence value. Here, the C-value is a result of real-time polymerase chain reaction for three heterozygous samples (# 1, 3, 5) and three homozygous samples (# 2, 4, 6). The average value of the RCt x RΔRn1 values of the prepared samples was 3.34. The correlation Raf1 is a value obtained by dividing RCt x RΔRn1 by C-values and distinguishing homozygotes and heterozygotes based on '1'.

In the present embodiment, it can be seen that the correlation Raf1 result value is larger than 1 in the heterozygote [A / B Hetero (50%)] and smaller than 1 in the homozygote [B / B Homo (100%)].

(-Δ-): Amplification curve of the internal control (IC), (-○-): Amplification curve of the foreign SNP trait (B), (-×-): Amplification curve of the domestic SNP trait (A).

Table 3 shows the repeated analysis of the gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero) identified in FIG. 2 using a 7500 Real Time PCR System (ABI). This is the result of applying various correlations to determine the genotype based on the Ct and fluorescence values measured in the amplification curve obtained from. Calculated values (ΔCt, RCt, ΔΔRn1, RΔRn1, ΔCt * ΔΔRn1, ΔCt * RΔRn1, RCt * ΔΔRn1, RCt * RΔRn1) calculated on the basis of the Ct value and the fluorescence value ΔRn As a result of applying the correlation using value), 100% homozygote and 50% heterozygote can be easily determined. have. Heterozygote values greater than 1 and homozygotes less than 1.

Figure 3 gDNA of 100% domestic sesame (A / A Homo), 100% foreign sesame (B / B Homo), 50% mixed sesame (A / B Hetero) using CFX96 Real-Time System (Bio-Rad) 3 times amplification curve (set 1, 2, 3). As a result of analysis of domestic 100% gDNA as a template, only the amplification curve (-△-) of the internal control was confirmed, and the result of analysis of 50% mixed gDNA and 100% gDNA in foreign countries as a template was shown as amplification curve of the internal control (-△-). ) And the amplification curve (-○-) of foreign SNP traits are confirmed at the same time.

(-Δ-): Amplification curve of the internal control (IC), (-○-): Amplification curve of the foreign SNP trait (B), (-×-): Amplification curve of the domestic SNP trait (A).

Table 4 shows the repeated analysis of the gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero), which were identified in FIG. 3, using the CFX96 Real-Time System (Bio-Rad). In addition, various correlations and relative coefficients are applied using the Ct and fluorescence values measured in the resulting amplification curve. Calculated values (ΔCt, RCt, ΔRFU1, RRFU1, ΔCt * ΔRFU1, ΔCt * RRFU1, RCt * ΔRFU1, RCt * RRFU1) calculated on the basis of the Ct value and the fluorescence value (RFU) As a result of applying the correlation using value), if the value is greater than 1, it can be determined as a 50% mixed heterozygote, and if it is less than 1, it can be regarded as a foreign 100% homozygote.

FIG. 4 shows gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero) 3 times using CFX96 Real-Time System (Bio-Rad). Repeated analysis was performed to compare genotypes by correlation using Ct and fluorescence values measured in the resulting amplification curves. Eight kinds of values (ΔCt, RCt, ΔRFU1, RRFU1, ΔCt * ΔRFU1, ΔCt * RRFU1, RCt * ΔRFU1, RCt * RRFU1) calculated based on the Ct value and the fluorescence value (RFU) are calculated. If the value divided by the value (C-value) is greater than 1, it can be determined as a 50% mixed heterozygote (A / B heterozygote), if less than 1 it can be determined as a foreign 100% homozygote (B / B homozygote). Depending on the correlations applied, genotype differences can be identified and genotypes can be more clearly distinguished when two values are used together than when Ct and fluorescence values are used respectively.

FIG. 5 is repeated analysis of gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero) 10 times under the same conditions using 7500 Real Time PCR System (ABI). This is the result of applying the correlation Raf1 (RCt x RΔRn1 / C-value) using the Ct and fluorescence values measured in the amplification curve. The result of applying the correlation Raf1 was 1.22 ± 0.05 for heterozygotes [A / B Heterozygote (50%)] and 0.8 ± 0.02 for homozygotes [B / B Homozygote (100%)]. not big. In other words, it can be seen that the results of real-time polymerase chain reaction under the same conditions (analyzer, PCR reaction conditions (temperature, time) and reagents (5x qPCRMix, 10x Primer Mix, etc.)) are reproducible.

