CN113930486A

CN113930486A - Digital PCR (polymerase chain reaction) detection method for human MED12 gene mutation and application

Info

Publication number: CN113930486A
Application number: CN202010675646.5A
Authority: CN
Inventors: 江萤; 童慧娟; 黄昕
Original assignee: Mingshi Medical Technology Ningbo Co ltd; Mingchi Biotechnology Shanghai Co ltd
Current assignee: Mingshi Medical Technology Ningbo Co ltd; Mingchi Biotechnology Shanghai Co ltd
Priority date: 2020-07-14
Filing date: 2020-07-14
Publication date: 2022-01-14

Abstract

The invention provides a digital PCR detection method for human MED12 gene mutation and application thereof. Specifically, a preferred primer pair, an amplification method, a nucleic acid probe and a detection system aiming at the sequence of MED12G44 are provided, and a kit for detecting MED12 gene mutation is further provided. According to the invention, through the optimized primer pair, probe and corresponding reaction conditions, the MED12 gene mutation can be detected with high sensitivity and strong specificity on different samples.

Description

Digital PCR (polymerase chain reaction) detection method for human MED12 gene mutation and application

Technical Field

The invention relates to the field of gene detection, in particular to a digital PCR (polymerase chain reaction) detection method for human MED12 gene mutation and application thereof.

Background

The MED12(MED complete 12, MED12) gene is located on the X chromosome, and the human MED12 gene is composed of 45 exons and has a length of about 25000 bp. Under physiological conditions, MED12 regulates the transcription and expression of related genes to realize the functions of regulating the growth, differentiation and the like of cells. Therefore, once the MED12 gene sequence is mutated, related diseases can be caused.

Hysteromyoma is a common benign tumor in gynecology, and the most main clinical manifestations of hysteromyoma are abnormal uterine bleeding, pelvic pain and anemia, and the influence on the quality of life of women is not negligible. Foreign studies have reported high-frequency mutations in the mesocomplex subunit 12(MED 12) gene in uterine fibroids, wherein the gene mutation is present in focal tissues of about 70% of patients with uterine fibroids, and most (> 90%) of the gene mutation is located at glycine 44 (MED12 p.g. 44) of the MED12 gene.

At present, MED12 mutation has been found in various tumors, and MED12 gene mutation has been found in breast fibroepithelial tumors in addition to uterine fibroids.

The study finds that the uterine fibroids positive to MED12 mutation are generally associated with the serosa type, and the tumor number is inversely proportional to the fetal number; while uterine fibroids without the MED12 mutation, the number correlated with the history of pelvic inflammatory disease. In addition, MED12 positive mutant uterine fibroids were less bulky and more histopathologically routine than negative lesions. Therefore, mutation detection aiming at MED12 can help a clinician to better classify uterine fibroids and predict tumor number and tissue morphology.

Although no tumor targeting drug aiming at MED12 mutation exists in the current market, the possibility of generation of related drugs in the future is not excluded, and detection of MED12 mutation of related tumors is helpful for guiding medication and other treatment means in the future.

Although tumor tissue and tumor cytology samples are the best samples for mutation detection, such samples are difficult to obtain. Detecting free nucleic acid (cfDNA) in blood plasma, also called 'liquid biopsy', avoids the need of tumor tissue biopsy, and is a very useful diagnostic application in clinic. The use of fluid biopsies offers the possibility of repeated blood sampling, allowing changes in cfDNA to be tracked during tumorigenesis or during cancer treatment, thereby monitoring changes in disease status.

However, the use of cell-free nucleic acids (e.g., cfDNA) as biomarkers in tumor patients presents certain difficulties, and in particular, the accurate and specific detection of gene mutations using cfDNA detection currently presents significant technical challenges. First, the cfDNA content in blood varies from person to person and is mostly very low, and among them, the quality of tumor-derived free nucleic acid (ctDNA) is more uneven and the content is high.

Moreover, the specificity of cfDNA detection methods is to be improved. Douillard et al report that the detection of EGFR mutations using plasma only matched the results of tumor tissue detection by 65%.

In addition, although there are some methods for detecting MED12 gene mutation based on cfDNA, the sensitivity and specificity of these methods are not yet satisfactory.

Therefore, there is an urgent need in the art to develop a method for detecting RAS gene mutation based on cfDNA with high sensitivity and high specificity.

Disclosure of Invention

The invention aims to provide a method for detecting MED12 gene mutation with high sensitivity and high specificity based on cfDNA.

In a first aspect of the present invention, there is provided a reagent for detecting a gene mutation, comprising a first primer pair for detecting a MED12G44 mutation, wherein the first primer pair comprises primers shown in SEQ ID Nos. 1 and 2.

In another preferred example, the sequence of the MED12G44 is located in NG _ 012808.1: 5786-5882.

In another preferred example, the nucleic acid sequence of the wild-type sequence of MED12G44 is shown as SEQ ID No. 8.

In another preferred example, the MED12G 44D mutation is glycine G to aspartic acid D (i.e., G44D) at position 44 of the amino acid sequence of MED12 protein.

In another preferred example, the MED12G 44V mutation is a mutation of glutamine Q at position 61 of the amino acid sequence of MED12 protein to arginine R (i.e., G44R).

In another preferred example, the MED12G 44S mutation is glycine G to aspartic acid D (i.e., G44D) at position 44 of the amino acid sequence of MED12 protein.

In another preferred example, the MED12G 44C mutation is a mutation of glutamine Q at position 61 of the amino acid sequence of MED12 protein to arginine R (i.e., G44R).

In another preferred example, the MED12G 44D mutation is guanine G mutation to adenine a at position 131 of the MED12 gene nucleic acid sequence (MED12 c.131g > a).

