CN112921097A - Gene detection kit for fibroblast/myofibroblast tumors and application thereof - Google Patents
Gene detection kit for fibroblast/myofibroblast tumors and application thereof Download PDFInfo
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- CN112921097A CN112921097A CN202110425768.3A CN202110425768A CN112921097A CN 112921097 A CN112921097 A CN 112921097A CN 202110425768 A CN202110425768 A CN 202110425768A CN 112921097 A CN112921097 A CN 112921097A
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Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/118—Prognosis of disease development
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
Abstract
The invention discloses a gene detection kit for fibroblast/myofibroblast tumors and application thereof, wherein the gene detection kit comprises a gene for detection and a corresponding primer. The invention arranges and summarizes the known genes for detecting tumors derived from the fibroblasts and the myofibroblasts, the kit comprises the genes for detecting the tumors derived from the fibroblasts and the myofibroblasts comprehensively, and the second-generation DNA sequencing detection is utilized, so that the number of gene detection or the number of detection sites of a patient can be reduced, the cost is saved, and the use is convenient.
Description
Technical Field
The invention relates to the technical field of tumor detection, in particular to a gene detection kit for fibroblast/myofibroblast tumors and application thereof.
Background
Some tumors of fibroblast and myofibroblast origin can only be diagnosed morphologically as either a fibroblast or myofibroblast tumor, but cannot be diagnosed next. Immunohistochemistry is very sensitive but lacks specificity. Gene detection is often an important tool in determining the criteria for disease diagnosis and the direction of progression. High throughput or whole exon sequencing, although it is of a wide sequencing range, is expensive and difficult to determine mutations in genes. Therefore, the second generation sequencing shows obvious advantages.
However, there is no relevant gene detection kit for second-generation sequencing aiming at tumors derived from fibroblasts or myofibroblasts. Furthermore, with the progress of research, some new genes are gradually discovered, and the existing disease diagnosis cannot be satisfied by the original second-generation sequencing technology, so that a new gene detection kit is urgently needed.
Disclosure of Invention
The invention aims to provide a gene detection kit for fibroblast/myofibroblast tumors and application thereof, wherein the kit comprises a plurality of genes of tumors derived from fibroblast and myofibroblast, and can reduce the number of gene detection or detection sites of patients by using second-generation DNA sequencing detection, thereby saving cost and being convenient to use.
The invention is realized by the following technical scheme:
a gene detection kit for fibro/myofibroblast tumors comprises the following genes:
YWHAE-ROS, USP, TRIM-RET, TPR-NTRK, TPM-ALK, TPM-NTRK, TPM-ALK, TP, TFG-ROS, TFG-ALK, TERT, STRN-NTRK, SEC 31L-ALK, SEC 31-USP, RRBP-ALK, RB, RANBP-ALK, PPP 6R-USP, PPFIBP-ALK, NPM-ALK, NCOA-RET, MYH-USP, MDM, KIF 5-RET, JAK, IGF, HNRNPA-ALK, GSTP, GAB-ABL, FUS-CREB3L, FN-EGF, FGFR, FCHSD-ALK, EWSR-CREB 3L, ETV-PDGFRB, ETV-NTRK, EML-ALK, EMILIN-PDGFD, EGFR, DCNNFD-CREB, CTA 6-CLT, CATV-COLTC-COL, CCTC-ALK, CCTC-COL, CCTP-COLD, BCR-CREB, BCR-C, APC, ANTXR2, and AHRR-NCOA 2;
also comprises a primer pair for detecting the gene, and the corresponding primer sequence is shown as SEQ ID No.1-SEQ ID No. 108.
The genes in the kit of the invention are all existing genes, and can be directly used for literature inquiry through enumerated gene names.
The inventive concept of the present application resides in:
the gene that can be used for detecting fibroblast and myofibroblast source tumour that knows at present is put in order and is concluded, and this kit has included comparatively comprehensive gene that is used for detecting fibroblast and myofibroblast source tumour, utilizes the next generation DNA sequencing to detect, can reduce patient's gene detection figure or detect the reduction of site number, practices thrift the cost, facilitates the use.
The application reasonably designs corresponding primers for second-generation DNA sequencing aiming at each gene, and can better realize the detection of fibroblast and myofibroblast derived tumors. In the second-generation DNA sequencing, different primer pairs have certain influence on the test result, the same gene can be provided with the primer pairs, and in the application, the primer pair with better effect is selected through experiments.