FIG. 6 compares the results of experiments using reagents (5x qPCRMix, 10x Primer Mix) and three batches (set 1, set 2 and set 3) having different analysis dates. In each batch, 100% foreign sesame seed (B / B Homo) and 50% mixed sesame seed (A / B Hetero) gDNA were analyzed four times under the same conditions using 7500 Real Time PCR System (ABI). The correlation Raf1 (RCt x RΔRn1 / C-value) was applied using the Ct and fluorescence values measured at. As a result of the experiment, it can be seen that the calculated C-value of each batch is changed, but the result is the same as the case of applying the average C-value calculated as their average value.

Example  2

Domestic homozygotes (A / A homozygote, 100% domestic), domestic homozygotes (B / B homozygote, 100% domestic) and mixed heterozygotes using FenDEL probes that can select and amplify only internal controls and foreign SNP traits This study is to determine the effect of the amount of gDNA used as a template in the real-time polymerase chain reaction for determining A / B heterozygote (50%). The effects of the amount of gDNA on the trait determination were analyzed using the measured Ct and fluorescence values, respectively, when using 5ul (6.9ng) of sesame gDNA and 3ul (4.1ng). To this end, a CFX96 Real-Time System (Bio-Rad) analyzer was used, and the PCR reactant composition was as follows.

RT-PCR Reactant Composition

Each reaction tube contains 5 ul (6.9 ng) or 3 ul (4.1 ng) sesame gDNA and 2 ul of 10x primer mix (10 uM of internal control front primer, 10 uM of internal control rear primer, 1.25 uM of internal control TaqMan probe , 6 uM target gene front primer, 6 uM target gene rear primer, 2.25 uM FenDEL probe, 5 uM target gene TaqMan probe), and 4 ul 5x qPCR Mix and sterile water were mixed to a final total dose of 20 ul.

7 shows 6.9 ng (set 1, 2), 4.1 ng of 100% domestic sesame seeds (A / A Homo), 100% foreign sesame seeds (B / B Homo), and 50% mixed sesame seeds (A / B Hetero), respectively. Real-time polymerase chain reaction amplification curves used (sets 3 and 4). The result of analysis of domestic 100% gDNA as a template shows only the amplification curve of the internal control (-△-), and the result of analysis of 50% mixed and foreign 100% gDNA as a template shows the amplification curve of the internal control (-△-). And amplification curves (-○-) of foreign SNP traits are confirmed at the same time.

(-△-): Amplification curve of internal control (IC), (-○-): Amplification curve of foreign SNP trait (B), (-×-): Amplification curve of domestic SNP trait (A)

Table 5 uses the Ct and fluorescence values measured in real time polymerase chain reaction amplification curves using gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero). This is the result of applying various correlations. Regardless of the amount of gDNA used as a template, values calculated based on Ct value and fluorescence value (RFU) (ΔCt, RCt, ΔRFU1, RRFU1, ΔCt * ΔRFU1, ΔCt * RRFU1, RCt * ΔRFU1, RCt * RRFU1) and each As a result of applying the correlation using the average value of C-values, if the value is greater than 1, it is 50% A / B heterozygote. If it is less than 1, it is 100% homozygous / B homozygote).

Example  3

Domestic homozygotes (A / A homozygote, 100% domestic), foreign homozygotes (B /) by real-time polymerase chain reaction using ARMS primers that can select and amplify only the internal control (IC) and foreign SNP traits B homozygote, 100% foreign) and mixed heterozygotes (A / B heterozygote, 50%). The analyzer was used 7500 Real Time PCR System (ABI), PCR reaction composition is as follows.

RT-PCR Reactant Composition

Each reaction tube contains 5ul (1.38ng / ul) of sesame gDNA and 2ul of 10x Primer Mix (6uM internal control anterior primer, 6uM internal control anterior primer, 1uM internal control TaqMan probe, 10uM target gene anterior ARMS primer, 10 uM target gene posterior primer, 5 uM target gene TaqMan probe) and 4 ul 5x qPCR Mix were mixed with sterile water to a final total volume of 20 ul.

FIG. 8 shows amplification of gDNA of 100% domestic sesame seeds (A / A Homo), 100% foreign sesame seeds (B / B Homo), and 50% mixed sesame seeds (A / B Hetero) twice (set 1, 2) It is a curve. The result of analysis of domestic 100% gDNA as a template shows only the amplification curve of the internal control (-△-), and the result of analysis of 50% mixed and foreign 100% gDNA as a template shows the amplification curve of the internal control (-△-). And amplification curves (-○-) of foreign SNP traits are confirmed at the same time.

