Single-sample tumor somatic mutation discrimination and TMB detection method based on NGS platform

A somatic cell mutation and single-sample technology, applied in the field of bioinformatics analysis, can solve the problems of insufficient bioinformatics filtering methods in public databases, false positives in the discrimination process, etc., and achieve the effect of expanding treatment options and ensuring accuracy

Active Publication Date: 2022-07-01
JIANGSU SIMCERE MEDICAL DEVICE CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0006] In summary, the discrimination of somatic mutations in a single tumor sample and the calculation of TMB are greatly affected by the limitations of the current public database and the still incomplete bioinformatics filtering method, and there are many false positives in the discrimination process

Method used

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  • Single-sample tumor somatic mutation discrimination and TMB detection method based on NGS platform
  • Single-sample tumor somatic mutation discrimination and TMB detection method based on NGS platform
  • Single-sample tumor somatic mutation discrimination and TMB detection method based on NGS platform

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experiment example

[0076] Experimental example, the establishment of the method system of this application

[0077] like figure 1 As shown, the single-sample somatic mutation discrimination and TMB calculation of this application includes the following steps:

[0078] 1. Extract DNA from a single sample of tumor tissue and capture tumor-related genes in tumor-related gene regions by hybridization capture (such as using human tumor multi-gene detection Panel);

[0079] 2. Sequence the captured tumor-related genes through the NSG platform to obtain high-throughput sequencing raw data and conduct quality control to remove low-quality sequencing sequences;

[0080] 3. Compare the quality-controlled sequencing data to the human reference genome hg19, and remove repetitive sequences;

[0081] 4. Mutation detection: Based on the human reference genome alignment data analysis and acquisition of single nucleotide variation (SNV) and small insertion deletion variation (INDEL), and calculate the allele f...

Embodiment 1

[0113] The specific somatic mutation information of the positive standard in this example is shown in Table 1 below, wherein the frequency of somatic mutation is mainly distributed in 1%-2%. In this example, a total of 20 cases of HD789 are gDNA standard samples, which simulate formalin-fixed and paraffin-embedded (FFPE) tissue samples to test the detection performance of this method. DNA sequencing data were obtained for all samples using the human tumor multi-gene detection panel target capture method, and the target capture range covered the positive sites in the standard, and the sequencing depth was 1500X.

[0114] Table 1 Somatic mutation information of HD789 standard

[0115]

[0116] The sequencing data of the 20 standard samples were subjected to the quality control of the sequencing data, and the BWA (v0.7.17) MEM algorithm was used for the comparison and analysis of the human reference genome. Single-sample somatic mutation detection and discriminant analysis. ...

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Abstract

The invention relates to the technical field of signal analysis, and particularly provides a single-sample tumor somatic mutation discrimination method based on an NGS platform and a corresponding TMB detection method.According to the method, a mutation detection result is obtained based on NGS platform data, and the mutation detection result is obtained through comparison of a public database and a self-built national human mutation database; and on the basis of a method for constructing a statistical distribution model based on allele copy numbers calculated by a single sample, single-sample tumor somatic cell mutation judgment is carried out, so that TMB calculation is realized.

Description

technical field [0001] The present application belongs to the field of bioinformatics analysis, and in particular relates to a single-sample tumor somatic mutation discrimination method based on an NGS platform and a corresponding TMB detection method. Background technique [0002] Next Generation Sequencing (NGS) of tumor samples is widely used to discover biologically important mutations and guide clinical targeted therapy and medication. These mutations are divided into somatic mutation (Somatic mutation) and germline mutation (Germline mutation). Somatic mutation generally exists only in tumor cells and is not passed on to offspring, while germline mutation occurs in fertilized eggs and exists in tumor cells at the same time. and normal cells, can be passed on to offspring. The carcinogenesis of cells and the development of tumors are usually related to the long-term accumulation of gene mutations in somatic cells, but not all somatic mutations lead to cancerous cells. ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/50G16B50/00G16B20/30G16B20/20
CPCG16B20/50G16B20/30G16B20/20G16B50/00
Inventor 叶雷邓望龙雷燕萍秦勇卜范峰李诗濛任用
Owner JIANGSU SIMCERE MEDICAL DEVICE CO LTD
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