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A method, device and storage medium for detecting tumor mutation load

A technology of mutation load and detection method, applied in the directions of proteomics, genomics, instruments, etc., can solve the problems of long cycle, inability to effectively distinguish somatic mutation from germ cell mutation, and unsuitable for clinical application, etc.

Active Publication Date: 2020-01-14
裕策医疗器械江苏有限公司
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  • Claims
  • Application Information

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Problems solved by technology

In terms of research, the method of whole exome sequencing is usually used 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 application
Moreover, 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; big impact

Method used

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  • A method, device and storage medium for detecting tumor mutation load
  • A method, device and storage medium for detecting tumor mutation load
  • A method, device and storage medium for detecting tumor mutation load

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preparation example Construction

[0165] In order to ensure that the capture area of ​​the gene chip can truly and accurately reflect the changing trend of tumor mutation load on the whole human genome, this application specifically provides a preparation method of the gene chip, including the design of the capture area of ​​the chip, which specifically includes the following steps:

[0166] The statistical steps of exon mutation probability include:

[0167] 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;

[0168] 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.

[0169] 2) In the ICGC database, the number of mutated bases on each exon of each ge...

Embodiment 1

[0185] 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.

[0186] The design process of the target capture chip is:

[0187] 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.

[0188]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 ge...

Embodiment 2

[0201] 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.

[0202] 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 insert fr...

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Abstract

A tumor mutation load detection method and device and a storage medium are disclosed. The tumor mutation load detection method of the present invention comprises a logoff data processing step, a datafiltering and quality control step, a sequence alignment and quality control step, a somatic mutation detection and filtering step, a mutation result annotation step, a tumor purity prediction step, asample pairing quality control step and a tumor mutation load prediction step. The detection method of the present application can distinguish somatic mutations, but also filter out false positive mutations in the case of fully considering the clonality and subclonality of mutations, so that the resulting TMB value can more accurately reflect the total degree of gene mutation in tumor cells. Thetumor mutation load detection method of the present application has significant clinical guiding significance for immunotherapy medication, and the tumor mutation load detection method of the presentapplication specifically annotates the mutation frequency of the Chinese population, laying a foundation for subsequent medication guidance applicable to the Chinese population.

Description

technical field [0001] The present application relates to the field of tumor mutation load detection, in particular to a tumor mutation load detection method, device and storage medium. 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 as 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 TMB levels in different tu...

Claims

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Application Information

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IPC IPC(8): G16B20/50G16B20/20
Inventor 李淼王佳茜陈龙昀杨洁高志博
Owner 裕策医疗器械江苏有限公司
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