CN117402975A - Probe, kit and drop-off ddPCR method for quantitatively detecting IDH1 gene mutation - Google Patents

Probe, kit and drop-off ddPCR method for quantitatively detecting IDH1 gene mutation Download PDF

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CN117402975A
CN117402975A CN202311722602.3A CN202311722602A CN117402975A CN 117402975 A CN117402975 A CN 117402975A CN 202311722602 A CN202311722602 A CN 202311722602A CN 117402975 A CN117402975 A CN 117402975A
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drop
mutation
idh1
primer
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舒迎霜
王冰
杨春燕
商宇红
李旋
周启明
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Beijing Qiuzhen Medical Equipment Co ltd
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Abstract

The invention belongs to the technical field of gene detection, and in particular relates to quantitative detectionIDH1Probes, kits and drop-off ddPCR methods for gene mutation. The invention is based onIDH1Designing two probes with different fluorescent signals in a hotspot mutation region of a gene No.4 exon, wherein a Drop-off probe is positioned on the hotspot mutation region, and the probes are complementary with a wild type sequence and are not complementary with mutation sites; the Reference probe is located outside the mutation hot spot region and is complementary to both the mutant and wild type sequences. As long as the Drop-off probe coverage area is mutated, the probe cannot be combined with a template sequence, the Reference probe can still be combined with the probe and amplified, and finally the mutation type can be distinguished by the fluorescence signal intensity of the liquid Drop measured by a detection instrument and the position in two-dimensional coordinates,Wild type and negative, realizationIDH1Detection of gene mutation.

Description

Probe, kit and drop-off ddPCR method for quantitatively detecting IDH1 gene mutation
Technical Field
The invention belongs to the technical field of gene detection, and particularly relates to a probe, a kit and a drop-off ddPCR method for quantitatively detecting IDH1 gene mutation.
Background
The IDH1 gene is located on chromosome 2 of human genome, is used as key gene involved in cell metabolism, and its coded protein isocitrate dehydrogenase 1 is cytosolic enzyme, mainly consists of 414 amino acids, and can combine two NADP + The molecule and 154 water molecules, and contains C-terminal tripeptide, alanine-lysine-leucine, are type 1 peroxisome targeting sequences, which can target proteins to peroxisomes. The protein is mainly present in cytoplasm, peroxisome and endoplasmic reticulum, and can catalyze oxidative decarboxylation of isocitrate to alpha-ketoglutarate (alpha-KG). NADP consumption by catalytic processes + NADPH is produced, and the catalytic products alpha-KG and NADPH can relieve oxidative damage of cells caused by oxidative stress and play an important role in the process of cell detoxification. In addition to the above functions, IDH1 catalyzes the β -oxidation of unsaturated fatty acids in the peroxisome of hepatocytes.
IDH1 is the most frequent gene for mutation of metabolic genes (metabic genes) in human cancers, and mutant IDH1 interferes with normal metabolism and epigenetic regulation of cells, and is ubiquitous in many myeloid malignancies, and studies indicate that IDH1 (R132C and R132H) or IDH2 (R172 and R140) somatic mutations are detected in about 20% of patients with Acute Myeloid Leukemia (AML). While normal IDH1 protein plays a key role in the food nutrition metabolism process, mutant IDH1 protein in AML patients additionally converts alpha-KG produced by the catalysis of IDH1 into metabolite 2-hydroxyglutarate (2-HG) during the metabolism process, and the process consumes NADPH to generate NADP + .2-HG is an oncogenic molecule, and the latter can inhibit the former target due to competitive inhibition caused by the structural similarity of alpha-KG and 2-HG, thus, the alpha-KG is used as a base in AML patientsThe signaling pathways of the agent are often disrupted, resulting in epigenetic deregulation of histone and DNA methylation, chromatin remodeling, blocking of cell differentiation and other transformation effects, leading to the development of tumors. In addition, besides AML, research shows that IDH1 mutation is closely related to diseases such as glioma, cartilage tumor, chondrosarcoma, glioma and the like, and IDH genes are already listed in NCCN guidelines and Chinese glioma guidelines, which clearly indicate that IDH1/2 is a key index of molecular typing of glioma, and has important significance for individual treatment and clinical prognosis judgment of glioma.