In another preferred example, the MED12G 44V mutation is that the guanine G at position 131 of the nucleic acid sequence of the MED12 gene is mutated into thymine T (MED12 c.131G > T).

In another preferred example, the MED12G 44S mutation is guanine G mutation to adenine a at position 130 of the MED12 gene nucleic acid sequence (MED12 c.130g > a).

In another preferred example, the MED12G 44C mutation is that guanine G at position 130 of the nucleic acid sequence of the MED12 gene is mutated into thymine T (MED12 c.130G > T).

In another preferred example, the MED12G 44D mutant nucleic acid sequence is shown as SEQ ID NO. 9.

In another preferred example, the MED12G 44V mutant nucleic acid sequence is shown as SEQ ID No. 10.

In another preferred example, the MED12G 44S mutant nucleic acid sequence is shown as SEQ ID NO. 11.

In another preferred example, the MED12G 44C mutant nucleic acid sequence is shown as SEQ ID No. 12.

In another preferred embodiment, the reagent further comprises a first probe used in conjunction with the first primer pair, wherein the first probe is selected from the group consisting of: the probe shown in SEQ ID No. 3, the probe shown in SEQ ID No. 4, the probe shown in SEQ ID No. 5, the probe shown in SEQ ID No. 6, the probe shown in SEQ ID No. 7 or the combination thereof.

In another preferred embodiment, the first probe and the second probe are single-stranded nucleic acid probes.

In another preferred embodiment, the structure (5'-3') of the first probe is represented by formula I:

Z1-Z2-Z3 I

wherein the content of the first and second substances,

z1 is a fluorophore;

z2 is a specific complementary nucleic acid sequence;

z3 is a quencher group;

"-" is a bond, a linker, or a linker of 1-3 nucleotides.

In another preferred embodiment, the Z2-specific nucleic acid sequence targets the wild-type MED12G44 site.

In another preferred embodiment, the Z2-specific nucleic acid sequence targets the mutant MED12G 44D site.

In another preferred embodiment, the Z2-specific nucleic acid sequence targets the mutant MED12G 44V site.

In another preferred embodiment, the Z2-specific nucleic acid sequence targets the mutant MED12G 44S site.

In another preferred embodiment, the Z2-specific nucleic acid sequence targets the mutant MED12G 44C site.

In another preferred embodiment, the sequence of Z2 is selected from the group consisting of:

TGGTTATTGAAACCTTG(SEQ ID No:3)；

TGGTTATTGAAATCTG(SEQ ID No:4)；

TGGTTATTGAAAACTG(SEQ ID No:5)；

TGGTTATTGAAACTTTGTG(SEQ ID No:6)；

TGGTTATTGAAACATTGTG(SEQ ID No:7)。

in another preferred embodiment, the fluorescent groups are independently located at the 5 'end, the 3' end and the middle of the nucleic acid probe.

In another preferred embodiment, the fluorescent group and the quenching group are independently located at the 5 'end, the 3' end, and/or the middle portion.

In another preferred embodiment, the fluorophore comprises a fluorophore crosslinked with a DNA probe.

In another preferred embodiment, the fluorescent group is selected from the group consisting of: FAM, VIC, HEX, FITC, BODIPY-FL, G-Dye100, FluorX, Cy3, Cy5, Texas Red, or combinations thereof.

In another preferred embodiment, the quencher group is selected from the group consisting of: DABCYL, TAMRA, BHQ 1, BHQ 2, BHQ3, MGB, BBQ-650, TQ1-TQ6, QSY 7carboxylic acid, TQ7, eclipse, or combinations thereof.

In another preferred embodiment, the nucleic acid probe is WTP-MED 12G44 (SEQ ID NO: 3).

In another preferred embodiment, the nucleic acid probe is MTP-MED 12G 44D (SEQ ID No: 4).

In another preferred embodiment, the nucleic acid probe is MTP-MED 12G 44V (SEQ ID No: 5).

In another preferred embodiment, the nucleic acid probe is MTP-MED 12G 44S (SEQ ID No: 6).

In another preferred embodiment, the nucleic acid probe is MTP-MED 12G 44C (SEQ ID No: 7).

In a second aspect of the present invention, there is provided a kit comprising the reagent for detecting a gene mutation according to the first aspect.

In another preferred embodiment, the kit further comprises a first probe for use in conjunction with the first primer pair.

In another preferred embodiment, the first primer pair and the first probe are as described above.

In another preferred embodiment, the kit comprises a first primer pair shown in SEQ ID Nos. 1 and 2 and a first probe shown in SEQ ID Nos. 3, 4, 5, 6 and 7.

In a third aspect of the present invention, there is provided a use of the reagent for detecting gene mutation according to the first aspect or the kit according to the second aspect for preparing a diagnostic product for judging whether a subject has a tumor with a gene mutation.

In another preferred example, the product is tested against cfDNA samples.

In another preferred example, the cfDNA is from blood, plasma, or serum of the subject.

In another preferred embodiment, the genetic mutation is a MED12 genetic mutation.

In another preferred embodiment, the subject is a tumor patient.

In another preferred embodiment, the tumor is selected from the group consisting of: uterine fibroids, fibroepithelial tumors of the breast, or combinations thereof.

In a fourth aspect of the present invention, there is provided a method for detecting whether a sample to be tested contains a gene mutation, comprising the steps of:

(S1) providing a PCR reaction system, wherein the PCR reaction system contains a sample to be detected as a template and a primer pair for amplification, the primer pair is a first primer pair for detecting MED12G44 mutation, and the first primer pair comprises primers shown in SEQ ID Nos. 1 and 2;

a reagent for detecting a mutation in a gene according to the first aspect;

(S2) performing a PCR reaction on the PCR reaction system of step (S1), thereby obtaining an amplification product;

(S3) analyzing the amplification product generated in the step (S2), thereby obtaining an analysis result of whether the test sample contains a gene mutation.

