Construction method of prognosis evaluation model of intrahepatic cholangiocarcinoma patient
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A technology for prognostic assessment and method construction, applied in the field of bioinformatics, can solve problems that have not yet been
Active Publication Date: 2021-01-26
浙江高美基因科技有限公司
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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 invention provides a construction method of a model for predicting the survival rate of a patient with intrahepatic cholangiocarcinoma. The construction method comprises the following steps of 1)providing DNA methylation sequencing data of the intrahepatic cholangiocarcinoma; 2) analyzing the DNA methylation sequencing data, and screening out a plurality of related promoter regions of the intrahepatic cholangiocarcinoma; and 3) establishing a model for predicting the survival rate of the intrahepatic cholangiocarcinoma patient by utilizing the plurality of related promoter regions of theintrahepatic cholangiocarcinoma. By conducting DNA methylation prognostic labeling on intrahepatic cholangiocarcinoma patients, the DNA methylation markers serve as independent variables, the patientsare distinguished into a high death rate group and a low death risk group, and experimental verification shows that the construction method of the model can be used for predicting the total postoperative survival rate of the intrahepatic cholangiocarcinoma patients, and can be used for predicting the postoperative survival rate of the intrahepatic cholangiocarcinoma patients; an individualized adjuvant therapy strategy is provided for a patient with the 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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