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Gene chip for detecting tumor mutation load, and preparation method and device thereof

A gene chip and mutation load technology, which is applied in the field of gene chip and its preparation for tumor mutation load detection, can solve the problems of unsuitability for clinical application, high cost, and long cycle, so as to reduce the amount of sequencing data, reduce detection costs, The effect of saving experiment cost

Active Publication Date: 2018-12-18
裕策医疗器械江苏有限公司
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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 detecting tumor mutation load, and preparation method and device thereof
  • Gene chip for detecting tumor mutation load, and preparation method and device thereof
  • Gene chip for detecting tumor mutation load, and preparation method and device thereof

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preparation example Construction

[0055] In order to ensure that the capture area of ​​the chip can truly and accurately reflect the changing trend of tumor mutation burden on the whole human genome, the present application especially provides the preparation method of the gene chip of the present application, including the design of the capture area of ​​the chip, specifically 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 in each exon of each gene in the COSMIC database, and divide the number of mutated bases in the exon by the total length of the corresponding exon, that is, to obtain the occurrence of the exon Probability of mutated bases, marked as pa;

[0058] Among them, the COSMIC database reference S.A.Forbesetal., "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) Count the...

Embodiment 1

[0086] Traditional tumor mutation burden detection usually adopts whole exome sequencing, which has the disadvantages of high cost and long cycle. 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 this 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 ICGC database (https: / / icgc.org / ), count how many samples are mutated on each exon of each gene, and divide the number of mutant samples by the total number of samples to get each ...

Embodiment 2

[0102] Traditional tumor genome detection methods usually use tumor single-sample detection, and studies have found that this method cannot effectively distinguish somatic mutations from germline mutations. This defect has little impact on conventional targeted detection, but has a greater impact on tumor mutational burden detection. In order to solve this problem, the paired detection method was adopted in this case, and the tumor tissue and control samples were simultaneously detected, and the somatic mutation was obtained with the subsequent analysis method. Among them, the control samples were adjacent tissues or peripheral blood.

[0103] This example introduces the sequencing sequence error correction technology in the experimental method: the current mainstream next-generation sequencing method uses the 150bp Paired End method to sequence, resulting in two 150bp reads. Due to the characteristics of the library construction method, the length of the inserted fragment is...

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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 tumor mutation load detection, in particular to a gene chip for tumor mutation load detection and a preparation method and device thereof. 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 mutational burden (abbreviated TMB) is an indicator of the total genetic mutation level in tumor cells, usually expressed as the total number of tumor somatic mutations contained in each megabase (Mb) of tumor genomic region. Different types of tumors and different populations of 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 TMB levels in different ...

Claims

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Application Information

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IPC IPC(8): C12Q1/6858C12Q1/6886C12M1/34
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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