In another preferred example, the analysis result is a qualitative result.

In another preferred example, the PCR reaction system is a digital PCR reaction system.

In another preferred embodiment, the digital PCR is ddPCR.

In another preferred embodiment, the concentration of the target nucleic acid molecule to be detected in the ddPCR in the microdroplet is 1 to 1X 10¹⁵Copy/ml, preferably 1 to 10¹⁰Copy/ml, more preferably 1 to 10⁵Copy/ml.

In another preferred example, in step (S2), the annealing temperature of the PCR reaction is 56 ± 2 ℃, preferably 56 ± 1 ℃, more preferably 56 ± 0.5 ℃.

In another preferred embodiment, the PCR reaction system further comprises a first probe used in combination with the first primer pair, wherein the first probe is selected from the group consisting of: the probe shown in SEQ ID No. 3, the probe shown in SEQ ID No. 4, the probe shown in SEQ ID No. 5, the probe shown in SEQ ID No. 6, the probe shown in SEQ ID No. 7 or the combination thereof.

In another preferred embodiment, the probe for detecting the wild-type gene (SEQ ID No:3) employs a first fluorescent marker (e.g., HEX, FAM).

In another preferred example, the probes for detecting mutant genes (SEQ ID Nos: 4, 5, 6, 7) employ the same second fluorescent label (e.g., HEX, FAM), and the first fluorescent label and the second fluorescent label are different.

In another preferred embodiment, the method is non-diagnostic and non-therapeutic.

In another preferred embodiment, the method is an in vitro method.

In another preferred embodiment, the method has a detection accuracy of 0.06% -1%, preferably 0.0625% -0.08%.

It is to be understood that within the scope of the present invention, the above-described features of the present invention and those specifically described below (e.g., in the examples) may be combined with each other to form new or preferred embodiments. Not to be reiterated herein, but to the extent of space.

Drawings

FIG. 1 shows the result of PCR electrophoresis of MED 125 pair primers (M: DNA Marker)

FIG. 2 shows annealing temperature optimization of Taqman-ddPCR method for detecting MED12G 44D mutation, wells F09, F05, and F01 represent annealing temperature gradients 60 deg.C, 58 deg.C, and 56 deg.C. Wherein A is the 1-D amplitude profile of the FAM channel detection positive control (containing G44D 100% gene mutation); b, HEX channel detection G44D mutation negative control 1-D amplitude diagram.

FIG. 3 shows annealing temperature optimization of Taqman-ddPCR method for detecting MED12G 44V mutation, wells B09, B05, B01 represent annealing temperature gradients 60 deg.C, 58 deg.C, 56 deg.C. Wherein A is the 1-D amplitude profile of the FAM channel detection positive control (containing G44V 100% gene mutation); b is a 1-D amplitude chart of the HEX channel for detecting G44V mutant gene negative control.

FIG. 4 shows annealing temperature optimization of Taqman-ddPCR method for detecting MED12G 44S mutation, wells D09, D05, D01 represent annealing temperature gradients 60 deg.C, 58 deg.C, 56 deg.C. Wherein A is the 1-D amplitude profile of the FAM channel detection positive control (containing G44S 100% gene mutation); wherein B is a 1-D amplitude chart of a HEX channel detection G44S mutation-containing gene negative control group.

FIG. 5 shows annealing temperature optimization of Taqman-ddPCR method for detecting MED12G 44C mutation, wells H09, H05, H01 represent annealing temperature gradient 60 ℃, 58 ℃, 56 ℃. Wherein A is FAM channel detection positive control (containing G44C 100% gene mutation); b is a 1-D amplitude chart of a HEX channel detection G44C mutation-containing gene negative control group.

FIG. 6 shows the validation of the concentration of the MED12 gene G44D mutation assay. As can be seen from the figure, the linearity of the detection method in all detection concentrations (0.06% -1%) is very good, namely the sensitivity of the method reaches 0.06%.

FIG. 7 shows the validation of the concentration of the MED12 gene G44V mutation assay. As can be seen from the figure, the linearity of the detection method in all detection concentrations (0.06% -1%) is very good, namely the sensitivity of the method reaches 0.06%.

FIG. 8 shows the validation of the concentration of the MED12 gene G44S mutation assay. As can be seen from the figure, the linearity of the detection method in all detection concentrations (0.06% -1%) is very good, namely the sensitivity of the method reaches 0.06%.

FIG. 9 shows the validation of the concentration of the MED12 gene G44C mutation detection. As can be seen from the figure, the linearity of the detection method in all detection concentrations (0.06% -1%) is very good, namely the sensitivity of the method reaches 0.06%.

Figure 10 shows that case "MS 1082" was MED12 negative by digital PCR detection. Two-dimensional diagrams (2D amplitude diagrams of FAM-HEX channels) for detection of G44D, G44V, G44S, and G44C, respectively, are from top to bottom. Where green is the wild type signal.

FIG. 11 shows a two-dimensional plot of the digital PCR detection of MED12G 44D for case "MS 1096" (2D plot of FAM-HEX channel). Blue and orange are mutation signals, indicating that the case "MS 1129" was MED12G 44D positive by digital PCR.

Fig. 12 shows a two-dimensional map of the case "MS 1087" detected by digital PCR detection MED12G 44V (2D map of FAM-HEX channel). Blue and orange are mutation signals, indicating that case "MS 1087" was MED12G 44V positive by digital PCR.

Fig. 13 shows a two-dimensional map of the case "MS 1123" detected by digital PCR detection MED12G 44S (2D map of FAM-HEX channel). Blue and orange are mutation signals, indicating that the case "MS 1123" was MED12G 44S positive by digital PCR.