The gene detection kit is applied to next generation gene sequencing.
The gene detection kit is applied to the second generation gene sequencing of tumors derived from fibroblasts and myofibroblasts.
Specifically, the detection source corresponding to each gene can be queried by literature, for example: USP6 can be used to detect tenosynovitis and myositis ossificans, pseudofibromatosis of the toes and fasciitis nodosa; CTNNB1 can be used for detecting ligament-like fibroma; RB1 can be used for cell-rich angiofibromas, myofibroblastoma, and myxofibrosarcoma; APC can be used for Gardner fibroids; STRN3-NTRK3 for detecting adult fibrosarcoma; the specific query is shown in table 1:
TABLE 1
The kit adopts the second-generation sequencing technology when in application, the second-generation sequencing technology is the prior art, and the specific sequencing process is as follows:
tissue sections 4um thick were excised from paraffin samples, DNA was extracted according to the protocol of the QIAamp DNA kit, and sequence and copy number variations were detected by cancer genomic analysis. The entire exon sequences and selected intron sequences were captured using the solution phase Agilent SureSelect hybridization capture kit (Agilent Technologies, inc., Santa Clara, CA) and massively parallel sequenced using an Illumina HiSeq 2500 sequencer (Illumina, inc., San Diego, CA). Mutation calls were performed using MUTECT and GATK software (Broad Institute, Cambridge, MA, USA), and copy number changes were assessed using VISCCAPcopy (Dana Farber Cancer Institute, Boston, MA, USA). Structural variations including large insertions/deletions and rearrangements were detected using the brekmer and confirmed by manual inspection at INTEGRATED GENOME VIEWER.
Compared with the prior art, the invention has the following advantages and beneficial effects:
1. the invention arranges and summarizes the known genes for detecting tumors derived from the fibroblasts and the myofibroblasts at present, combines the rearranged gene USP6, comprises more comprehensive genes for detecting the tumors derived from the fibroblasts and the myofibroblasts, and can reduce the number of gene detections or the number of detection sites of a patient by using second-generation DNA sequencing detection, thereby saving the cost and being convenient to use.
2. The kit is suitable for the second generation sequencing of tumors from which fibroblasts or myofibroblasts are considered morphologically to search mutant genes for diagnosis, prognosis or related important driver genes.
Detailed Description
In order to make the objects, technical solutions and advantages of the present invention more apparent, the present invention is further described in detail below with reference to examples, and the exemplary embodiments and descriptions thereof are only used for explaining the present invention and are not used as limitations of the present invention.
Example (b):
a gene detection kit for fibro/myofibroblast tumors comprises the following genes:
YWHAE-ROS, USP, TRIM-RET, TPR-NTRK, TPM-ALK, TPM-NTRK, TPM-ALK, TP, TFG-ROS, TFG-ALK, TERT, STRN-NTRK, SEC 31L-ALK, SEC 31-USP, RRBP-ALK, RB, RANBP-ALK, PPP 6R-USP, PPFIBP-ALK, NPM-ALK, NCOA-RET, MYH-USP, MDM, KIF 5-RET, JAK, IGF, HNRNPA-ALK, GSTP, GAB-ABL, FUS-CREB3L, FN-EGF, FGFR, FCHSD-ALK, EWSR-CREB 3L, ETV-PDGFRB, ETV-NTRK, EML-ALK, EMILIN-PDGFD, EGFR, DCNNFD-CREB, CTA 6-CLT, CATV-COLTC-COL, CCTC-ALK, CCTC-COL, CCTP-COLD, BCR-CREB, BCR-C, APC, ANTXR2, and AHRR-NCOA 2;
also comprises a primer pair for detecting the gene, and the corresponding primer sequence is shown as SEQ ID No.1-SEQ ID No. 108.
Primers for each gene are shown in table 2:
TABLE 2
The above-mentioned embodiments are intended to illustrate the objects, technical solutions and advantages of the present invention in further detail, and it should be understood that the above-mentioned embodiments are merely exemplary embodiments of the present invention, and are not intended to limit the scope of the present invention, and any modifications, equivalent substitutions, improvements and the like made within the spirit and principle of the present invention should be included in the scope of the present invention.