There are various detection methods for IDH1 gene mutation, mainly Sanger sequencing, second generation sequencing, real-time fluorescent quantitative PCR, traditional ddPCR (microdroplet digital PCR, droplet Digital PCR) and the like. Among them, sanger sequencing is the most classical method for detecting IDH1 gene mutation and is also the gold standard for detecting gene mutation. The direct sequencing method based on the dideoxy sequencing principle can most intuitively show the change of the gene sequence in the form of a base peak diagram, has comprehensive detection types and is also the earliest mutation detection means. The second generation sequencing has the advantages of high flux, high sensitivity and the like, but the experimental operation is difficult and the cost is high. The real-time fluorescent quantitative PCR is a detection method for judging whether mutation exists or not by using a Ct value based on the PCR, and has the advantages of strong specificity, high sensitivity, accurate quantification, simple and convenient operation, full-closed reaction and the like, but absolute quantification cannot be performed and the risk of false positive possibly exists. The traditional ddPCR method has high sensitivity, can directly reflect the mutation load level of IDH1, but can only detect one known mutation by a pair of probes, can not detect multiple mutations on the same hot spot at the same time, and can possibly generate omission.
Disclosure of Invention
The invention aims at a probe, a kit and a drop-off ddPCR method for quantitatively detecting IDH1 gene mutation, and the primer and the probe can realize detection of a plurality of known mutation sites on the IDH1 gene, and have high sensitivity and simple test operation.
The invention provides a probe for detecting IDH1 gene mutation, which comprises a Drop-off probe and a Reference probe, wherein the nucleotide sequence of the Drop-off probe is shown as SEQ ID NO.1, and the nucleotide sequence of the Reference probe is shown as SEQ ID NO. 2; the 5 'end of the Drop-off probe and the Reference probe is marked with a fluorescent group, and the 3' end is marked with a fluorescence quenching group; the Drop-off probe and the Reference probe bear different fluorophores.
Preferably, the 5 'end of the Drop-off probe is marked with a fluorescent group VIC, and the 3' end is marked with a fluorescence quenching group BHQ1; the Reference probe is marked with a fluorescent group FAM at the 5 'end and a fluorescence quenching group BHQ1 at the 3' end.
The invention also provides a primer for detecting IDH1 gene mutation, the nucleotide sequence of the forward primer of the primer is shown as SEQ ID NO.3, and the nucleotide sequence of the reverse primer is shown as SEQ ID NO. 4.
The invention also provides a drop-off ddPCR kit for quantitatively detecting IDH1 gene mutation, which comprises the probe and the primer for detecting IDH1 gene mutation.
Preferably, the primer for detecting IDH1 gene mutation comprises the primer according to the technical scheme.
Preferably, the kit further comprises a dPCR enzyme and a buffer.
Preferably, the kit further comprises an IDH1 mutant plasmid and an IDH1 wild-type plasmid.
The invention also provides application of the probe, the primer or the kit in preparation of products for detecting IDH1 gene mutation.
Preferably, the IDH1 gene mutation comprises one or more of R132C, R132G, R132H, R L and R132S.
The invention also provides a drop-off ddPCR method for quantitatively detecting IDH1 gene mutation, which comprises the following steps:
mixing genomic DNA of a sample to be detected, a primer, a probe, dPCR enzyme and a buffer solution to obtain ddPCR reaction mixed solution;
mixing the ddPCR reaction mixed solution with an oil phase, and preparing the obtained mixture by a droplet preparation instrument to generate micro-reaction droplets;
introducing the micro-reaction liquid drops into a chip, performing PCR amplification reaction, collecting signals of the micro-droplets in the chip after the PCR amplification reaction, and calculating to obtain the mutation frequency of the IDH1 gene in the sample to be detected;
the probe comprises the probe according to the technical scheme.
