CN113862368A - Primer composition and kit related to gene detection of tumor chemotherapy drugs - Google Patents
Primer composition and kit related to gene detection of tumor chemotherapy drugs Download PDFInfo
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Abstract
The invention discloses a tumor chemotherapy drug gene detection primer composition, a kit and a detection method thereof, the kit aims at tumor chemotherapy drug individualized genes and comprises ABCB1, ATIC, CBR3, CDA, DPYD, ERCC1, GSTP1, MTHFR, MTRR, NQO1, SOD2, TP53, UGT1A1, UMPS, XPC and XRCC1, 22 pairs of primers or a combination containing part of the primers, and a forward primer and a reverse primer of each pair of primers comprise an amplification primer pair and other sequences connected with the 5' end of the amplification primer pair. The specific sequences of the forward primer and the reverse primer of each pair of primers are selected from the sequences shown in SEQ ID NO.1-44, and a kit for detecting the individualized genes of the tumor chemotherapeutic drugs is provided. The kit and the specific primer group can quickly, accurately and once detect the individual mutation gene hot spot area of the tumor chemotherapeutic drug, can detect samples such as blood and the like, and can be well used for guiding chemotherapeutic drugs and selecting chemotherapeutic schemes.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to a primer composition and a kit related to gene detection of tumor chemotherapy drugs.
Background
The drug effect has individual differences, and the influencing factors comprise physiological factors, pathological factors, environmental factors and genetic factors, wherein the genetic factors mainly depend on individual gene polymorphism, including single nucleotide polymorphism and copy number polymorphism, and the polymorphism can influence pharmacokinetics and pharmacodynamics through drug metabolic enzyme, drug transport protein, drug receptor, pathogenic gene and the like, so that the individual differences of the drug curative effect and toxicity are caused.
Chemotherapy is a common means for tumor treatment, but chemotherapy patients still have the condition of poor chemotherapy effect or large toxic and side effect, and patients who relapse or transfer after tumor treatment also have the condition that the original chemotherapy scheme is invalid.
Next-Generation Sequencing (NGS), also called second-Generation Sequencing, is a high-throughput detection technique that can sequence hundreds of thousands or even hundreds of millions of DNA molecules at a time, which has been developed in recent years, and is now widely used in the fields of prenatal detection, tumor mutation analysis and medication guidance, pathogen microorganism screening, and the like. The Illumina platform is the most common NGS sequencer in China at present, and has higher market share. Domestic MGI platforms also each have unique advantages, and domestic application rates are also steadily increasing.
Prior to NGS sequencing, it is often necessary to enrich and amplify specific regions of sample DNA, a process known as library construction. The multiplex PCR technology does not need to preprocess the sample, a small amount of sample or a sample degraded to a certain degree can be used, and the multiplex PCR technology is suitable for most clinical conditions; meanwhile, the library building process is simple, can be completed within hours, and has low overall cost. However, the multiplex PCR technology puts higher requirements on the design of an amplification primer pool, and a large amount of primer dimers are easily generated by slight errors, so that target fragments are sharply reduced, or the operation of tube division is forced, thereby weakening the original advantages.
Disclosure of Invention
The invention aims to provide a tumor chemotherapeutic drug individualized gene, which comprises ABCB1, ATIC, CBR3, CDA, DPYD, ERCC1, GSTP1, MTHFR, MTRR, NQO1, SOD2, TP53, UGT1A1, UMPS, XPC and XRCC1, and comprises 22 pairs of primers or a combination comprising a part of primers, wherein a forward primer and a reverse primer of each pair of primers comprise an amplification primer pair and other sequences connected with the 5' end of the amplification primer pair. The structure of each primer in the primer composition of the invention is schematically shown in FIG. 1.
The invention provides a kit for detecting tumor chemotherapeutic drug genes, which comprises specific primers of the tumor chemotherapeutic drug genes, DNA polymerase, PCR buffer solution, dNTP and the like. The composition of the kit is detailed in table 1.