(-△-): Amplification curve of internal control (IC), (-○-): Amplification curve of foreign SNP trait (B), (-×-): Amplification curve of domestic SNP trait (A)

Table 6 shows the repeated analysis of the gDNA of 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero) twice, and the Ct and fluorescence values measured in the obtained amplification curve. This is the result of applying various correlations using. Calculated values (ΔCt, RCt, ΔΔRn1, RΔRn1, ΔCt * ΔΔRn1, ΔCt * RΔRn1, RCt * ΔΔRn1, RCt * RΔRn1) calculated based on the Ct value and the fluorescence value ΔRn As a result of applying the correlation using -value), if the value is greater than 1, it can be judged as 50% mixed heterozygote, and if it is less than 1, it can be regarded as 100% homozygote. .

Example  4

As a result of PCR amplification by selecting foreign SNP traits, this test is to confirm the correlation between heterozygotes and homozygotes that can be applied to reaction conditions in which the fluorescence value at the end of PCR is greater than the fluorescence value of the internal control. The CFX96 Real-Time System (Bio-Rad) analyzer was used, and the PCR reaction composition was as follows.

RT-PCR Reactant Composition

Each reaction tube contains 5ul (1.38ng / ul) of sesame gDNA and 2ul of 10x Primer Mix (1.5uM internal control anterior primer, 1.5uM internal control anterior primer, 1.25uM internal control TaqMan probe, 6uM target gene anterior) Primers, 6uM target gene posterior primer, 2.25uM FenDEL probe, 5uM target gene TaqMan probe) and 4ul of 5x qPCR Mix and sterile water were mixed to a final total volume of 20ul.

FIG. 9 shows the amplification curves of gDNA of 100% domestic sesame seeds (A / A Homo), 100% foreign sesame seeds (B / B Homo) and 50% mixed sesame seeds (A / B Hetero), and Ct measured in each amplification curve. This is the result of applying the correlation Raf2 (RCt / RRFU2 / C-value) to determine the SNP genotype based on the value and fluorescence value. As a result of applying the correlation Raf2, it can be seen that if the value is greater than 1, it is a heterozygote [A / B Hetero (50%)], and if it is less than 1, it is a homozygote [B / B Homo (100%)].

(-△-): Amplification curve of internal control (IC), (-○-): Amplification curve of foreign SNP trait (B), (-×-): Amplification curve of domestic SNP trait (A)

Example  5

In order to measure the mixing ratio of foreign SNP traits, the RCt, ΔΔRn, and RCt / ΔΔRn values of the standard samples with 70% and 80% mixing rates of the foreign sesame gDNA were calculated, respectively. A calibration curve of was prepared. Based on each calibration curve, the mixing rate of the unknown test sample (actually, 80% foreign mixed sample) was measured. The 7500 Real Time PCR System (ABI) was used as an analyzer, and the PCR reactant composition was as follows.

RT-PCR Reactant Composition

Each reaction tube contains 5ul (1.38ng / ul) of sesame gDNA and 2ul of 10x Primer Mix (1uM internal control anterior primer, 1uM internal control anterior primer, 1.25uM internal control TaqMan probe, 10uM target gene anterior primer, 10 uM target gene posterior primer, 2.25 uM FenDEL probe, 3.5 uM target gene TaqMan probe), and 4 ul 5x qPCR Mix and sterile water were mixed to a final total volume of 20 ul.

10 is a real-time polymerization of the amplification curve (A) of two standard samples (70% foreign SNP transgenic, 80% foreign SNP transgenic mixture) and five foreign mixed 80% samples for measuring the mixing ratio of foreign SNP traits Enzyme chain reaction amplification curve (B).

FIG. 11 shows the calibration curve using the relative Ct value (RCt), the relative fluorescence value (ΔΔRn2) and the correlation value (RCt / ΔΔRn2) using the two values calculated as a result of the real-time polymerase chain reaction amplification of the standard sample. Using this calibration curve, the foreign SNP trait mixing ratio of five foreign 80% mixed samples was calculated.

