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Biomarker detection method and system for predicting tumor immune treatment effect

A biomarker and immunotherapy technology, applied in the field of biomarker detection to predict the effect of tumor immunotherapy, can solve problems such as mismatch repair function microsatellite instability, and achieve the effect of improving accuracy and applicability

Pending Publication Date: 2020-11-24
深圳裕策生物科技有限公司
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  • Application Information

AI Technical Summary

Problems solved by technology

Comparing the potential indicators for evaluating the efficacy of immune checkpoint inhibitor PD-1, such as PD-L1 expression, tumor mutation burden (TMB), mismatch repair function deficiency / microsatellite instability (dMMR / MSI), and some exploratory indicators For example, intratumoral heterogeneity (ITH), loss of leukocyte antigen heterozygosity (HLALOH), evolutionary diversity of HLA-class I genes (HED), tumor lymphoid infiltrating cells (TIL), etc. cannot fully obtain immune checkpoint inhibitors. effective screening of beneficial patients

Method used

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  • Biomarker detection method and system for predicting tumor immune treatment effect
  • Biomarker detection method and system for predicting tumor immune treatment effect
  • Biomarker detection method and system for predicting tumor immune treatment effect

Examples

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Effect test

Embodiment 1

[0034] This embodiment provides a biomarker detection method for predicting the effect of tumor immunotherapy, such as figure 1 As shown, it includes the following steps:

[0035] S1. Obtain whole exome sequencing (WES) data of tumor samples and control blood samples.

[0036] Specifically, the original WES sequencing off-machine data of tumor samples and control blood samples were obtained, and the WES sequencing data were obtained after splicing and low-quality data quality control processing.

[0037] S2. Align the sequencing data with the sequence of the reference genome of the control blood sample to obtain an alignment result.

[0038] Compare the WES sequencing data obtained in step S1 with the reference genome, and remove redundancy to obtain the comparison result. In this embodiment, the reference genome is the hg19 genome, and the comparison process uses bwa (Burrow-WheelerAligne) software Then use the picard tool to remove redundancy and get the bam file of the co...

Embodiment 2

[0050] This example provides a biomarker detection method for predicting the effect of tumor immunotherapy, taking the tumor in the immunotherapy cohort of non-small cell lung cancer as an example, the specific detection method is as follows:

[0051] S1. Obtain the WES raw sequencing off-machine data of the tumor tissue samples and control blood samples of the non-small cell lung cancer immunotherapy cohort of 69 patients, and obtain the WES sequencing data after removing joints and quality control processing of low-quality data.

[0052] S2. Aligning the sequencing data of 69 cases with the sequence of the reference genome hg19 to obtain an alignment file.

[0053] S3. Use the comparison results to detect somatic cell mutations, obtain information on somatic cell mutations, depth, mutation frequency, and somatic copy number variations of 69 patients, and obtain tumor purity, tumor ploidy, and HLA-class I genes Typing information.

[0054] S4. Using the detection results obt...

Embodiment 3

[0059] This example provides a biomarker detection method for predicting the effect of tumor immunotherapy, taking nasopharyngeal carcinoma immunotherapy cohort tumors as an example, the specific detection method is as follows:

[0060] S1. Obtain the original WES sequencing off-machine data of the tumor tissue samples and control blood samples of the nasopharyngeal carcinoma immunotherapy cohort of 61 patients, and obtain the WES sequencing data after removing joints and quality control processing of low-quality data.

[0061] S2. Aligning the sequencing data of 61 cases with the sequence of the reference genome hg19 to obtain an alignment file.

[0062] S3. Using the comparison results, somatic mutation detection was performed to obtain somatic mutation, depth, mutation frequency and somatic copy number variation information of 61 patients, as well as obtain tumor purity, tumor ploidy and HLA-class I genes Typing information.

[0063] S4. Using the detection results obtaine...

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Abstract

The invention discloses a biomarker detection method for predicting a tumor immune treatment effect. The method comprises the following steps: detecting a plurality of biomarkers on the basis of second-generation sequencing detection tissue whole exome sequencing (WES) data, and constructing a prediction model for comprehensively predicting a tumor immune treatment effect. Compared with a traditional method capable of only detecting a single biomarker, the method provided by the invention effectively improve the accuracy and applicability of predicting the curative effect of the inhibitor at the immune checkpoint.

Description

technical field [0001] The invention belongs to the technical field of bioinformatics, and relates to a biomarker detection method, in particular to a biomarker detection method for predicting the effect of tumor immunotherapy. Background technique [0002] Cancer is a disease with a high mortality rate, and it is also one of the most important non-communicable diseases in the world. In my country, nearly 4.3 million people are diagnosed with cancer every year, and more than 2.8 million people die of cancer. In medicine, cancer refers to malignant tumors originating from epithelial tissue. Generally speaking, "cancer" generally refers to all malignant tumors. Cancer has biological characteristics such as abnormal cell differentiation and proliferation, uncontrolled growth, invasion, and metastasis. Its occurrence is a multi-factor and multi-step complex process, which is divided into three processes: carcinogenesis, carcinogenesis, and evolution, which are closely related to...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886C12Q1/6869G16B20/20G16B30/00
CPCC12Q1/6886C12Q1/6869G16B20/20G16B30/00C12Q2600/156C12Q2535/122
Inventor 陈龙昀易坚金皓玄苏小凡高志博
Owner 深圳裕策生物科技有限公司
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