The beneficial effects are that:
the invention provides a probe for detecting IDH1 gene mutation, which comprises a Drop-off probe and a Reference probe, wherein the nucleotide sequence of the Drop-off probe is shown as SEQ ID NO.1, and the nucleotide sequence of the Reference probe is shown as SEQ ID NO. 2; the 5 'end of the Drop-off probe and the Reference probe is marked with a fluorescent group, and the 3' end is marked with a fluorescence quenching group; the Drop-off probe and the Reference probe bear different fluorophores. According to the invention, two probes with different fluorescent signals are designed according to the hot spot mutation region of the No.4 exon of the IDH1 gene, wherein the Drop-off probes are positioned on the hot spot mutation region, and the probes are complementary with a wild type sequence and are not complementary with mutation sites; the Reference probe is located outside the mutation hot spot region and is complementary to both the mutant and wild type sequences. As long as the Drop-off probe coverage area is mutated, the probe cannot be combined with a template sequence, and the Reference probe can still be combined and amplified at the moment, and finally, the mutation type, the wild type and the negative type can be distinguished according to the fluorescence signal intensity of the liquid Drop measured by a detection instrument and the position of the liquid Drop in two-dimensional coordinates; the wild type carries two fluorescent signals, namely a Drop-off probe and a Reference probe; mutant forms carry only the Reference probe fluorescent signal; negative with no fluorescent signal.
On the basis, the detection of multiple mutations of the mutation hot spot of the 4 th exon of the IDH1 gene can be realized by combining primer amplification, and compared with Sanger sequencing, the detection method has high sensitivity and is simpler than the second generation sequencing experiment operation.
Drawings
In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings that are required to be used in the embodiments will be briefly described below.
FIG. 1 is a 2D scattergram of IDH1 gene mutation detection in example 1;
FIG. 2 is a 2D scatter plot of the IDH1 mutant type plasmid assay of example 2;
FIG. 3 is a plot of the detected 2D scatter plot after dilution of the wild-type plasmid to 1% in example 2;
FIG. 4 is a plot of the detected 2D scatter plot after dilution of the wild-type plasmid to 0.5% in example 2;
FIG. 5 is a plot of the detected 2D scatter plot after dilution of the wild-type plasmid to 0.2% in example 2;
FIG. 6 is a plot of the detected 2D scatter plot after dilution of the wild-type plasmid to 0.1% in example 2;
FIG. 7 is a plot of the detected 2D scatter plot after dilution of the wild-type plasmid to 0.05% in example 2;
FIG. 8 is a 2D scatter plot of the negative samples of example 2;
FIG. 9 is a linear relationship between the theoretical mutation frequency and the actual mutation frequency of IDH1 in example 2.
Detailed Description
The invention provides a probe which comprises a Drop-off probe and a Reference probe, wherein the nucleotide sequence of the Drop-off probe is shown as SEQ ID NO.1, and the nucleotide sequence of the Reference probe is shown as SEQ ID NO. 2; the 5 'end of the Drop-off probe and the Reference probe is marked with a fluorescent group, and the 3' end is marked with a fluorescence quenching group; the Drop-off probe and the Reference probe bear different fluorophores.
In the invention, the nucleotide sequence of the Drop-off probe is shown as SEQ ID NO.1, specifically 5'-TGGGTAAAACCTATCATCATAGGTC-3', the 5 'end of the Drop-off probe is preferably marked with a fluorescent group VIC, the 3' end of the Drop-off probe is preferably marked with a fluorescent quenching group BHQ1, and the sequence after marking the fluorescent group is as follows: 5'-VIC-TGGGTAAAACCTATCATCATAGGTC-BHQ1-3'. The nucleotide sequence of the Reference probe is shown as SEQ ID NO.2, specifically 5'-ATGGGGATCAAGTAAGTCATGTTGG-3', the 5 'end of the Reference probe is preferably marked with a fluorescent group FAM, the 3' end of the Reference probe is marked with a fluorescence quenching group BHQ1, and the marked sequence is as follows: 5'-FAM-ATGGGGATCAAGTAAGTCATGTTGG-BHQ1-3'.
According to the invention, two probes are designed aiming at the mutation hot spot region of the No.4 exon of the IDH1 gene, one probe is positioned outside the mutation hot spot region, when the mutation hot spot region generates base mutation, deletion and insertion, the Drop-off probe positioned in the mutation hot spot region cannot be tightly combined with a template, and the Reference probe can still be combined and amplified with the template at the moment, so that the detection of multiple mutation of the mutation hot spot of the No.4 exon of the IDH1 gene, including unknown mutation sites, is realized.