(-△-): Amplification curve of internal control (IC), (-○-): Amplification curve of foreign SNP trait (B), (-×-): Amplification curve of domestic SNP trait (A)

Based on the Ct and fluorescence values measured in real-time polymerase chain reaction analysis results of two standard samples, RCt, ΔΔRn2, and RCt / ΔΔRn2 values were calculated, respectively (FIG. 11 (A)). A calibration curve (calibration line 1 (RCt value), calibration curve 2 (ΔΔRn2 value), calibration curve 3 (RCt / ΔΔRn2 value)) was prepared respectively (FIG. 11C). In addition, the foreign SNP trait mixing ratios of five prepared unknown test samples (actually 80% mixed with foreign SNP traits) were analyzed using the respective calibration curves (FIG. 11 (B)). As a result of analysis, the mixing rate was average 74.868% when using calibration curve 1 (RCt value) [error range 3.294 ~ 8.045 (average 5.132)], 78.752% when calibration curve 2 (ΔΔRn2 value) was used (0.344 ~ 3.821 (average 2.737)] And when using the calibration curve 3 (RCt / ΔΔRn2 value) it can be seen that 78.907% [0.114 ~ 2.75 (average 1.798)].

As shown in FIG. 10 and FIG. 11, a calibration curve may be prepared by using relative Ct values and relative fluorescence values based on Ct values and fluorescence values that can be measured by real-time polymerase chain reaction. However, it can be seen that the quantitative method using the relative Ct value and the relative fluorescence value can reduce the error between experiments and provide more accurate mixing rate calculation results.

Claims (17)