Sequence listing
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<213> Artificial sequence 74 (Artificial sequence)
<400> 74
ccccaacagg ttgaccacgt tcag 24
<210> 75
<211> 25
<212> DNA
<213> Artificial sequence 75 (Artificial sequence)
<400> 75
cttacatgaa ccacatcatg gtctc 25
<210> 76
<211> 23
<212> DNA
<213> Artificial sequence 76 (Artificial sequence)
<400> 76
acagccacaa gcatcttgtc ctt 23
<210> 77
<211> 20
<212> DNA
<213> Artificial sequence 77 (Artificial sequence)
<400> 77
tgatgttttg aggcgtcttg 20
<210> 78
<211> 20
<212> DNA
<213> Artificial sequence 78 (Artificial sequence)
<400> 78
acggaagtac tgggggttct 20
<210> 79
<211> 21
<212> DNA
<213> Artificial sequence 79 (Artificial sequence)
<400> 79
ctgcagacaa gcataaagat g 21
<210> 80
<211> 19
<212> DNA
<213> Artificial sequence 80 (Artificial sequence)
<400> 80
gcttgctcag cttgtactc 19
<210> 81
<211> 21
<212> DNA
<213> Artificial sequence 81 (Artificial sequence)
<400> 81
gccacgtctt ccagatttct a 21
<210> 82
<211> 21
<212> DNA
<213> Artificial sequence 82 (Artificial sequence)
<400> 82
cagttccaca gccacaattt c 21
<210> 83
<211> 20
<212> DNA
<213> Artificial sequence 83 (Artificial sequence)
<400> 83
actgacaaac cagcaggaag 20
<210> 84
<211> 18
<212> DNA
<213> Artificial sequence 84 (Artificial sequence)
<400> 84
agcgtcttca cagccact 18
<210> 85
<211> 20
<212> DNA
<213> Artificial sequence 85 (Artificial sequence)
<400> 85
atggccatgg aaccagacag 20
<210> 86
<211> 21
<212> DNA
<213> Artificial sequence 86 (Artificial sequence)
<400> 86
tgggaggtat ccacatcctc t 21
<210> 87
<211> 21
<212> DNA
<213> Artificial sequence 87 (Artificial sequence)
<400> 87
cagcaaggtc agcttctagt t 21
<210> 88
<211> 21
<212> DNA
<213> Artificial sequence 88 (Artificial sequence)
<400> 88
cagttccaca gccacaattt c 21
<210> 89
<211> 19
<212> DNA
<213> Artificial sequence 89 (Artificial sequence)
<400> 89
tcgagggcca agacgaaga 19
<210> 90
<211> 21
<212> DNA
<213> Artificial sequence 90 (Artificial sequence)
<400> 90
agtatgtcct tccgctcctg t 21
<210> 91
<211> 29
<212> DNA
<213> Artificial sequence 91 (Artificial sequence)
<400> 91
gagtgctttg gagcttgtct gtttacctg 29
<210> 92
<211> 22
<212> DNA
<213> Artificial sequence 92 (Artificial sequence)
<400> 92
gcttgggtcg ttgggcattc cg 22
<210> 93
<211> 20
<212> DNA
<213> Artificial sequence 93 (Artificial sequence)
<400> 93
aatcgcctct ggaaaaggat 20
<210> 94
<211> 20
<212> DNA
<213> Artificial sequence 94 (Artificial sequence)
<400> 94
ccttccatcg gatctcgtaa 20
<210> 95
<211> 20
<212> DNA
<213> Artificial sequence 95 (Artificial sequence)
<400> 95
cggaagctgc cagagaactt 20
<210> 96
<211> 20
<212> DNA
<213> Artificial sequence 96 (Artificial sequence)
<400> 96
tcgatggtgt tccgtgaagg 20
<210> 97
<211> 20
<212> DNA
<213> Artificial sequence 97 (Artificial sequence)
<400> 97
ctggagaaca tcgccctgta 20
<210> 98
<211> 23
<212> DNA
<213> Artificial sequence 98 (Artificial sequence)
<400> 98
agcacacttc aggcagcgtc ttc 23
<210> 99
<211> 25
<212> DNA
<213> Artificial sequence 99 (Artificial sequence)
<400> 99
tttcctttac ttactacacc tcaga 25
<210> 100
<211> 23
<212> DNA
<213> Artificial sequence 100 (Artificial sequence)
<400> 100
ccatccacaa aatggatcca gac 23
<210> 101
<211> 20
<212> DNA
<213> Artificial sequence 101 (Artificial sequence)
<400> 101
cgctcgccct gaacccagtg 20
<210> 102
<211> 23
<212> DNA
<213> Artificial sequence 102 (Artificial sequence)
