Application of gene combination in preparation of products for graded detection of human tumor homologous recombination defect, tumor mutation load and microsatellite instability

A technology of homologous recombination and mutation load, which is applied in the determination/inspection of microorganisms, biochemical equipment and methods, etc., can solve the problems of high cost and huge medical expenses, achieve cost saving, improve sequencing depth and accuracy, and popularize wide range of effects

Pending Publication Date: 2022-08-05
PEKING UNIV FIRST HOSPITAL
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Although the traditional detection methods of homologous recombination deficiency (HRD), tumor mutation burden (TMB) and microsatellite instability (MSI) are reliable, they have the following obvious defects when detecting

Method used

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  • Application of gene combination in preparation of products for graded detection of human tumor homologous recombination defect, tumor mutation load and microsatellite instability
  • Application of gene combination in preparation of products for graded detection of human tumor homologous recombination defect, tumor mutation load and microsatellite instability
  • Application of gene combination in preparation of products for graded detection of human tumor homologous recombination defect, tumor mutation load and microsatellite instability

Examples

Experimental program
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Effect test

Embodiment 1

[0041] Example 1 Gene panel (Panel) for human tumor homologous recombination deficiency (HRD), tumor mutational burden (TMB) and microsatellite instability (MSI) grading

[0042] The inventors mainly used the exome sequencing high-throughput database of Peking University First Hospital patients to screen, and confirmed a method for human tumor homologous recombination deficiency (HRD), tumor mutational burden (TMB) and microsatellite instability. (MSI) graded gene panel (panel), the gene panel includes gene set A and gene fragment set B;

[0043] The gene set A includes: ASAH1, ASXL1, BCOR, BRAF, CALML6, CCDC136, CIDEC, COX18, CSF1R, CYP3A5, DEK, DNMT3A, EGR1, FAM71E2, FGFR1, FKBP7, FLT1, FLT3, FLT4, GNAQ, GLIS1, IDH2, IFITM3, IMMT, KDR, KIT, KMT2A, KNOP1, KRT76, KRT9, KRTAP10-10, KRTAP10-8, MAF, MECOM, MFRP, MLLT3, MNS1, MRTFA, MTOR, MYH11, NF1, NUP214, PDGFRA, PDGFRB, PML, PRB2, PROSER3, RAF1, RARA, RBM15, RET, REXO1, RPN1, RUNX1T1, SCYL1, SLC16A6, SRC, STAG2, TCEAL5, TET2,...

Embodiment 2

[0051] Example 2 A method for human pancancer homologous recombination deficiency (HRD), tumor mutational burden (TMB) and microsatellite instability (MSI) grading and prediction

[0052] This example provides a method for the hierarchical detection of homologous recombination deficiency, tumor mutational burden and microsatellite instability in human tumors, including using the gene panel in Example 1 to perform human pancancer (Pancancer) ) Homologous recombination deficiency (HRD), tumor mutational burden (TMB) and microsatellite instability (MSI) grading and prediction, the specific steps are as follows:

[0053] (1) Take pan-cancer (here pan-cancer is defined as all cancer types in the TCGA pan-cancer data, including adrenal cancer, urothelial cancer, breast cancer, cervical cancer, bile duct cancer, colon cancer, lymphoma, esophageal cancer, Plasmoblastoma, head and neck squamous cell carcinoma, renal chromophobe carcinoma, renal clear cell carcinoma, renal papillary cel...

Embodiment 3

[0057] As an alternative embodiment, in the present invention, the genes in the gene panel (panel) in Example 1 are allowed to be selected and recombined to form a new gene panel, and the criterion is to select from the gene set A gene, then at least one of the genes has a gene mutation or copy number variation, indicating that the pan-cancer patient is a high-grade group, or a gene segment selected from the gene segment set B, then at least one region of the gene copy number increases , indicating that the pan-cancer patients are a high-grade group; on the contrary, there is no gene mutation or copy number variation in the genes selected in gene set A, and there is no copy number increase in the selected fragments in gene fragment set B, The pan-cancer patients were in the low-grade group. EXPERIMENTAL EXAMPLE 1 Gene combinations and detection methods for human tumor homologous recombination deficiency (HRD), tumor mutational burden (TMB) and microsatellite instability (MSI) ...

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Abstract

The invention relates to the field of grading detection of tumors, in particular to application of a gene combination to preparation of products for grading detection of human tumor homologous recombination defects, tumor mutation loads and microsatellite instability, and the gene combination is composed of a gene set A and a gene fragment set B, the gene combination is obtained from actual high-throughput sequencing data of a first hospital of Beijing University through specific pairing clustering analysis, the data from the real world has higher reliability and credibility, and homologous recombination defect, tumor mutation load and microsatellite instability grading and prediction can be accurately carried out on the pan cancer.

Description

technical field [0001] The invention relates to the field of tumor grading detection, in particular to the use of a gene combination to prepare a grading detection product of human tumor homologous recombination defect, tumor mutation load and microsatellite instability. Background technique [0002] Homologous recombination deficiency (HRD), Tumor Mutation Burden (TMB), and Microsatellite Instability (MSI) are important factors commonly used in clinical immunotherapy for malignant tumors and the efficacy of PARP inhibitors. index. Usually, different sequencing methods are needed to obtain complete information for the above three types of indicators. Usually, for homologous recombination defect (HRD) and microsatellite instability (MSI), it is necessary to design a special sequencing panel for targeted sequencing of genes in specific regions, and finally calculate the final HRD score and MSI score to judge HRD and MSI; usually for tumor mutational burden (TMB), whole-exome...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886C12Q1/6869
CPCC12Q1/6886C12Q1/6869C12Q2600/112C12Q2600/156C12Q2600/158C12Q2535/122
Inventor 熊耕砚周利群
Owner PEKING UNIV FIRST HOSPITAL
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