Fig. 14 shows a two-dimensional plot of the digital PCR detection MED12G 44C detection of case "MS 1073" (2D plot of FAM-HEX channel). Blue and orange are mutation signals, indicating that case "MS 1073" was MED12G 44C positive by digital PCR.

FIG. 15 shows a two-dimensional graph (2D graph of FAM-HEX channel) of MED 124 gene mutations (G44D + G44V + G44S + G44C) detected by digital PCR in case "MS 1070". Blue and orange are mutation signals, indicating that case "MS 1070" is MED12 positive by digital PCR.

Detailed Description

The inventor of the invention can effectively improve the gene mutation detection effect by extensive and deep research, particularly by optimizing a primer sequence and a probe and combining a digital PCR platform, breaks through the problems of low accuracy, low sensitivity and the like of pathological tissues as starting materials in the existing gene mutation detection technology, and provides a method for detecting MED12 gene mutation with high specificity, high sensitivity and strong anti-interference capability. On this basis, the present inventors have completed the present invention.

Specifically, the invention provides a detection method for MED12G 44D, G44V, G44S and G44C mutant genes, namely a digital PCR detection system is established by providing 1 pair of specially optimized probes for a primer pair at the G44 site of MED12 and specially optimized probes for the mutant genes of MED12G 44D, G44V, G44S and G44C, so that the mutation condition of the MED12 gene is qualitatively and quantitatively detected. When the method and the reagent are used for detecting MED12 gene mutation, the unexpected high sensitivity and high specificity are realized, and samples with different difficulties can be detected.

Term(s) for

In order that the disclosure may be more readily understood, certain terms are first defined. As used in this application, each of the following terms shall have the meaning given below, unless explicitly specified otherwise herein. Other definitions are set forth throughout the application.

The term "about" can refer to a value or composition that is within an acceptable error range for the particular value or composition as determined by one of ordinary skill in the art, which will depend in part on how the value or composition is measured or determined. For example, as used herein, the expression "about 100" includes 99 and 101 and all values in between (e.g., 99.1, 99.2, 99.3, 99.4, etc.).

As used herein, the term "comprising" or "includes" can be open, semi-closed, and closed. In other words, the term also includes "consisting essentially of …," or "consisting of ….

Sequence identity is determined by comparing two aligned sequences along a predetermined comparison window (which may be 50%, 60%, 70%, 80%, 90%, 95% or 100% of the length of the reference nucleotide sequence or protein) and determining the number of positions at which identical residues occur. Typically, this is expressed as a percentage. The measurement of sequence identity of nucleotide sequences is a method well known to those skilled in the art.

Digital PCR (digital PCR) technology

Digital PCR (digital PCR) technology, which is an absolute method of nucleic acid quantification based on a single-molecule PCR method for counting, is a method of nucleic acid quantification. The method mainly adopts a micro-fluidic or micro-droplet method in the current analytical chemistry hot research field to disperse a large amount of diluted nucleic acid solution into micro-reactors or micro-droplets of a chip, wherein the number of nucleic acid templates in each reactor is less than or equal to 1. Thus, after PCR cycling, the fluorescent signal of each droplet is analyzed after amplification is completed, the reactor with the nucleic acid molecule template gives the fluorescent signal, and the reactor without the template has no fluorescent signal. Based on the relative proportions and the volume of the reactor, the nucleic acid concentration of the original solution can be deduced.

Digital PCR enables accurate quantitative analysis and detection of target nucleic acid molecules with high sensitivity, compared to conventional qPCR. The method of analyzing the results of conventional qPCR is an analog method, wherein the digital PCR method, the results of which are analyzed by a digital method (since the resulting signal has a value of "0" or "1"), has the advantage that large volume samples can be analyzed, different samples can be detected simultaneously, and different tests can be performed simultaneously. The digital PCR technique is a technique that can absolutely quantify a DNA sample using a single-molecule counting method without a standard curve, and can perform more accurate absolute quantification of a single droplet per well by PCR (see Gudrun Pohl and le-Ming Shih, Principle and application of digital PCR, Expert rev. mol. digital.4 (1),41-47 (2004)). The digital PCR has the advantages of high sensitivity, accurate quantification without a standard curve, simple operation and the like.

In digital PCR, each droplet containing a sample gene template, amplification primers, and fluorescent probes prepared to be available for dilution to an average copy number of 0.5-1 is dispensed into a single well and miniemulsion PCR is performed. Then, the well count showing the fluorescent signal was a value of "1" because the sample having the gene copy number of 1 was dispensed into the well and shows the fluorescent signal after amplification, while the well count showing no signal was "0" because the sample having the gene copy number of 0 was dispensed into the well and shows no fluorescent signal due to no amplification. In this way, absolute quantification can be achieved.

Primer and method for producing the same

A primer is a macromolecule with a specific nucleotide sequence, which is stimulated to be synthesized at the beginning of nucleotide polymerization and is linked with a reactant in a covalent bond mode. The primers are typically two oligonucleotide sequences synthesized by man, one primer complementary to one DNA template strand at one end of the target region and the other primer complementary to the other DNA template strand at the other end of the target region.

In the present invention, in order to improve the sensitivity of the detection system, the corresponding gene segment in the detection system is amplified in advance, and thus a primer corresponding to the sequence in which the mutation is located is designed.

In a preferred example, 1 pair of primers is respectively designed on the upstream and downstream of the G44 site of MED12 gene aiming at the sequence of MED12G44, and the optimal primer pairs are finally determined to be SEQ ID Nos. 1 and 2 through experimental tests.

