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Cancer-related biomarker based on cfDNA sequencing and data analysis as well as application of cancer-related biomarker based on cfDNA sequencing and data analysis in cfDNA sample classification

A cancer-related biomarker technology, applied in the field of tumor markers and classification biology, can solve the problems of no improvement and high recurrence rate

Active Publication Date: 2020-06-09
SOUTHEAST UNIV
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Problems solved by technology

ESCA predicts 5-year survival of between 15% and 20%, showing little improvement in recent decades due to high recurrence rates, early metastatic tendencies, and limited knowledge of biomarkers and potential therapeutic targets

Method used

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  • Cancer-related biomarker based on cfDNA sequencing and data analysis as well as application of cancer-related biomarker based on cfDNA sequencing and data analysis in cfDNA sample classification
  • Cancer-related biomarker based on cfDNA sequencing and data analysis as well as application of cancer-related biomarker based on cfDNA sequencing and data analysis in cfDNA sample classification
  • Cancer-related biomarker based on cfDNA sequencing and data analysis as well as application of cancer-related biomarker based on cfDNA sequencing and data analysis in cfDNA sample classification

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Embodiment

[0046] Discovery and classification of biomarkers (markers) for esophageal cancer based on cfDNA sequencing and data analysis

[0047] 1. Materials and methods

[0048] 1.1. Prepare various joints:

[0049] All oligonucleotides were synthesized by Shanghai Sangon Biotechnology Co., Ltd. (Table 1, 2, 4). To prepare the barcode T linker (BTA), oligonucleotides Barcode 1-20 were annealed with oligonucleotide BTA-universal oligo (Table 1) and dissolved in ddH at a concentration of 100 μM 2 O, then mix equimolarly in a PCR tube. To prepare single-stranded adapters (SSA), the oligonucleotides SSA-PN-3N and SSA-PNrev (Table 2) were dissolved at a concentration of 100 μM in ddHO 2 O, then mix equimolarly in PCR tubes. Finally, all mixtures were denatured in a water bath at 95 °C for 5 min and then gradually cooled to 25 °C to anneal into various joints.

[0050] Table 1: Oligonucleotide cassettes used to prepare BTA adapters

[0051]

[0052]

[0053] Notes: 5'-[phos] for ...

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Abstract

The invention discloses a cancer-related biomarker based on cfDNA sequencing and data analysis as well as application of the cancer-related biomarker based on the cfDNA sequencing and the data analysis in cfDNA sample classification. According to the cancer-related biomarker based on the cfDNA sequencing and the data analysis as well as the application of the cancer-related biomarker based on thecfDNA sequencing and the data analysis in the cfDNA sample classification, a novel method is used for finding new biomarkers of cancers from plasma cfDNA (cfDNA ); related epigenetic and genetic markers are identified by performing sequencing and bioinformatics analysis on cfDNA samples from cancer patients and healthy people; and the cfDNA samples can be accurately classified by a support vectormodel established by analyzing epigenetic markers with machine learning, namely that full DNA samples from cancer individuals or healthy individuals are obtained. The cancer-related biomarker (or marker) based on the cfDNA sequencing and the data analysis disclosed by the invention is a novel molecular biomarker for cancer diagnosis, prognosis and treatment. In addition, the invention provides a novel approach for finding new cancer molecular markers from the cfDNA through combination of SALP-Seq and machine learning.

Description

technical field [0001] The invention relates to the field of tumor markers and classification biotechnology, in particular to a cancer biomarker based on cfDNA-based sequencing and data analysis and its new classification method in cfDNA sample classification and its application. Background technique [0002] Cancer is an important public health problem worldwide. Its morbidity and mortality are increasing year by year, and the treatment effect is poor, seriously affecting people's health and quality of life. According to GLOBOCAN, there were approximately 18.08 million new cancer cases and 9.56 million deaths worldwide in 2018, the majority of whom lived in low- and middle-income countries. It is estimated that by 2025, there will be approximately 20 million new cases of cancer each year. The latest cancer statistics show that in 2019, 1,762,450 new cancer cases and 606,880 cancer deaths are expected to occur in the United States. Although previously the incidence of can...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886C12Q1/6869G16B30/00G16B40/00
CPCC12Q1/6869C12Q1/6886G16B30/00G16B40/00
Inventor 王进科刘世财
Owner SOUTHEAST UNIV
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