The invention also provides a primer for detecting IDH1 gene mutation, the nucleotide sequence of the forward primer of the primer is shown as SEQ ID NO.3, and the primer specifically comprises the following components: 5'-GCCATTATCTGCAAAAATATCCCCC-3' the nucleotide sequence of the reverse primer is shown as SEQ ID NO.4, and specifically comprises the following steps: 5'-TACAAGTTGGAAATTTCTGGGCCAT-3'.
The invention also provides a drop-off ddPCR kit for quantitatively detecting IDH1 gene mutation, which comprises the probe and the primer for detecting IDH1 gene mutation. The primer for detecting IDH1 gene mutation preferably comprises the primer according to the technical scheme. The kit of the present invention preferably further comprises a dPCR enzyme and a buffer, the source and brand of which are not particularly limited, and reagents conventionally used in the art for drop-off ddPCR detection may be employed. The kit of the invention preferably further comprises an IDH1 mutant plasmid and an IDH1 wild type plasmid; the IDH1 mutant plasmid and the IDH1 wild type plasmid can be used for positive control and negative control for detecting IDH1 gene mutation respectively.
The invention also provides application of the probe, the primer or the kit in preparation of products for detecting IDH1 gene mutation. The known mutation site in the IDH1 gene mutation of the present invention preferably includes one or more of R132C, R132G, R132H, R L and R132S, more preferably a plurality of R132C, R132G, R132H, R L and R132S, and still more preferably R132C, R132G, R132H, R L and R132S.
The invention also provides a drop-off ddPCR method for quantitatively detecting IDH1 gene mutation, which comprises the following steps:
mixing genomic DNA of a sample to be detected, a primer, a probe, dPCR enzyme and a buffer solution to obtain ddPCR reaction mixed solution;
mixing the ddPCR reaction mixed solution with an oil phase, and preparing the obtained mixture by a droplet preparation instrument to generate micro-reaction droplets;
introducing the micro-reaction liquid drops into a chip, performing PCR amplification reaction, collecting signals of the micro-droplets in the chip after the PCR amplification reaction, and calculating to obtain the mutation frequency of the IDH1 gene in the sample to be detected;
the probe comprises the probe according to the technical scheme.
The invention mixes the genome DNA of the sample to be tested, the primer, the probe, the dPCR enzyme and the buffer solution to obtain the ddPCR reaction mixed solution. The specific step of extracting the genomic DNA of the sample to be detected is not particularly limited, and the genomic DNA can be extracted by adopting a conventional extraction method in the field, such as extraction by adopting a kit. The genome DNA, the primer, the probe, the dPCR enzyme and the buffer solution of the sample to be tested form the amplification system of the drop-off ddPCR, and the volume of each component is preferably as follows according to 30 mu L: 1-15. Mu.L of genomic DNA of a sample to be tested, 7.5. Mu.L of 4 XMaxMix, 3.3. Mu.L of upstream primer, 3.3. Mu. L, drop-off probe 0.45. Mu. L, reference probe 0.45. Mu.L of downstream primer and the balance of water. The primer of the invention preferably comprises the primers shown in SEQ ID NO.3 and SEQ ID NO. 4.
After the ddPCR reaction mixture is obtained, the ddPCR reaction mixture is mixed with an oil phase. The volume ratio of the ddPCR reaction mixed solution to the oil phase is preferably 3:16.
after the mixing, the micro-reaction liquid drops are prepared from the obtained mixture by a micro-drop preparation instrument. The steps and processes for preparing the micro-reactive droplets are not particularly limited, and conventional steps and processes in the art may be employed.
After the micro-reaction liquid drops are obtained, the micro-reaction liquid drops are led into a chip for PCR amplification reaction, and the micro-droplets in the chip after the PCR amplification reaction are subjected to signal collection, so that the IDH1 gene mutation frequency in the sample to be detected is calculated, wherein the calculation formula of the gene mutation frequency is FAM copy number/(FAM copy number+VIC copy number). The PCR amplification procedure of the present invention preferably comprises: hot start at 95 ℃ for 10min; denaturation at 94℃for 30s, annealing at 60℃for 1min, total 40 cycles, and instrument cooling at 12℃for 5min.