Probe needle

As used herein, the terms "probe", "nucleic acid probe" and "gene probe" are used interchangeably and refer to a nucleic acid sequence (DNA or RNA) complementary to a gene of interest, having a detectable label and known sequence. The gene probe is combined with target gene by means of molecular hybridization to produce hybridization signal, and the target gene can be displayed from vast genome. According to the principle of hybridization, a nucleic acid sequence as a probe must have at least the following two conditions: firstly, the single-stranded DNA is required to be subjected to denaturation treatment if the double-stranded DNA is double-stranded; ② should carry easily detectable marks. The nucleic acid probe may include the entire gene or may be only a part of the gene; the DNA itself may be used, or the RNA transcribed therefrom may be used. In the present invention, the probe also refers to a modified primer, and the modified primer has chemical modification groups at two ends or in the middle, and these chemical modifications have special functions including but not limited to: signal indicating effect, enhancing the linking effect with the reactant, etc.

Z1-Z2-Z3 I

Wherein the content of the first and second substances,

z1 is a fluorophore;

z2 is a specific complementary nucleic acid sequence;

z3 is a quencher group;

"-" is a bond, a linker, or a linker of 1-3 nucleotides.

TGGTTATTGAAACCTTG(SEQ ID No:3)；

TGGTTATTGAAATCTG(SEQ ID No:4)；

TGGTTATTGAAAACTG(SEQ ID No:5)；

TGGTTATTGAAACTTTGTG(SEQ ID No:6)；

TGGTTATTGAAACATTGTG(SEQ ID No:7)。

Modification of primers and probes

In the present invention, the nucleic acid sequence of the primer includes an unmodified or modified primer sequence.

In a preferred embodiment of the present invention, the modification is selected from: phosphorylation (Phosphorylation), Biotin (Biotin), Digoxigenin (Digoxigenin), internal amino modification, 5 'amino modification, 3' amino modification, Thiol (Thiol), Spacer, thio (phosphinothioate), DeoxyUridine (dU), deoxyhypoxanthine (dI), or combinations thereof.

Phosphorylation modification: 5' phosphorylation can be used for linker, cloning and gene construction as well as ligase catalyzed ligation reactions. 3 'phosphorylation is also used to prevent DNA polymerase catalyzed DNA strand extension reactions in related experiments that are resistant to 3' exonuclease digestion.

Biotin modification: the primer biotin label can be used for non-radioactive immunoassay to detect protein, intracellular chemical staining, cell separation, nucleic acid separation, hybridization to detect specific DNA/RNA sequence, ion channel conformation change and the like.

New modification of Gegao: the digoxigenin is linked to the C5 position of uracil via an 11-atom spacer, and the hybridized digoxigenin probe can be detected by an anti-digoxigenin antibody. The probe labeled with the digoxigenin can be used for various hybridization reactions, such as DNA-DNA hybridization (Southern blotting), DNA-RNA hybridization (Northern blotting), Dot hybridization (Dot blotting), clone hybridization, in situ hybridization and enzyme-linked immunoassay (ELISA).

Internal amino modification: internal modifications were made primarily by adding C6-dT aminol inker to thymine residues. The modified amino group is 10 atoms away from the backbone and can be used for further labeling and enzyme attachment (e.g., alkaline phosphatase), currently providing internal amino modification mediated dT-Dabcyl, dT-Biotin and dT-Digoxingin modifications.

5' amino modification: can be used for preparing functionalized oligonucleotides, and is widely applied to DNA chips (DNA Microarray) and multi-label diagnostic systems. Both 5'C6 amino modifications, which can be used to attach compounds that do not affect the function of the oligonucleotide even when it is close to it, and 5' C12 amino modifications, which can be used to attach affinity purification groups and fluorescent labels, especially when fluorescence may be quenched by labels that are too close to the DNA strand, are currently provided.

3' amino modification: 3' C6 amino modifications are currently provided. It can be used to design new diagnostic probes and antisense nucleotides, for example, the 5 'end can be labeled with highly sensitive 32P or fluorescein while the 3' end can be modified with an amino group for additional ligation. In addition, 3 'modification can inhibit 3' exonuclease enzymolysis, and thus can be used for antisense experiments.

And (3) sulfydryl modification: the 5' -thiol group is similar to the amino group modification in many respects. Sulfhydryl groups can be used to attach various modifications such as fluorescent labels and biotin. For example, thiol-linked fluorescent probes can be prepared in the presence of iodoacetic acid and maleimide derivatives. 5' Thiol modification predominantly uses a 5' Thiol modifying monomer (5' -Thiol-Modifier C6-CE Phosphoramidite or Thiol-Modifier C6S-S CE Phosphoramidite). Modification with the 5' -thio-Modifier C6-CE monomer must be followed by oxidation with silver nitrate to remove the protecting group (trityl), while modification with the thio-Modifier C6S-S CE monomer must be followed by reduction of the disulfide bond to the Thiol group with DTT.

Modification of the middle arm: the Spacer can provide necessary spacing for oligonucleotide labeling to reduce the interaction between a labeling group and the oligonucleotide, and is mainly applied to the research of DNA hairpin structures and double-stranded structures. C3 spacer is used primarily to mimic the three-carbon spacing between the 3 'and 5' hydroxyl groups of ribose, or to "replace" an unknown base in a sequence. 3'-Spacer C3 was used to introduce a 3' Spacer to prevent the 3 'exonuclease and 3' polymerase from acting. Spacer 18 is commonly used to introduce a strong hydrophilic group.

And (3) thio modification: thio-modified oligonucleotides are used primarily in antisense experiments to prevent degradation by nucleases. All thioates can be chosen, but as the number of thioated bases increases, the Tm of the oligonucleotide decreases, and to reduce this effect, 2-5 bases at both ends of the primer can be thioated, and typically 3 bases each of 5 'and 3' can be chosen for thioation.

Deoxyuridine pyrimidine modification: deoxyuridine pyrimidines may be inserted into oligonucleotides to increase the melting temperature of the duplex and thus increase duplex stability. The melting point of the double chain can be increased by 1.7 ℃ by replacing each deoxythymine with deoxyuracil.

