Application of m5c modification regulating genome in preparation of tumor prognosis assessment reagent or kit

A prognostic assessment and kit technology, which is applied in the field of medical biological detection, can solve the problems of little understanding of the role and mechanism of immunotherapy efficacy assessment, and achieve the effects of high repeatability, sensitive detection and easy operation.

Active Publication Date: 2022-07-12
FUDAN UNIV SHANGHAI CANCER CENT
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Problems solved by technology

[0006] At present, although m5c has been found to be related to the development and development of different types of tumors, its role and mechanism in evaluating the efficacy of immunotherapy are still poorly understood
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  • Application of m5c modification regulating genome in preparation of tumor prognosis assessment reagent or kit
  • Application of m5c modification regulating genome in preparation of tumor prognosis assessment reagent or kit
  • Application of m5c modification regulating genome in preparation of tumor prognosis assessment reagent or kit

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Embodiment Construction

[0044] The present invention will now be described in detail with reference to the embodiments and accompanying drawings, but the implementation of the present invention is not limited thereto.

[0045] 1. Data preprocessing

[0046] 1. Download TCGA LUAD SNV data (MuTect2 Annotation) for a total of 570 samples.

[0047] 2. Download the TCGA LUAD CNV data for a total of 544 samples, use the hg38 reference group-based re-annotation through bedtools software, and extract the annotation results of 13 gene CNVs.

[0048] 3. Download the TCGA LUAD FPKM, and convert it into TPM data through further processing, a total of 572 samples and a total of 513 cases of clinical data on the follow-up time and follow-up status of patients. Among them, 513 were tumor samples and 59 were normal samples.

[0049] 4. Download the expression profile data (246 samples) of GSE31210 in the NCBI GEO database and the clinical data of the patient's follow-up time and follow-up status, a total of 246 sa...

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Abstract

The invention relates to the technical field of medical biological detection, and provides the application of m5c modified and regulated genome in the preparation of a tumor prognosis assessment reagent or kit, wherein the tumor is lung adenocarcinoma, and the genome includes NSUN2, NSUN5, DNMT1, DNMT3A, DNMT3B, TET2 and ALYREF; further provided a prognostic evaluation kit, consisting of a reverse transcription system, a primer system and an amplification system; also provided a prognostic evaluation system, including a prognostic evaluation kit and an m5c‑score model installed on a terminal vector, The m5c‑score model includes a PCA analysis module, a score extraction module, and an m5c‑score calculation module. The PCA analysis module analyzes each gene based on the expression of the above genes; the score extraction module extracts the PC1 and PC2 scores of each gene; m5c‑score The score calculation module calculates the m5c‑score of the sample.

Description

technical field [0001] The invention belongs to the technical field of medical biological detection, and relates to the application of m5c modification regulation gene group in tumor prognosis evaluation. Background technique [0002] RNA in eukaryotes carries more than 100 chemical modifications, of which about 60% are RNA methylation modifications, and among the methylation modifications, N5-methylcytosine (m5c) is the most common modification. m5c is methylated on the fifth N of cytosine nucleotide, which is mainly distributed in CG-rich regions, and there are a large number of m5c methylation sites in coding RNA and non-coding RNA. m5c is highly abundant and stable in transfer RNA (transfer RNA, tRNA) and ribosomal RNA (rRNA), and its functions have been confirmed to be involved in the regulation of stem cell stress, cytotoxic stress, messenger RNA (mRNA) Nuclear and cell development and gene expression. [0003] m5c is well conserved in mammalian mRNA, but the genes i...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886C12N15/11
CPCC12Q1/6886C12Q2600/158C12Q2600/118
Inventor 祝鸿程赵快乐张军华刘明张致远曾怡瑄李芳芳翟瑞萍
Owner FUDAN UNIV SHANGHAI CANCER CENT
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