In the method of identifying mutations using real-time PCR,
(A) real-time PCR for screening and amplifying a specific mutant trait of the test sphere in one tube and performing a real-time PCR for the internal control by designating one of the genes in the genome containing the specific mutation as an internal control;
(B) performing real-time PCR on a standard sample in which a homozygote sample and a heterozygote sample for a specific mutant trait are present in a specific molar ratio under the same conditions and the same type as in the above (a);
(C) obtaining at least one of the Ct value measured in the internal control PCR and the test PCR, and ΔRn and RFU, which are fluorescence values at the end of PCR;
(D) RCt (relative Ct), which is the larger value divided by the smaller of the Ct value measured by the internal control PCR and the Ct value measured by the test PCR, ΔCt (delta Ct) ), Obtaining RΔRn, RRFU, which is a large value divided by a small value of fluorescence values, ΔΔRn, ΔRFU, which is a value obtained by subtracting a small value from a large value of fluorescence values, and multiplying these values or dividing these values by one or more ;
(E) obtaining one or more of each Ct value and each fluorescence value ΔRn and RFU for the homozygous sample and the heterozygous sample from the PCR result for the standard sample;
(F) Ct value, homofluorescence value ΔRn value or RFU value of homozygous sample and heterozygous sample in the standard sample, ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU and their relative values Or obtaining a C-value which is a value obtained by dividing a relative value and an average value of each of these values;
(G) Ct value, ΔRn value, RFU value, their relative values ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU, and their relative values obtained from (D) and the control group, or their relative values. Dividing the value by the corresponding C-value of step (bar); And
(H) dividing into a heterozygote if the value obtained in step (g) is greater than 1 and homozygous if less than 1; and identifying a mutation using real-time PCR.
The method according to claim 1,
Wherein said mutation is at least one of insertion, deletion, substitution and single nucleotide polymorphism (SNP) of a base.
The method according to claim 1,
The mutation is a mutation present in plants, animals, microorganisms, human bodies, agricultural products and processed products thereof.
The method according to claim 1,
Real time PCR for screening and amplifying a specific mutant trait is one selected from FenDEL-PCR, ARMS-PCR, TaqMan-PCR, MGB-TaqMan-PCR and PNA-PCR.
The method according to claim 1,
Characterized by selecting a house keeping gene as an internal control.
The method according to claim 1,
Steps (B), (E) and (B) are performed separately from the other steps, so that at least one of each Ct value and each fluorescence value ΔRn and RFU for the homozygous standard sample and the heterozygous standard sample, or in the standard sample. Each mean value of the homozygous sample and the heterozygous sample is ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU, and relative values of the Ct, fluorescence, ΔRn, or RFU Characterized in that the C-value is provided protocolized.
To carry out the method of any one of claims 1 to 5
Primers and probes for internal controls;
Standard sample including homozygous sample and heterozygous sample;
Primers and probes for the standard sample; And
Real-time PCR kit comprising a; primers and probes that can distinguish the mutant trait of the test sample.
To carry out the method of claim 6
Each Ct value and each fluorescence value for homozygous and heterozygous standard samples or at least one of ΔRn and RFU, or Ct values for homozygous and heterozygous samples in standard samples, ΔRn or RFU values for fluorescence, and these values Protocols in which relative values ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU and their relative values are multiplied or divided by relative values and the average of these values are recorded as C-values;
Primers and probes for internal controls; And
Real-time PCR kit comprising a; primers and probes that can distinguish the mutant trait of the test sample.
In the method of identifying mutations using real-time PCR,
(A) real-time PCR for screening and amplifying a specific mutant trait of the test sphere in one tube and performing a real-time PCR of the internal control with one of the genes in the genome containing the specific mutation as an internal control;
(B) real-time PCR of homohomygote standard and heterozygote standard samples and one or more standard samples where homozygotes and heterozygotes exist in a specific molar ratio for the specific mutant trait. Performing the same conditions and the same model;
(C) obtaining at least one of the Ct value measured in the internal control PCR and the test PCR, and ΔRn and RFU, which are fluorescence values at the end of PCR;
(D) RCt (relative Ct), which is the larger value divided by the smaller of the Ct value measured by the internal control PCR and the Ct value measured by the test PCR, ΔCt (delta Ct) ), Obtaining RΔRn, RRFU, which is a large value divided by a small value of fluorescence values, ΔΔRn, ΔRFU, which is a value obtained by subtracting a small value from a large value of fluorescence values, and multiplying these values or dividing these values by one or more ;
(E) obtaining one or more of each Ct value and each fluorescence value ΔRn and RFU for each standard sample after PCR with respect to the standard sample;
(F) Ct, fluorescence, ΔRn, or RFU, relative values of ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU, and their relative values; Obtaining a C-value, which is each average of the values of the relative values;
(G) preparing a calibration curve for the standard sample using the values obtained in step (f);
(H) Ct value, ΔRn value or RFU value of the internal control and test sphere obtained in step (D), their relative values ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU and their relative values or their relative values Dividing the value divided by the corresponding C-value of the step (f) respectively; And
(I) substituting the value obtained in step (h) into the calibration curve obtained in step (g) to calculate the homozygote / heterozygote mixing rate of the test zone; How to check.
The method according to claim 9,
Wherein said mutation is at least one of insertion, deletion, substitution and single nucleotide polymorphism (SNP) of a base.
The method according to claim 9,
The mutation is a mutation present in plants, animals, microorganisms, human bodies, agricultural products and processed products thereof.
The method according to claim 9,
Real time PCR for screening and amplifying a specific mutant trait is one selected from FenDEL-PCR, ARMS-PCR, TaqMan-PCR, MGB-TaqMan-PCR and PNA-PCR.
The method according to claim 9,
Characterized by selecting a house keeping gene as an internal control.
The method according to claim 9,
The steps (B), (E), (B) and (G) are performed separately from the other steps, so that the homozygous standard sample, the heterozygote standard sample, and the homozygote and the heterozygote exist in one or more standard samples in a specific molar ratio. ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, the relative value of the Ct value, the fluorescence value of ΔRn, or the RFU value of at least one of each Ct value and each fluorescence value of ΔRn and RFU or of a homozygous and heterozygous sample in a standard sample. C-value, which is the mean value of the product of RRFU and the relative value, or the relative value divided, or the calibration curve created for the standard sample.
To carry out the method of any one of claims 9 to 13
Primers and probes for internal controls;
A standard sample comprising a homozygote sample, a heterozygote sample, and two or more mixed samples in which the homozygote and the heterozygote are mixed at a predetermined ratio;
Primers and probes for the standard sample; And
Real-time PCR kit comprising a; primers and probes that can distinguish the mutant trait of the test sample.
To carry out the method of claim 14
One or more of each Ct value and each fluorescence value ΔRn and RFU, or a homozygous sample in a standard sample, for a homozygous standard sample, a heterozygous standard sample, and one or more standard samples where the homozygous and heterozygotes exist in a specific molar ratio C-value, or C-value, which is the average value of each product of Ct, fluorescence, ΔRn, or RFU, ΔCt, RCt, ΔΔRn, ΔRFU, RΔRn, RRFU, and their relative values A protocol in which a calibration curve created for a sample is recorded;
Primers and probes for internal controls; And
Real-time PCR kit comprising a; primers and probes that can distinguish the mutant trait of the test sample.
The method according to claim 15,
The kit is a real-time PCR kit, characterized in that for discriminating or determining the degree of incorporation of any one of agricultural products, livestock products, aquatic products and processed products thereof.

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