And (3) deoxyhypoxanthine modification: deoxyhypoxanthine is a naturally occurring base that, while not a true universal base, when combined with other bases, is relatively more stable than other base mismatches. The binding capacity of the deoxyinosine with other bases is dI: dC > dI: dA > dI: dG > dI: dT., and the deoxyinosine is preferentially bound with dC under the catalysis of DNA polymerase.

cfDNA

Free nucleic acid (cfDNA) in blood plasma, also called liquid biopsy, avoids the need for biopsy of tumor tissue, and is a very useful diagnostic application in clinic. The use of fluid biopsies offers the possibility of repeated blood sampling, allowing changes in cfDNA to be tracked during tumorigenesis or during cancer treatment, thereby monitoring changes in disease status (Cell-free nucleic acids as biologizers in cancer patients). However, there are currently significant technical challenges to accurately and specifically detect gene mutations using cfDNA detection. First, the cfDNA content in blood varies from person to person and is mostly very low, and among them, the quality of tumor-derived free nucleic acid (ctDNA) is more uneven and the content is high. Moreover, the specificity of cfDNA detection methods is to be improved. Douillard et al reported that detection of EGFR mutations using plasma only matched the results of tumor tissue detection by 65%.

The main advantages of the invention include:

1. the sensitivity is high: because the method adopts a digital PCR platform, the reaction system can be divided into about 20000 micro-reactions, single copy mutation can be detected theoretically, and the method has the sensitive advantage that other technologies cannot compete. The detection method can reach the lowest detection limit of 0.06 percent through verification.

2. The specificity is strong: the designed specific primers can specifically amplify wild type and mutant templates at target positions aiming at the sequence of the G44 locus of the MED12 gene; the designed specific probes cover mutation sites, 5 pieces (in total) are respectively designed aiming at wild types and mutant types of MED12G44 sites, HEX fluorescent group modification is carried out at the 5' end of the wild type probe, FAM fluorescent group modification is carried out at the 5' end of the mutant type probe, meanwhile, MGB is carried at the 3' end of the MED12 probe, a template with a base difference can be effectively distinguished, and the design of the primers and the probes greatly improves the detection specificity.

3. The requirements on the type and quality of the sample are loose, and the interference resistance is strong. Due to the high sensitivity, the sample type applicable to the invention can be used for preparing a peripheral blood sample (the sample is easy to obtain, but has low DNA content and is broken) besides a fresh tissue sample and a paraffin section which are commonly used in a common method; and, because of the uniqueness of the digital PCR platform, the reaction system can be divided into about 20000 small systems, and the interfering substance can be divided into about 20000 parts, so that the influence of the interfering substance on the reaction can be greatly reduced, and the sample with more complex background can be detected. This is not possible with other platforms.

4. The positive interpretation method is simple: as the method of absolute quantification is adopted, a comparison standard curve is not required to be set, and whether the target mutation template is contained or not can be judged according to a two-dimensional graph of fluorescence according to the result (Table 1).

TABLE 1 table of test results

The invention will be further illustrated with reference to the following specific examples. It should be understood that these examples are for illustrative purposes only and are not intended to limit the scope of the present invention. Experimental procedures without specific conditions noted in the following examples, generally followed by conventional conditions, such as Sambrook et al, molecular cloning: the conditions described in the laboratory Manual (New York: ColdSpringHarbor laboratory Press,1989), or according to the manufacturer's recommendations. Unless otherwise indicated, percentages and parts are percentages and parts by weight.

Unless otherwise specified, materials and reagents used in examples of the present invention are commercially available products.

Primer, probe and sequence of amplified fragment

In the examples, the nucleic acid sequence information of the primers, probes and amplified DNA fragments used are shown in Table 2:

table 2: nucleic acid sequences of primers, probes and DNA fragments

Example 1 screening of primer pairs

A plurality of primer pairs (the primers are synthesized by Shanghai Biotechnology Limited) are respectively designed according to the sequence of the MED12 target site (G44), and the specific sequence is shown in the following table 3.

TABLE 3 screening of 5 primer pairs for amplification of MED12G44

The screening PCR system comprises 0.2ul Taq HS polymerase, 2ul 10 XHS PCR buffer, 1.6ul dNTP mixture, 1ul upstream primer, 1ul downstream primer, 5.5ul tgDNA (human leukocyte genomic DNA as template), and water to 20 ul.

Screening the PCR program: 95 ℃ for 10min, 30 cycles (94 ℃ for 30s, 56 ℃ for 30s, 72 ℃ for 20 s).

Through PCR screening, the amplification efficiency of the G44 primer pair 2(MED12-F2/MED12-R2) on a target fragment is high (a band is bright), an amplification product is short, no primer dimer is generated, the overall effect is best, and the primer pair can be used as a primer pair for MED12 gene mutation detection. See fig. 1.

Example 2 optimization of Taqman probes and digital PCR reaction program

In this example, Taqman probes were synthesized and optimized, and the digital PCR reaction program was optimized based on the optimized Taqman probes.

2.1 Taqman probes

In this example, the MED12 gene mutations detected were nucleotide mutations corresponding to G44D, G44V, G44S, G44C (table 4);

table 4: MED12 gene mutation information sheet

Detection site	Type of mutation	COSMIC numbering	Genetic alteration
				G44D	Point mutation	COSM131596	c.131G>A
G44V	Point mutation	COSM131597	c.131G>T
				G44S	Point mutation	COSM131594	c.130G>A
G44C	Point mutation	COSM131593	c.130G>T

Based on the genome sequence and mutation site of human MED12, corresponding Taqman probes are designed and optimized, namely WTP-G44(SEQ ID No:3), MTP-G44D (SEQ ID No:4), MTP-G44V (SEQ ID No:5), MTP-G44S (SEQ ID No:6) and MTP-G44C (SEQ ID No:7), and the specific information of the probes is shown in Table 2.

