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New method for lung adenocarcinoma biomarker screening, prognosis model construction and biological verification

A biomarker, lung adenocarcinoma technology, applied in the field of model construction and biological verification

Active Publication Date: 2021-07-16
JILIN UNIV
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Problems solved by technology

Although high-throughput methods can reduce experimental loss and improve efficiency, how to effectively select the best markers in the face of tens of thousands of dimensional features is still a key problem to be solved in related fields

Method used

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  • New method for lung adenocarcinoma biomarker screening, prognosis model construction and biological verification
  • New method for lung adenocarcinoma biomarker screening, prognosis model construction and biological verification
  • New method for lung adenocarcinoma biomarker screening, prognosis model construction and biological verification

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Embodiment Construction

[0050] see Figure 1 to Figure 3 Shown:

[0051] The novel method for lung adenocarcinoma biomarker screening, prognostic model construction and biological verification provided by the present invention comprises the following steps:

[0052] Step 1. Perform data preprocessing on the original gene expression matrix. First, use the matching file to annotate, and change the probe name to the gene name. The process of data preprocessing is as follows:

[0053] 1) Deleting transcriptome signature genes with a deletion rate of more than 20%;

[0054] 2) Delete transcriptome signature genes whose variance is close to 0;

[0055] 3) Use KNN filling method to fill in the transcriptome characteristic genes with a deletion rate of more than 20%;

[0056] 4), use the Z-score method to normalize the expression matrix obtained in 3)

[0057] Finally, a transcriptome expression data matrix containing 57,000 genes and 513 samples was obtained.

[0058] Step 2: Perform biomarker screeni...

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Abstract

The invention discloses a new method for lung adenocarcinoma biomarker screening, prognosis model construction and biological verification. The method comprises the following steps: 1, carrying out data preprocessing on an original gene expression matrix; 2, carrying out biomarker screening on the data obtained after preprocessing; 3, constructing a prognosis model by using the lung adenocarcinoma prognosis marker subjected to the multi-step feature selection; 4, carrying out signal analysis on the selected marker after modeling. The invention has the beneficial effects that 45 gene markers are verified by using a linear support vector machine model, AUC and ACC which are poorly verified by five folds are used as model evaluation indexes, and the final result is that AUC is equal to 0.98, and ACC is equal to 0.92. The result is obviously superior to that of most traditional gene marker selection methods, the marker related to the lung cancer can be found out, the lifetime of a lung cancer patient can be accurately predicted, meanwhile, a channel related to lung adenocarcinoma occurrence can be explored, and the occurrence mechanism of lung adenocarcinoma can be explored.

Description

technical field [0001] The invention relates to a new method for model construction and biological verification, in particular to a new method for lung adenocarcinoma biomarker screening, prognosis model construction and biological verification. Background technique [0002] Currently, lung cancer is a malignant tumor with the highest mortality and morbidity in the world. In addition, lung cancer has a high degree of malignancy and poor prognosis, with a 5-year survival rate of only 8%. There are various treatment methods for lung cancer. Traditional treatment methods include drug therapy, surgery, radiotherapy, and chemotherapy. After entering the 21st century, molecular targeted therapy has made a major breakthrough, and the effect of treating cancer-specific factors is far better than traditional therapy. Therefore, finding specific biomolecules related to the pathogenesis of cancer is also a current research hotspot in the field of tumor biology. [0003] In recent ye...

Claims

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Application Information

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IPC IPC(8): G16B20/00G06K9/62G06N20/10
CPCG16B20/00G06N20/10G06F18/2411
Inventor 刘元宁赵曦张浩钟晓丹王林宇
Owner JILIN UNIV
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