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Biomarker for esophageal cancer typing and application thereof

A biomarker, esophageal cancer technology, applied in the field of medical detection, can solve the problems of poor differentiation, wrong pathological determination, low qualification rate, etc., and achieve the effect of ensuring accurate, convenient and precise treatment

Pending Publication Date: 2022-03-22
深圳康华君泰生物科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] Limited tissue samples and the need to evaluate an increasing number of therapeutically targetable markers have greatly increased current diagnostic needs, and studies of histological diagnostic reproducibility have shown intra- and inter-pathologist variability: pathology Misjudged results, poorly differentiated tumors, and contradictory immunohistochemical results, etc., challenge the accuracy of current precision medicine in esophageal cancer
[0005] At the same time, the latest 2021 National Solid Tumor Somatic Cell High-throughput Sequencing (Large Panel) Testing Laboratory Interstitial Evaluation Report shows that the national testing laboratory pass rate is only 49.2%, and it is expected that the pass rate of genome or exome sequencing will be even higher. Low, this data greatly shows that the current quality control of drug recommendations for patients based on pathological and genetic testing needs to be improved urgently

Method used

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  • Biomarker for esophageal cancer typing and application thereof
  • Biomarker for esophageal cancer typing and application thereof
  • Biomarker for esophageal cancer typing and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0043] Based on the TCGA public database, a preliminary screening of variant gene markers for pathological subtypes of esophageal cancer was performed.

[0044] The screening method is as follows.

[0045] 1. Obtain the whole exome sequencing data of the tumor tissue of patients with esophageal cancer from the TCGA database.

[0046] In this example, the whole exome sequencing data of 184 patients with esophageal cancer (including 88 cases of adenocarcinoma and 96 cases of squamous cell carcinoma) were downloaded, and seven different software were used: MuTect, VarScan, MuSE, Radia and SomaticSniper to detect SNPs respectively Mutation site: VarScan, Pindel, and Indelocator were used to detect InDels respectively, and finally the mutation site that was simultaneously called by at least two mutation software in the sample was used as the candidate mutation site.

[0047] 2. According to the data set of adenocarcinoma group and the data set of squamous cell carcinoma group, the...

Embodiment 2

[0057] For the potential markers obtained in Example 1, clinical samples were analyzed and verified.

[0058] The verification process is as follows.

[0059] 1. Acquisition of tissue samples: 184 cases of esophageal cancer (96 cases of squamous cell carcinoma, 88 cases of squamous cell carcinoma) related FFPE section samples were collected from Jinan University.

[0060] 2. Sample sequencing analysis: FFPE tissue samples were subjected to whole-genome sequencing analysis by a third party (Brightcode Biotechnology Company).

[0061] 3. Establishing a model: using the information of all target markers in Example 1, the independent verification set, namely 96 cases of squamous cell carcinoma and 88 cases of adenocarcinoma patient tissue samples were detected and judged, and the random forest model was used for modeling analysis. Modeling process such as figure 1 As shown, according to the 7:3 segmentation, 20 repetitions, the AUC of the model is as high as 0.9489, and the mode...

Embodiment 3

[0066] Select 28 samples clinically judged as esophageal cancer, use the 10 MARKER combination models established in the above-mentioned Example 2 for analysis, and compare the analysis results with the judgment results of clinical experts, the results are shown in the table below.

[0067] Table 3 clinical verification results

[0068]

[0069]

[0070] It can be seen from the above results that using the biomarkers of the present invention, the above model can be used to determine the classification of squamous cell carcinoma or adenocarcinoma in lung small cell carcinoma more accurately, and the consistency with expert judgment is more than 91.3%.

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Abstract

The invention relates to a biomarker for esophageal cancer typing and application thereof, and relates to the technical field of medical detection. The biomarker comprises at least five kinds of genes such as GAS7, LRP1B, MAP2K4, FOXP1, WWOX and the like. When the biomarkers are used for carrying out typing diagnosis on esophageal squamous carcinoma and esophageal adenocarcinoma, the diagnostic power AUC can reach 0.9447 when 5 markers are used, the diagnostic power AUC can reach 0.9789 when 10 markers are used, the diagnostic power AUC can reach 0.9714 when 20 markers are used, and the diagnostic power AUC can reach 0.9489 when all the markers are used, so that the biomarkers have excellent diagnostic power and can be used for diagnosis of esophageal squamous carcinoma and esophageal adenocarcinoma. The invention provides a method for discriminating two pathological subtypes based on molecular level, provides mutual verification for pathological diagnosis results, ensures that the case diagnosis results are correct, and is convenient for subsequent precise treatment.

Description

technical field [0001] The invention relates to the technical field of medical detection, in particular to a biomarker for esophageal cancer typing and its application. Background technique [0002] Esophageal cancer is the eighth most common cancer in the world and the sixth leading cause of death. In China, the incidence of esophageal cancer has declined in recent years, but the mortality rate has always ranked fourth. Esophageal cancer is a malignant disease with poor prognosis. The overall 5-year survival rate of esophageal cancer at each stage is about 14%. Histologically, esophageal cancer is divided into tumors of epithelial and non-epithelial origin. More than 90% of esophageal cancers are squamous cell carcinoma (SCC) or adenocarcinoma. In terms of histological types, squamous cell carcinoma is the main type of esophageal cancer in my country, accounting for more than 90%, while adenocarcinoma is the main type in the United States and Europe, accounting for about ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886G06K9/62G16B20/50G16B50/30
CPCC12Q1/6886G16B20/50G16B50/30C12Q2600/112G06F18/24323
Inventor 刘鑫贾富建刘康
Owner 深圳康华君泰生物科技有限公司
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