The drop-off ddPCR method of the present invention preferably includes a drop-off ddPCR method for diagnostic or non-diagnostic purposes.
The technical solutions provided by the present invention are described in detail below with reference to the drawings and examples for further illustrating the present invention, but they should not be construed as limiting the scope of the present invention.
Example 1
A drop-off ddPCR kit and a method for quantitatively detecting IDH1 gene mutation comprise the following steps:
1 example of tissue DNA for detecting IDH 1R 132H gene mutation by high throughput sequencing (NGS) is selected, and a using method of the kit is introduced.
The kit combines a liquid drop type digital PCR technology with a Taqman fluorescent probe method, and detects 5 mutations on the No.4 exon of the IDH1 gene, wherein specific mutation sites comprise: R132C, R132G, R H, R132L, R132S.
The kit comprises 2 reagents, wherein the reagent 1 mainly comprises the following components: enzyme, buffer, and enzyme and buffer were purchased from Beijing New Biotechnology Co., ltd., product number 23010, 380. Mu.L/tube; the reagent 2 mainly comprises the following components: a primer and a probe; detecting the sample type: FFPE organization.
The primer is as follows: IDH1 forward primer: 5'-GCCATTATCTGCAAAAATATCCCCC-3', IDH1 reverse primer: 5'-TACAAGTTGGAAATTTCTGGGCCAT-3';
the probe is as follows: drop-off probe: 5'-VIC-TGGGTAAAACCTATCATCATAGGTC-BHQ1-3', reference probe: 5'-FAM-ATGGGGATCAAGTAAGTCATGTTGG-BHQ1-3'.
The specific experimental method comprises the following steps:
1. extraction of tissue DNA: DNA was extracted according to the tissue DNA extraction kit procedure, and the extracted DNA was quantified using Qubit, QIAxcel, to detect fragment size.
2. Digital PCR detection
The PCR reaction system was prepared as shown in Table 1 using the DNA template extracted in step 1, wherein 4 XMaxMix was purchased from Biotechnology Inc. of Beijing as a finished product reagent, and the product number was 23010.
TABLE 1 PCR reaction System
The prepared PCR reaction system was mixed with 10. 10 s, and the mixture was subjected to instantaneous centrifugation.
3. Micro-droplet preparation
The reaction system was prepared by adding 160. Mu.L of the droplet-forming oil and 30. Mu.L of the above-described reaction system, in accordance with the instructions of the micro-droplet-forming kit (kit model 10001 available from Biotechnology Co., ltd. In Beijing).
4. PCR amplification
The resulting 8 rows containing microdroplets were capped and placed on a PCR apparatus for amplification, and the PCR amplification procedure is shown in Table 2.
TABLE 2 PCR amplification procedure
5. Result detection
And (3) placing the amplified chip on a biological reader for detection, and analyzing the data to obtain a final 2D scatter diagram (figure 1) and FAM and VIC related data.
The result shows that: in 30ng of DNA, the FAM copy number was 2469 copies, the VIC copy number was 10264.6 copies, and the mutation frequency was 19.39% as calculated by the formula of mutation frequency=FAM/(FAM+VIC), and positive. It can be seen that the results of the detection using the method of the present invention are consistent with those obtained using high throughput sequencing.
Example 2
The sensitivity test of the kit comprises the following steps:
sensitivity tests were performed using IDH 1-containing mutant plasmid DNA and wild-type plasmid DNA as templates.
Plasmid samples are self-synthesized, and the plasmid construction method comprises the following steps: plasmid vector was prepared by cutting vector pUC57 using double cleavage (Nde I/Sph I); screening NGS to detect a sample containing IDH1 hot spot mutation, designing a primer according to the sequence of a mutation region, and designing a forward primer: 5'-TGAGATGGACGCCTATTTGT-3' (SEQ ID NO. 5), reverse primer: 5'-GTGATGCCACCAACGACCAA-3' (SEQ ID NO. 6); amplifying and enriching the target gene fragment by using a pcr method, and detecting the accuracy of the size of the target gene fragment by using agarose gel electrophoresis; respectively recovering plasmid vector DNA and target gene DNA fragments after electrophoresis, linking the vector and the target gene by using T4 DNA ligase, adding a connection product into competent cells DH5 alpha, standing on ice for 30min, performing heat shock conversion at 42 ℃, adding LB culture medium, shaking for 45-60min by a shaking table at 200rpm and 37 ℃, coating onto a screening plate, culturing overnight at 37 ℃, picking up 5 single colonies, performing enzyme digestion identification, and carrying out first generation sequencing for further verification after identification.
