Development of multi-cancer screening technology based on cfDNA

①　Project Background

Liquid biopsy technology is a non-invasive screening new technology for diagnosing diseases through body fluids such as blood, saliva, and urine, which has the characteristics of being non-invasive, efficient, and accurate. In recent years, liquid biopsy technology has been widely used in many fields such as early screening, companion diagnostics, personalized treatment, and prognosis monitoring of tumors. The most common liquid biopsy is the detection of circulating free DNA (cell-free DNA, cfDNA), which is the detection of DNA released into the blood by tumor necrosis or apoptosis. In the blood of tumor patients, a part of cfDNA comes from dead tumor cells, which contain changes in the tumor cells' genome (point mutations, insertions, deletions, etc.) and epigenome (DNA methylation, etc.) that can be detected through second-generation sequencing, PCR, and other technical platforms.

DNA methylation is an important way of gene epigenetic modification, which refers to the chemical modification process in which the active methyl group is transferred to specific bases in the DNA chain by DNA methyltransferase (DNMT) catalysis, with S-adenosylmethionine as the methyl donor. On the human genome, there are about 280 million CpG sites, of which 60-80% of cytosines are methylated. Changes in DNA methylation patterns are closely related to the occurrence, development, and cell carcinogenesis of tumors. Methylation changes occur earlier than mutations and are a characteristic change in the early development of tumors. Moreover, the number of methylation sites related to tumor genes is large, and they exist in clusters in the genome, which is easy to detect, has a high sensitivity, and the methylation pattern has tissue specificity, which can achieve cancer tissue tracing and is easy to distinguish from variations caused by aging, with a high degree of specificity.

A multi-cancer screening strategy based on cfDNA methylation detection, which completes the screening of multiple cancers and tissue tracing at the same time with one test, has a relatively low screening cost and is a non-invasive operation, and the acceptance of the population is expected to be greatly improved. Therefore, a multi-cancer screening strategy based on liquid biopsies of cfDNA methylation detection is particularly suitable for low-sanitary resource areas with a heavy burden of tumor diseases.

②　Technical solution

Directly sequence cfDNA based on Nanopore sequencing. Nanopore sequencing does not require a high amount of DNA input, making it suitable for low-concentration, low-abundance cfDNA samples. This makes it an ideal choice for non-invasive detection methods such as cfDNA. The portable nanopore sequencing platform does not require complex sample processing steps and PCR amplification, offering advantages of low library construction cost and a rapid sequencing workflow. Nanopore sequencing can not only analyze DNA sequences but also utilize it to detect DNA methylation patterns. By measuring the changes in current when DNA molecules pass through the nanopore, nanopore sequencing can capture epigenetic information such as methylation, which has great potential for early diagnosis and monitoring of diseases.

③　Project goals

 Screening of epigenetic biomarkers with high sensitivity, high specificity and good tissue traceability;

 Integrating cfDNA methylation biomarkers, epidemiological and clinical diagnosis and treatment information, a multi-modal, multi-dimensional multi-cancer screening risk prediction model was constructed and verified to achieve effective prediction of cancer risk.