TABLE 1 kit composition
Composition of | Principal Components | Quantity (12) | Volume of |
Amplification reaction solution 1 | DNA polymerase, dNTPs, buffer | 1 tube | 150μL |
Amplification reaction solution 2 | DNA polymerase, dNTPs, buffer | 1 tube | 360μL |
Primer combination | Primer and method for producing the same | 1 tube | 60μL |
Joint A | Aqueous solution containing universal primer | 4 tubes | 12 mu L/tube |
Joint B | Aqueous solution containing universal primer | 3 tube | 16 mu L/tube |
The invention also provides a kit for detecting the individualized genes of the tumor chemotherapy drugs, which comprises at least one pair of two pairs of linkers, wherein the two pairs of linkers respectively correspond to two sequencing platforms, namely Illumina and MGI, and DNA fragments matched with the sequence shown in SEQ ID NO.45 or the sequence shown in SEQ ID NO.46 are contained in the linkers.
The method is simple, is convenient to operate, can complete the construction of the NGS library within hours, and has low overall cost. The invention is helpful to realize the conversion of the reagent from laboratory to clinical application and in-vitro diagnosis reagent, and has good application prospect
Drawings
FIG. 1 is a schematic diagram of the structure of each primer in the primer composition of the present invention.
Detailed Description
The primer composition of the tumor chemotherapeutic drug gene of this example 1 is specifically shown in table 2:
TABLE 2
The kit for detecting the individualized genes of the tumor chemotherapeutic drugs specifically amplifies a plurality of genes related to the tumor chemotherapeutic drugs in a DNA sample of a tumor patient by a multiplex PCR method, and mainly comprises the following steps:
1. sample preparation
The applicable range of the sample comprises samples such as whole blood, plasma, serum and the like. Samples such as whole blood, plasma, serum and the like were extracted from genomic DNA using a Qiagen tissue DNA extraction kit, and the specific procedures were as specified in the kit procedures. Each time, 200. mu.L of whole blood is extracted, and the blood plasma and blood serum are not less than 800. mu.L. The extracted DNA was dissolved in Tris-HCl (10mmol/L, pH 8.0), the mass extracted was measured by UV spectrophotometer and the concentration was determined. The kit recommends that the accounting quantity adopted by each reaction is 20ng-50 ng.
2. Library construction
2.1 first round PCR reaction
Gene-specific PCR reactions were prepared as shown in Table 3 below, and the corresponding DNA samples were added to each tube.
TABLE 3
The PCR reaction was run according to the procedure of Table 4 below.
TABLE 4
2.2 first round PCR product purification
2.2.1 the tubes were removed from the PCR machine and centrifuged quickly to spin the liquid to the bottom of the tube.
2.2.2 adding 1.2 times volume of purified magnetic beads into each tube, shaking and mixing evenly and centrifuging quickly. The mixture was allowed to stand at room temperature for 5 minutes.
2.2.3 transfer each tube to a magnetic rack and stand at room temperature for 5 minutes or until the liquid is clear. The supernatant was carefully aspirated, taking care to avoid hitting the beads.
2.2.4 Add 150. mu.L 70% ethanol per tube wash, incubate for 30 seconds and aspirate the ethanol, taking care to avoid touching the beads. The washing was repeated once.
2.2.5 cover the tube, place each tube on the magnetic rack after rapid centrifugation, carefully suck the remaining ethanol in the tube. 2.2.6 at room temperature for 2-3 minutes until the beads are dry. Add 64. mu.L of ribozyme-free water to each tube, cover the tube, shake and mix well and centrifuge quickly.
2.2.7 transfer each tube to a magnetic rack and allow to stand at room temperature for 5 minutes. Transfer supernatant to a new tube.
2.3 second round PCR reaction
The adaptor-added PCR reaction solution was prepared as shown in Table 5 below.
TABLE 5
The PCR reaction was run according to the procedure of Table 6 below.