2.2 optimization of the digital PCR reaction program

The digital PCR reaction program was further optimized based on the optimal primer pair (SEQ ID Nos: 1 and 2) determined in example 1 and the optimized probe determined in example 2.1. The digital PCR reaction program optimization experiment needs comprehensive analysis of the digital PCR amplification conditions of the wild type template and the mutant type template along with the change of the annealing temperature. The optimum annealing temperature should satisfy two conditions: negative controls (wild-type template) were clean in background (FAM channel without microdroplets), positive and negative signals within mutant templates were easily distinguished (FAM and HEX channel fluorescence intensity was high).

The experimental method is as follows:

the following PCR system was arranged in the reagent preparation area: 11ul of 2 XDddPCR Supermix (No dUTP), 1.1ul of upstream primer (MED12-F), 1.1ul of downstream primer (MED12-R), 0.55ul of probe 1(WTP-G44), 0.55ul of probe 2(MTP-G44D/MTP-G44V/MTP-G44S/MTP-G44C), 5.5ul of template, and adding water to supplement to 22 ul.

The templates were added to the sample preparation area in the following order: negative control and positive control. The negative control is normal human leukocyte genome (tgDNA), and the positive control is genomic DNA solution containing the corresponding mutation sequence of MED12G 44.

In the droplet generation zone, droplet generation is performed as required by the instrument.

In the sample analysis zone, a PCR reaction is performed and analysis is performed.

PCR program for ddPCR optimization experiments: 95 ℃ for 10min, 40 cycles {94 ℃ for 30s, annealing temperature gradient (60 ℃, 58 ℃ and 56 ℃) for 15s, 72 ℃ for 15s }, 98 ℃ for 10min, and temperature rise and fall rate of 2 ℃/s.

And after the PCR is finished, setting according to the instrument and experiment requirements, selecting a FAM/HEX detection channel, and starting to read the plate.

The results are shown in FIGS. 2 to 5. Wherein, the FAM channel indicates the MTP probe to detect the microdroplet of the mutant template and the fluorescence intensity (Amplitude) thereof, and the HEX channel indicates the WTP probe to detect the microdroplet of the wild template and the fluorescence intensity (Amplitude) thereof. The FAM-HEX double positive microdroplets represent the presence of both wild type and mutant templates. The number of droplets passing through the FAM channel can be used for presuming whether the mutant template exists in the digital PCR system and accurately calculating the copy number (copies/ul).

The results of fig. 2 to 5 show that annealing at 56 ℃ for 15s, digital PCR negative control is free of contamination, negative signals and positive signals are distinguished most obviously, the overall effect is good, and the optimal annealing temperature is obtained.

Example 3 verification of sensitivity of detecting MED12 Gene mutation by digital PCR method

Wild type template copy number (copies/ul), mutant template genomic copy number (copies/ul) and mutation rate (%) were calculated according to example 1, both diluted to 4000copies/ul with TE. The mutant genome template is doped with tgDNA, so that the proportions of the mutant templates are respectively 0.06%, 0.13%, 0.25%, 0.5% and 1%, and a gradient dilution template is prepared.

Verifying the digital PCR system: 11ul of 2 XDddPCR Supermix (No dUTP), 1.1ul of primer 1(MED 12-F), 1.1ul of primer 2(MED12-R), 0.55ul of probe 1(WTP-G44), 0.55ul of probe 2(MTP-G44D/MTP-G44V/MTP-G44S/MTP-G44C), 5.5ul of template, and adding water to complete to 22 ul.

The templates were added to the sample preparation area in the following order: blank control, negative control, gradient dilution template. Blank control is water, negative control is tgDNA, and gradient dilution template is wild type template doped with 0.06% -1% mutant template.

The PCR reaction system was formed into droplets in the same manner as in example 1. PCR was performed according to the optimized PCR program: 95 ℃ for 10min, 40 cycles (94 ℃ for 30s, 56 ℃ for 15s, 72 ℃ for 15s), 98 ℃ for 10min, and a heating and cooling rate of 2 ℃/s. Plate reading is started according to instrument requirements.

The digital PCR results are shown in FIGS. 6 to 9. The digital PCR method of the invention takes water or tgDNA as a template, has clean background and no pollution. In addition, the digital PCR method of the invention is characterized in that 0.06% -1% mutant template is doped into the wild template, the copy number of the wild template is detected to be normal, and the detection is carried outThe proportion of mutant template (mutant template divided by total template times 100%) is in line with the theoretical proportion, R²The value is greater than 0.98. Namely, the digital PCR method has accurate detection value within the sensitivity range of 0.06% -1%, namely, the lowest detection sensitivity of the digital PCR method is 0.06%.

Example 4 detection of MED12 mutation in patient by digital PCR method for guiding tumor-targeted drug administration

The cases "MS 1082", "MS 1096", "MS 1087", "MS 1123" and "MS 1073" are all patients with uterine fibroids. Plasma was separated by two centrifugation steps by collecting venous blood, and plasma free nucleic acid was extracted by a free nucleic acid extraction kit. The extracted nucleic acid was quantified by Qubit. After quantification, the samples were stored in a-20 ℃ freezer in a sample preparation room.

The digital PCR assay system of the invention is shown in example 2.

The templates were added to the sample preparation area in the following order: blank control, negative control, case free nucleic acid, positive control (1%).

The PCR reaction system was formed into droplets in the same manner as in example 1. PCR was performed according to the optimized PCR program: 95 ℃ for 10min, 40 cycles (94 ℃ for 30s, 56 ℃ for 15s, 72 ℃ for 15s), 98 ℃ for 10min, and a heating and cooling rate of 2 ℃/s. The instrument is opened, setup is performed as required, and plate reading is started. The MED12 test has clean background with blank control and negative control, and normal copy number and mutation ratio of the positive control.