The quantitative result of the IDH1 mutant plasmid is 1495.1 copies, and then the wild type plasmid is used to dilute the IDH1 mutant plasmid to 1%, 0.5%, 0.2%, 0.1%, 0.05%, NC (healthy human blood leukocyte DNA), each sample is repeated 3 times, each group of template DNA is detected according to the detection method in example 1, the IDH1 mutation frequency result is shown in table 3, the 2D scatter diagram of each template is shown in fig. 2-8, and the linear relation between the IDH1 theoretical mutation frequency and the actually detected mutation frequency is shown in fig. 9.
TABLE 3 detection results of template DNA of each group
As shown in FIG. 9, the theoretical mutation frequency has a good linear relationship with the actual mutation frequency, R 2 The kit cannot detect the mutation at a theoretical mutation frequency of 0.05%, but the lowest detection frequency of the kit is 0.1%.
Although the foregoing embodiments have been described in some, but not all, embodiments of the invention, it should be understood that other embodiments may be devised in accordance with the present embodiments without departing from the spirit and scope of the invention.

Claims (10)

1. The probe for detecting IDH1 gene mutation is characterized by comprising a Drop-off probe and a Reference probe, wherein the nucleotide sequence of the Drop-off probe is shown as SEQ ID NO.1, and the nucleotide sequence of the Reference probe is shown as SEQ ID NO. 2; the 5 'end of the Drop-off probe and the Reference probe is marked with a fluorescent group, and the 3' end is marked with a fluorescence quenching group; the Drop-off probe and the Reference probe bear different fluorophores.
2. The probe of claim 1, wherein the Drop-off probe is labeled with a fluorescent group VIC at the 5 'end and a fluorescence quenching group BHQ1 at the 3' end; the Reference probe is marked with a fluorescent group FAM at the 5 'end and a fluorescence quenching group BHQ1 at the 3' end.
3. A primer for detecting IDH1 gene mutation is characterized in that the nucleotide sequence of a forward primer of the primer is shown as SEQ ID NO.3, and the nucleotide sequence of a reverse primer is shown as SEQ ID NO. 4.
4. A drop-off ddPCR kit for quantitatively detecting IDH1 gene mutation, wherein the kit comprises the probe of claim 1 or 2 and a primer for detecting IDH1 gene mutation.
5. The kit according to claim 4, wherein the primer for detecting mutation of IDH1 gene is the primer according to claim 3.
6. The kit of claim 4 or 5, further comprising a dPCR enzyme and a buffer.
7. The kit of claim 4 or 5, further comprising an IDH1 mutant plasmid and an IDH1 wild-type plasmid.
8. Use of the probe of claim 1 or 2, the primer of claim 3 or the kit of any one of claims 4 to 7 for the preparation of a product for detecting IDH1 gene mutation.
9. The use of claim 8, wherein the IDH1 gene mutation comprises one or more of R132C, R132G, R132H, R L and R132S.
10. A drop-off ddPCR method for quantitatively detecting IDH1 gene mutation is characterized by comprising the following steps:
mixing genomic DNA of a sample to be detected, a primer, a probe, dPCR enzyme and a buffer solution to obtain ddPCR reaction mixed solution;
mixing the ddPCR reaction mixed solution with an oil phase, and preparing the obtained mixture by a droplet preparation instrument to generate micro-reaction droplets;
introducing the micro-reaction liquid drops into a chip, performing PCR amplification reaction, collecting signals of the micro-droplets in the chip after the PCR amplification reaction, and calculating to obtain the mutation frequency of the IDH1 gene in the sample to be detected;
the probe comprises the probe of claim 1 or 2.
CN202311722602.3A 2023-12-15 2023-12-15 Probe, kit and drop-off ddPCR method for quantitatively detecting IDH1 gene mutation Pending CN117402975A (en)

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Citations (6)

* Cited by examiner, † Cited by third party
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