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Method and device for detecting tmb

A technology of sequencing data and mutation sites, applied in genomics, instrumentation, sequence analysis, etc., can solve problems such as inaccurate TMB detection, and achieve the effect of improving accuracy and stability

Active Publication Date: 2021-07-30
北京橡鑫生物科技有限公司 +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0005] The main purpose of the present invention is to provide a method and device for detecting TMB, to solve the problem of inaccurate detection of TMB in the prior art

Method used

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  • Method and device for detecting tmb

Examples

Experimental program
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Embodiment 1

[0052] The present application provides an embodiment of a method for detecting TMB.

[0053] figure 1 is a flow chart of an optional method for detecting TMB according to an embodiment of the present invention, such as figure 1 As shown, the method includes:

[0054] Step S101, using the sequencing data of paired white blood cells to remove the germline mutation sites in the sequencing data of the sample to be tested to obtain a set of candidate somatic mutation sites;

[0055] Step S102, filtering the false positive somatic mutation sites in the set of candidate somatic mutation sites to obtain the set of somatic mutation sites to be tested, the false positive somatic mutation sites include at least one of the following: mutation sites caused by oxidative damage , the mutation site caused by background noise;

[0056] Step S103, dividing the number of mutation loads in the concentration of somatic mutation sites to be detected by all the lengths of the sequencing data in ...

Embodiment 2

[0084] Taking a clinical sample as an example, obtain the patient's tissue sample and its corresponding plasma sample, extract the DNA and build the database, and use the illumina sequencing platform to obtain the off-machine data sampA.R1.fastq.gz, sampA.R2 of the tissue respectively. fastq.gz; and its white blood cell data are sampB.R1.fastq.gz, sampB.R2.fastq.gz; after bwa comparison, marker duplication and base quality correction, sampA.final.bam and sampB are obtained. final. bam. Use sampA.final.bam and sampB.final.bam to detect samples according to the pairing mode of mutect2, and obtain sampA.result.vcf. Use sampA.final.bam to detect according to the non-pairing mode of mutect2, and get sampA.resultWithoutSampB.vcf. According to the filter module and calculation module described in the patent, the subsequent filtering and calculation of sampA.resultvcf is performed, and the final TMB value is 14.7; if the existing method is used to detect the module, the pairing mode ...

Embodiment 3

[0090] The present application also provides an embodiment of a device for detecting TMB.

[0091] image 3 is a schematic diagram of an optional device for detecting TMB according to an embodiment of the present invention, such as image 3 As shown, the device includes a detection module 10, a filtering module 20, and a TMB calculation module 30. The detection module 10 is used to remove germline mutation sites in the sequencing data of the sample to be tested by using the sequencing data of paired white blood cells to obtain candidate somatic cells. Mutation site set; filtering module 20, used to filter false positive somatic mutation sites in the set of candidate somatic mutation sites to obtain a set of somatic mutation sites to be tested. False positive somatic mutation sites include at least one of the following : mutation sites caused by oxidative damage, mutation sites caused by background noise; TMB calculation module 30, used to divide the number of load mutations i...

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Abstract

The invention provides a method and device for detecting TMB. The method comprises: using the sequencing data of paired white blood cells to remove the germline mutation sites in the sequencing data of the sample to be tested to obtain a set of candidate somatic mutation sites; filtering false positive somatic mutation sites in the set of candidate somatic mutation sites to obtain The set of somatic mutation sites to be detected, the false positive somatic mutation sites include at least one of the following: mutation sites caused by oxidative damage, mutation sites caused by background noise; load mutations that concentrate the somatic mutation sites to be detected The number is divided by all the lengths of the sequencing data in the exon region to obtain the TMB. The accuracy and stability of TMB are improved by making full use of paired leukocytes, background noise mutation frequency distribution database, and oxidative damage to remove false positive somatic mutations.

Description

technical field [0001] The invention relates to the field of gene sequencing data analysis, in particular to a method and device for detecting TMB. Background technique [0002] Tumor mutation burden (Tumor Mutation Burden, TMB) is an indicator that reflects the totality of tumor cells, usually expressed by the total number of tumor somatic mutations contained in each million bases (Mb) of the tumor genome region. Tumors with high levels of TMB represent more mutations in tumor cells, which further indicates that the number of tumor neoantigens (Neoantigen) in tumor cells that can be recognized by the immune system may be more, thereby helping immune cells to produce more effective tumor cells. lethal effect. [0003] The currently commonly used tumor mutation burden detection method is the strategy proposed by Lawrence's team in Nature in 2015, which judges the tumor mutation burden status by calculating the number of somatic mutations in the whole exome (average depth <...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B40/10G16B20/50G16B30/10G16B50/30
CPCG16B20/50G16B30/10G16B40/10G16B50/30
Inventor 董永芳郭璟楼峰曹善柏
Owner 北京橡鑫生物科技有限公司
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