TABLE 6
2.4 library purification and quality control
2.4.1 the tubes were removed from the PCR machine and centrifuged quickly to spin the liquid to the bottom of the tube.
2.4.2 adding 1 time volume of purified magnetic beads into each tube, shaking and mixing evenly and quickly centrifuging. The mixture was allowed to stand at room temperature for 5 minutes.
2.4.3 transfer each tube to a magnetic rack and stand at room temperature for 5 minutes or until the liquid is clear. The supernatant was carefully aspirated, taking care to avoid hitting the beads.
2.4.4 Add 150. mu.L 70% ethanol per tube wash, incubate for 30 seconds and aspirate the ethanol, taking care to avoid touching the beads. The washing was repeated once.
2.4.5 cover the tube, place each tube on the magnetic rack after rapid centrifugation, carefully suck the remaining ethanol in the tube. 2.4.6 at room temperature for 2-3 minutes until the beads are dry. Add 32. mu.L of ribozyme-free water to each tube, cover the tube, shake and mix well and centrifuge quickly.
2.4.7 the tubes were transferred to a magnetic rack and allowed to stand at room temperature for 5 minutes. Transfer supernatant to a new tube.
2.4.8 quantification of the library using Qubit; the library fragments were analyzed for size and purity using Qseq 100.
3. Sequencing on machine
3.1 Each library was diluted to 5nM in aliquots and mixed in small aliquots.
3.2 denaturation by addition of an equal volume of 0.2N NaOH and dilution to 15pM with HT1 solution.
3.3 Take 594. mu.L of the 15pM mixed library and add 6. mu.L of 12.5pM PhiX library control.
3.4 add 600 μ L of the above sample to the sequencing kit provided by the invention, load into illumina miseq sequencer for sequencing.
The above examples are merely illustrative for clearly illustrating the present invention and are not intended to limit the embodiments of the present invention. The scientific and technical terms used in this patent have the same meaning as understood by one of ordinary skill in the art.
Sequence listing
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agtctgactc ccctccagat tc 22
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Claims (9)
1. A tumor chemotherapy drug gene detection primer composition is characterized in that: the primer set comprises 22 pairs of primers or a combination containing a part of the primers, wherein a forward primer and a reverse primer of each pair of primers comprise an amplification primer pair and other sequences connected with the 5' ends of the amplification primer pair. The specific sequence of the forward primer and the reverse primer of each pair of primers is selected from the sequences shown in SEQ ID NO. 1-44.
2. The primer composition for gene detection of tumor chemotherapeutic drugs according to claim 1, wherein: the specific sequence of the forward primer and the reverse primer of each pair of primers is 18-25 base sequences in the sequence.
3. The primer composition for gene detection of tumor chemotherapeutic drugs according to claim 1, wherein: the forward primer of the amplification primer pair comprises 20-35 base sequences in the sequence shown in SEQ ID NO. 45.
4. The primer composition for gene detection of tumor chemotherapeutic drugs according to claim 1, wherein: the reverse primer of the amplification primer pair comprises 20-35 base sequences in the sequence shown in SEQ ID NO. 46.
5. A kit for gene detection of tumor chemotherapy drugs is characterized in that: comprising the primer composition of any one of claims 1-4.
6. The kit for gene detection of tumor chemotherapeutic drugs according to claim 5, wherein: including DNA polymerase, PCR buffer, dNTP and ultrapure water.
7. The kit for gene detection of tumor chemotherapeutic drugs according to claim 5, wherein: comprises at least one of two pairs of adaptors corresponding to the two sequencing platforms Illumina and MGI respectively, wherein the adaptor internally contains a DNA fragment matched with the sequence of any one of claims 3 or 4.
8. The use of the kit according to claim 5 or 6 for the genetic testing of tumor chemotherapeutic drugs, wherein: the kit is suitable for the molecular detection of peripheral blood DNA.
9. Use of the kit according to claim 5 or 6 for the detection of genes related to chemotherapeutic drugs for tumors based on the NGS method.
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