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Construction method of prognosis assessment model for patients with intrahepatic cholangiocarcinoma
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A technology for prognosis assessment and method construction, applied in the field of bioinformatics, can solve problems such as not yet available, and achieve the effect of high accuracy and strong correlation
Active Publication Date: 2021-05-11
浙江高美基因科技有限公司
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However, to date, there are no studies using promoter methylation as a biomarker to screen survival in ICC patients
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Embodiment 1
[0060] Example 1: Data Collection
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[0061] This embodiment mainly introduces the specific steps of collecting DNA methylation data of ICC samples. The specific implementation is as follows:
[0062] First, samples of patients with intrahepatic cholangiocarcinoma (ICC) were obtained from the biobanks of West China Hospital of Sichuan University, Zhongshan Hospital of Fudan University, and Tianjin Medical University Cancer Hospital. Immediately after surgery, the samples were placed in liquid nitrogen. Freeze and store at -80 °C or in liquid nitrogen. Then, the samples undergo the process of genomic DNA isolation, WGBS database generation, sequencing, quality control and WGBS data processing to obtain the DNA methylation data of ICC samples. The DNA methylation data include the average methylation value of the 4,000 bps promoter region.
[0063] It should be noted that, as shown in Table 1, 164 and 170 patients participated in the training cohort and the verification cohort respectively in the embodiment of the ...
Embodiment 2
[0070] Example 2: Data Analysis
[0071] Example 2 is mainly to analyze the DNA methylation data in Example 1, and screen out several ICC-related promoter regions. The specific implementation is as follows:
[0072] In total, this example identified 175,976 promoter regions obtained by WGBS in the training cohort, corresponding to 198,074 transcripts for 42,737 genes (coding and non-coding genes). The methylation level of each promoter region derived from the WGBS data was continuous and quantitative, and the methylation level of the promoter region was determined to be significantly associated with overall survival using a univariate Cox method (P < 0.01). Subsequently, 36,938 promoter regions were found to be meaningful in univariate Cox analysis. C-index (index of concordance, consistency index) is usually used to evaluate the performance of the model, therefore, we first calculate the C-index of each promoter region, and then select the top 5000 promoter regions ranked b...
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Abstract
The present invention provides a method for constructing a model for predicting the survival rate of patients with intrahepatic cholangiocarcinoma, comprising the following steps: 1) providing DNA methylation sequencing data of intrahepatic cholangiocarcinoma; 2) sequencing the DNA methylation Analyze the data and screen out several related promoter regions of intrahepatic cholangiocarcinoma; 3) use the several related promoter regions of intrahepatic cholangiocarcinoma to establish a model for predicting the survival rate of patients with intrahepatic cholangiocarcinoma . Through the prognostic markers of DNA methylation in patients with intrahepatic cholangiocarcinoma, the markers of DNA methylation are used as independent variables, and patients are divided into high mortality and low mortality risk groups. After experimental verification, this paper The invented model construction method can be used to predict the overall survival rate of patients with intrahepatic cholangiocarcinoma after surgery, and provide individualized adjuvant treatment strategies for patients with intrahepatic cholangiocarcinoma.
Description
technical field [0001] The application relates to the field of bioinformatics, in particular to a method for constructing a prognosis assessment model for patients with intrahepatic cholangiocarcinoma. Background technique [0002] Intrahepatic cholangiocarcinoma (ICC) accounts for 4.4%-12.0% of primary liver cancer patients, and is the second most malignant liver tumor with poor prognosis. The morbidity and mortality of ICC patients have continued to rise over the past few decades. For patients with ICC who can be surgically resected, surgical resection is the only chance to increase survival. According to statistics, the 5-year overall survival of some ICC patients after surgery is about 25.0%-39.8%. [0003] However, the high recurrence rate after surgical treatment (such as liver transplantation, hepatectomy, or radiofrequency ablation) leads to poor prognosis for patients. Even after resection of intrahepatic cholangiocarcinoma tissue, 57.9%-73.4% of ICC patients sti...
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