Classification method and system of immune-related disease molecular typing and subtype classifier
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A technology for immune-related diseases and molecular typing, applied in the field of precision medicine
Pending Publication Date: 2022-01-07
AFFILIATED HUSN HOSPITAL OF FUDAN UNIV
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However, judging from the existing reports, there are few studies on accurate and high-quality molecular typing of immune-related diseases
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Embodiment 1
[0083] Example 1, ulcerative colitis (Ulcerative colitis, UC).
[0084] A method for classifying UC molecular typing and subtype classifiers provided in this embodiment, including:
[0085] Data acquisition step: obtain the UC chip data set, and divide the UC chip data set into a training set, a verification set and a comparison set. In the present invention, UC chip datasets were obtained from the GEO database, GSE87466 (n=87), GSE107499 (n=47) and GSE75214 (n=74) were used as training sets, GSE83687 (n=28) and GSE126124 (n =18) was used as a typing validation set, and GSE114527 (n=15), GSE73661 (n=64) and GSE16879 (n=24) were used to compare treatment response rates. Only tissues from the colon were included, and only active UC and involved mucosal tissues were included, and normal samples were retained as a control group. A total of 208 mucosal tissues were included in the training set. The data were all log2 transformed. The therapeutic target pathway gene set was down...
Embodiment 2
[0109] Example 2, Crohn's disease (Crohn's disease, CD).
[0110] A classification method for Crohn's disease molecular typing and subtype classifier, comprising:
[0111] Data acquisition step: acquire the CD chip data set, and divide the CD chip data set into a training set, a verification set and a comparison set. In the present invention, CD chip datasets were obtained from the GEO database, GSE112366 (n=110), GSE75214 (n=51), GSE179285 (n=33) and GSE100833 (n=50) were used as training sets, GSE16879 (n =18) was used as a typing validation set and GSE112366 (n=66) was used to compare treatment response rates. Only tissues from the terminal ileum were included, and only active CD, involved mucosal tissues were included, and normal samples were retained as a control group. A total of 244 mucosal tissues were included in the training set. The data were all log2 transformed.
[0112] Molecular typing step: use a clustering algorithm to perform molecular typing in the train...
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Abstract
The invention provides a classification method and system of immune-related disease molecular typing and a subtype classifier, and the method comprises the steps: carrying out the molecular typing in a training set through a clustering algorithm, and obtaining a plurality of subtypes stably appearing in the training set and a marker gene of each subtype; carrying out enrichment analysis on marker genes of the subtypes, carrying out immune cell infiltration evaluation on the subtypes, and obtaining various subtype categories with stable immune characteristics according to analysis and evaluation results; comparing the treatment response rates of different subtype categories through the comparison set, and determining the subtype category needing to be recognized; constructing a support vector machine model by utilizing the feature genes obtained by screening and the optimal parameter combination; and identifying whether the to-be-classified immune-related disease data is a required subtype category or not. According to the invention, immune-related disease subtypes with stable characteristics can be identified, so that accurate drug selection and economic treatment are facilitated. The invention is applicable to molecular typing and subtype classification of various immune-related diseases, and is not limited to the embodiments herein.
Description
technical field [0001] The present invention relates to the technical field of precision medicine, in particular, to a classification method and system for immune-related disease molecular typing and subtype classifier based on artificial intelligence machine learning. Background technique [0002] Immune-related diseases refer to diseases caused by the imbalance of immune regulation in the body. There are many treatments for immune-related diseases, especially the increasing use of biologics such as monoclonal antibodies. However, it can be seen clinically that the prognosis of patients with different immune-related diseases is not the same, which reflects that there is extensive heterogeneity in the immune status of different patients with the same disease, and it is difficult to distinguish them based on clinical manifestations. Accurate classification for clinical prognosis and treatment. [0003] Take Ulcerative colitis (UC), a typical immune-related disease, as an ex...
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