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Gene chip for detection of tumor mutation load and its preparation method and device

A technology of gene chip and mutation load, applied in the field of gene chip for tumor mutation load detection and its preparation, can solve the problems of long cycle, high cost, unsuitable for clinical application, etc., to reduce detection cost, save experimental cost, and reduce The effect of sequencing data volume

Active Publication Date: 2019-10-25
裕策医疗器械江苏有限公司
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  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

At present, there is no such mature product in the market, and the whole exome sequencing method is usually used in research to analyze and detect TMB; however, the TMB detection method based on exome sequencing has the defects of high cost and long cycle, and is not suitable for clinical practice application

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  • Gene chip for detection of tumor mutation load and its preparation method and device
  • Gene chip for detection of tumor mutation load and its preparation method and device
  • Gene chip for detection of tumor mutation load and its preparation method and device

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preparation example Construction

[0055] In order to ensure that the chip capture area can truly and accurately reflect the changing trend of tumor mutation load on the whole human genome, the application specifically provides the preparation method of the gene chip of the application, including the design of the chip capture area, as follows: figure 1 shown, including the following steps:

[0056] The step 101 of exon mutation probability statistics includes:

[0057] 1) Count the number of mutated bases on each exon of each gene in the COSMIC database, and divide the number of mutated bases on the exon by the total length of the corresponding exon to obtain the occurrence of the exon The probability of mutating bases, marked as pa;

[0058] Among them, COSMIC database reference S.A.Forbes et al., "COSMIC: Exploring the world’s knowledge of somatic mutations in human cancer," Nucleic Acids Res., vol.43, no.D1, pp.D805–D811, Oct.2015.

[0059] 2) In the ICGC database, the number of mutated bases on each exon...

Embodiment 1

[0086] Traditional tumor mutation burden detection usually uses whole exome sequencing, which has the disadvantages of high cost and long cycle. In order to solve this problem, a targeted capture chip is designed in this example, which only captures specific gene sequences and performs sequencing, which effectively reduces the amount of sequencing data and achieves the purpose of saving costs and shortening the cycle.

[0087] The design process of the target capture chip is:

[0088] 1) According to the mutation information collected in the COSMIC database, count how many bases are mutated in each exon of each gene, divide the total number of mutations by the total length of the exon, and obtain the number of mutated bases in each exon probability.

[0089] 2) According to the sample data collected by the ICGC database (https: / / icgc.org / ), count how many samples are mutated on each exon of each gene, divide the number of mutation samples by the total number of samples, and g...

Embodiment 2

[0102] Traditional tumor genome detection methods usually use single-sample detection of tumors, and studies have found that this method cannot effectively distinguish between somatic mutations and germ cell mutations. This defect has little impact on conventional targeted detection, but has a greater impact on tumor mutation burden detection. In order to solve this problem, this example adopts the method of paired detection, and detects tumor tissue and control samples at the same time, and cooperates with subsequent analysis methods to obtain somatic mutations. Wherein, the control sample is paracancerous tissue or peripheral blood.

[0103] In this example, the sequencing sequence error correction technology is introduced in the experimental method: the current mainstream next-generation sequencing method uses the 150bp Paired End method for sequencing, and generates two 150bp reads. Due to the characteristics of the library construction method, the length of the inserted ...

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Abstract

The invention discloses a gene chip for detecting tumor mutation load, and a preparation method and a device thereof. The gene chip disclosed by the invention contains probes capturing 811 genes. According to the gene chip disclosed by the invention, according to a tumor genome database, 811 chip capture regions are designed; by specific capture sequencing of the 811 chip capture regions, the change trend of the tumor mutation load in a whole human genome can be truly and effectively reflected, and the method is specially suitable for analysis of the tumor mutation load in Chinese people. Thegene chip can replace traditional full exons for sequencing and detecting the tumor mutation load, shrinks the sequencing data size, reduces the detection cost of the tumor mutation load, shortens thedetection cycle, and provides a relatively cheap, fast, highly efficient and accurate solution for clinical detection of the tumor mutation load. The gene chip and a tumor mutation load detection method based on the gene chip have significant clinical guiding significance for immunotherapy medication.

Description

technical field [0001] The present application relates to the field of detection of tumor mutation burden, in particular to a gene chip for detection of tumor mutation burden and its preparation method and device. Background technique [0002] Tumors are diseases caused by mutations in the genome. Immune checkpoint inhibitors have opened up a new era of tumor treatment, but due to the lack of suitable clinical molecular markers, the beneficiary population of PD-1 / PD-L1 drugs cannot be efficiently screened, only 20%-30%. Tumor mutation burden (abbreviated TMB) is an index that reflects the degree of total gene mutation in tumor cells, usually expressed by the total number of tumor somatic mutations contained in each million bases (Mb) of the tumor genome region. Different types of tumors and different groups of people in the same tumor have different TMB levels, and in tumors with relatively high average TMB levels, not all patients have high TMB levels, and there are high T...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6858C12Q1/6886C12M1/34
CPCC12Q1/6858C12Q1/6886C12Q2600/156C12Q2600/166C12Q2535/122C12Q2545/113
Inventor 李淼王佳茜陈超张艳鹏高志博
Owner 裕策医疗器械江苏有限公司
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