Application of methylation status near HBV integration site in cancer detection

Abstract

The invention provides a new methylation detection and analysis method that can be applied to liver cancer detection scenarios. Not only excellent classification performance under conventional sequencing conditions can be obtained, but also very good performance under low-coverage sequencing conditions can be realized. The bias of the prior art that deep sequencing is needed for DNA methylation analysis of cfDNA is overcome, the sequencing cost is greatly reduced, the application scope of methylation sequencing technology is expanded, and basic data fro clinical application such as early screening for liver diseases, liver disease diagnosis, liver disease monitoring, liver disease patient classification, liver cancer treatment or surgical intervention evaluation are provided.

Description

technical field [0001] The invention relates to the technical field of molecular biology, in particular to a method for cancer-related detection by using the methylation status of the region near the HBV integration site. Background technique [0002] Cell-free peripheral blood DNA (cfDNA) are small double-stranded DNA fragments found in human plasma, urine, and other body fluids [1,2] that originate from apoptosis and necrosis [3]. cfDNA analysis is regarded as a way of "liquid biopsy" and has been used for genetic testing [4,5], early cancer detection [6,7], and disease prognosis prediction [8,9]. Apoptotic and necrotic tumor cells can release cfDNA into peripheral blood, which reflects tumor-associated genetic characteristics, including cfDNA fragment size (cfDNA size )[10], as well as mutations, copy number aberrations and epigenetic changes, etc.[8]. At the same time, cfDNA also carries tissue-specific information, which provides application prospects for the inferenc...

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Problems solved by technology

[0005] Whole-genome methylation sequencing (WGBS) has become the gold standard for DNA methylation analysis due to its single cytosine metric and high accuracy [33]. The amount of tumor DNA is very small, especially in patients with early-stage tumors and minimal residual lesions, which requires deep sequencing to generate more sensitive markers for early-stage tumor detection and surveillance, often requiring 30-100 multiple genome-wide coverage[ 29,31], the high cost of sequencing limits its large-scale application in current clinical settings

[0006] To screen tumors based on the methylation level of specific gene loci in cfDNA, this scheme is not based on the detection of methylation level in the whole genome, but only relies on the selection of some loci, but the heterogeneity of tumors (different Variations in human tumor genomes) are very large, so even if these tests show excellent specificity and sensitivity in the samples used in the study, after changing the sample, due to the selection of candidate loci that are not in the new clinical samples It must show the changes expected to be monitored but cannot achieve the performance in the research samples, so it is necessary to provide a method for establishing hypomethylation assessment through bioinformatics at the genome-wide level that does not depend on specific methylation marker sites

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