<400> 102
tgatgatcag ggcttccatg agg 23
<210> 103
<211> 22
<212> DNA
<213> Artificial sequence 103 (Artificial sequence)
<400> 103
cctcatccag cttttacatg gc 22
<210> 104
<211> 19
<212> DNA
<213> Artificial sequence 104 (Artificial sequence)
<400> 104
gcccgagcct ctttactgc 19
<210> 105
<211> 33
<212> DNA
<213> Artificial sequence 105 (Artificial sequence)
<400> 105
cgagctctgc cttatagcta tgtcagatca cag 33
<210> 106
<211> 35
<212> DNA
<213> Artificial sequence 106 (Artificial sequence)
<400> 106
ccgctcgagt aaggcacact gtgatagagc acttg 35
<210> 107
<211> 23
<212> DNA
<213> Artificial sequence 107 (Artificial sequence)
<400> 107
tgtgtccagg gcactttcag gaa 23
<210> 108
<211> 23
<212> DNA
<213> Artificial sequence 108 (Artificial sequence)
<400> 108
tcactcggag actcagctgc agg 23
Claims (3)
1. A gene detection kit for a fibroblast/myofibroblast tumor is characterized by comprising the following genes:
YWHAE-ROS, USP, TRIM-RET, TPR-NTRK, TPM-ALK, TPM-NTRK, TPM-ALK, TP, TFG-ROS, TFG-ALK, TERT, STRN-NTRK, SEC 31L-ALK, SEC 31-USP, RRBP-ALK, RB, RANBP-ALK, PPP 6R-USP, PPFIBP-ALK, NPM-ALK, NCOA-RET, MYH-USP, MDM, KIF 5-RET, JAK, IGF, HNRNPA-ALK, GSTP, GAB-ABL, FUS-CREB3L, FN-EGF, FGFR, FCHSD-ALK, EWSR-CREB 3L, ETV-PDGFRB, ETV-NTRK, EML-ALK, EMILIN-PDGFD, EGFR, DCNNFD-CREB, CTA 6-CLT, CATV-COLTC-COL, CCTC-ALK, CCTC-COL, CCTP-COLD, BCR-CREB, BCR-C, APC, ANTXR2, and AHRR-NCOA 2;
also comprises a primer pair for detecting the gene, and the corresponding primer sequence is shown as SEQ ID No.1-SEQ ID No. 108.
2. The use of the gene detection kit of claim 1 in next-generation gene sequencing.
3. The use of the gene detection kit of claim 1 in the second generation gene sequencing of tumors derived from fibroblasts and myofibroblasts.
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|---|---|---|---|
| CN202110425768.3A CN112921097A (en) | 2021-04-20 | 2021-04-20 | Gene detection kit for fibroblast/myofibroblast tumors and application thereof |
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN114317741A (en) * | 2021-11-24 | 2022-04-12 | 上海桐树生物科技有限公司 | Soft tissue sarcoma gene detection kit and system |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20060147911A1 (en) * | 2002-04-17 | 2006-07-06 | Brandt Burkhard H | Method for characterizing primary tumors |
| WO2015075196A1 (en) * | 2013-11-21 | 2015-05-28 | Assistance Publique - Hopitaux De Paris | Method for detecting chromosomal rearrangements |
| US20180073083A1 (en) * | 2015-03-12 | 2018-03-15 | Agency For Science, Technology And Research | A multigene assay |
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2021
- 2021-04-20 CN CN202110425768.3A patent/CN112921097A/en active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20060147911A1 (en) * | 2002-04-17 | 2006-07-06 | Brandt Burkhard H | Method for characterizing primary tumors |
| WO2015075196A1 (en) * | 2013-11-21 | 2015-05-28 | Assistance Publique - Hopitaux De Paris | Method for detecting chromosomal rearrangements |
| US20180073083A1 (en) * | 2015-03-12 | 2018-03-15 | Agency For Science, Technology And Research | A multigene assay |
Non-Patent Citations (7)
Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN114317741A (en) * | 2021-11-24 | 2022-04-12 | 上海桐树生物科技有限公司 | Soft tissue sarcoma gene detection kit and system |
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