The results of the test of the case nucleic acid samples are shown in Table 5 below.

MS1082 was judged negative (see fig. 10) and did not contain the G44D, G44V, G44S, G44C mutations.

MS1096 judged positive for G44D (see FIG. 11; mutation rate 1.64%);

case MS1087 judged positive for G44V (see FIG. 12; mutation rate 1.59%);

case MS1123 judged positive for G44S (see fig. 13; mutation rate 0.87%);

case MS1073 was judged positive for G44C (see fig. 14; mutation rate 1.36%).

In addition, in the case of hysteromyoma, "MS 1170" was examined in a quadruple combination (MED 12G 44D + G44V + G44S + G44C), and the result was judged to be positive for MED12G44 mutation (see FIG. 15, mutation rate of 1.42%)

The specific test data for the above cases are shown in table 5 below:

table 5: case testing Gene mutation results

Discussion:

at present, the methods for detecting gene mutation mainly include:

(1) high resolution melting curve (HRM). HRM is a gene analysis technology which forms different morphological melting curves based on different single nucleotide melting temperatures. The detection sensitivity is about 1-10%. However, due to the high false positive of the dye method, sequencing verification is required at the later stage, resulting in a longer detection period.

(2) Probe amplification block mutation method (ARMS-qPCR). The method distinguishes the template with some point mutation from the normal template by using the principle that the terminal base at the 3' end of the PCR primer must be complementary with the template DNA for effective amplification, and the sensitivity of the detection method is higher than HRM and is about 1 percent (CN 104099422A).

(3) Allele-specific Taqman polymerase chain reaction (CAST-PCR). CAST-PCR uses a section of specially designed MGB probe to prevent primer from combining with wild type DNA and selectively preferentially amplify mutant type DNA, and the sensitivity of said detection method is about 0.1% -1%(patent No. CN104099422A). Barbanon R. et al applied CAST-PCR technology to detect V600E and V600K mutation of BRAF gene in clinical sample, and the sensitivity of the method is 1%(Competitive allele- specific TaqMan PCR(Cast-PCR)is a sensitive,specific and fast method for BRAF V600mutation detection in Melanoma patients)。

In summary, most of the existing gene mutation detection technologies are dye-based or probe-based fluorescence quantitative PCR technologies, which have the problems of low sensitivity, low accuracy, complex positive interpretation method and the like, and have high requirements on the type and quality of a sample, for example, some methods require providing a tissue sample, and some methods can treat a plasma/serum sample but require a tumor three-stage or four-stage patient.

The invention uses digital PCR (digital PCR) technology, a sample is distributed to tens of thousands of mutually independent small droplets, each droplet respectively carries out PCR amplification on target molecules, and the fluorescent signals of the droplets are analyzed after the amplification is finished. The digital PCR has the advantages of high sensitivity, accurate quantification without a standard curve, simple operation and the like.

Aiming at 4 mutations at the G44 locus, the invention develops a high-sensitivity and high-specificity digital PCR method, and compared with the prior art such as HRM, Arms-qPCR, CAST-PCR and the like, the invention adopts a Taqman probe and combines a digital PCR method, thereby solving the problems of low sensitivity, poor specificity, high requirements on the type and quality of a sample, complex positive interpretation method and the like. The sensitivity of the method can reach 0.06% at most, and the method can accurately detect tissue and body fluid samples and can also process samples with high difficulty such as blood plasma/serum and the like.

All documents referred to herein are incorporated by reference into this application as if each were individually incorporated by reference. Furthermore, it should be understood that various changes and modifications of the present invention can be made by those skilled in the art after reading the above teachings of the present invention, and these equivalents also fall within the scope of the present invention as defined by the appended claims.

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Ming-Shi medical science and technology (Ningbo) Co Ltd

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Claims

1. A reagent for detecting a gene mutation, comprising a first primer pair for detecting MED12G44 mutation, wherein the first primer pair comprises primers shown in SEQ ID nos 1 and 2.

2. The reagent of claim 1, further comprising a first probe for use with the first primer pair, wherein the first probe is selected from the group consisting of: the probe shown in SEQ ID No. 3, the probe shown in SEQ ID No. 4, the probe shown in SEQ ID No. 5, the probe shown in SEQ ID No. 6, the probe shown in SEQ ID No. 7 or the combination thereof.

3. The reagent of claim 2, wherein the first probe has the structure (5'-3') according to formula I:

Z1-Z2-Z3 I

wherein the content of the first and second substances,

z1 is a fluorophore;

z2 is a specific complementary nucleic acid sequence;

z3 is a quencher group;

"-" is a bond, a linker, or a linker of 1-3 nucleotides.

4. A kit comprising the reagent for detecting a gene mutation according to claim 1.

5. The kit of claim 4, further comprising a first probe for use in conjunction with the first primer pair.

6. Use of the reagent for detecting gene mutation according to claim 1 or the kit according to claim 4 for preparing a diagnostic product for evaluating whether a subject has a tumor with a gene mutation.

7. A method for detecting whether a sample to be detected contains gene mutation is characterized by comprising the following steps:

a reagent for detecting a gene mutation according to claim 1;

8. The method of claim 7, wherein the PCR reaction system further comprises a first probe for use with the first primer pair, wherein the first probe is selected from the group consisting of: the probe shown in SEQ ID No. 3, the probe shown in SEQ ID No. 4, the probe shown in SEQ ID No. 5, the probe shown in SEQ ID No. 6, the probe shown in SEQ ID No. 7 or the combination thereof.

9. The method of claim 7, wherein the method detects an accuracy of 0.06% -1%, preferably 0.0625% -0.08%.