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Tumor marker screening method based on single base substitution characteristic and application

A technology of tumor markers and screening methods, applied in the field of quantification of related single base substitution features, can solve problems such as inability to find, different sites and types, etc.

Pending Publication Date: 2021-09-07
BERRY ONCOLOGY CO LTD +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Through a large number of investigations and previous studies, tumors will accumulate a large number of mutations in the process of occurrence and development, but due to the influence of the proportion of blood into the blood and the current mutation site detection algorithm, there are fewer high-reliability sites in the end, and even for the same tumor For tumors, the sites and types of base substitutions in different patients are different, so it is impossible to find fixed features as tumor markers

Method used

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  • Tumor marker screening method based on single base substitution characteristic and application
  • Tumor marker screening method based on single base substitution characteristic and application
  • Tumor marker screening method based on single base substitution characteristic and application

Examples

Experimental program
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Effect test

Embodiment 1

[0079] The enrolled samples of this embodiment come from another study of the inventor, in which several ideas of the inventor were verified simultaneously, and a total of 957 subjects were included, specifically 481 patients with liver cancer (HCC) and 476 patients. healthy control (NC) ( figure 1 ). Follow the steps below to extract plasma cell-free DNA (cfDNA):

[0080](1) Take 3ml of peripheral blood (collected and stored in Streck cell-free DNA blood collection tubes), Eppendorf centrifuge (5810R and 5427R, German), and centrifuge at 1600g at low speed for 10min at a low temperature of 4°C, and only take the supernatant; Then centrifuge at a high speed of 16000 g for 10 min, and take the supernatant to obtain the plasma sample. The cell-free DNA in the plasma was extracted with the kit MagMAXCell-Free DNA Isolation Kit (Thermo) and the nucleic acid extractor (Thermo Kingfisher FLEX, USA).

[0081] (2) DNA quality detection: DNA concentration was detected by Qubit 3 Nu...

Embodiment 2

[0083] Low-depth whole-genome sequencing was performed on the cfDNA samples of all subjects prepared in Example 1. The sequencing process is as follows:

[0084] (1) WGS library construction and on-machine sequencing: Take 5ng cfDNA to construct a pre-library with an Enzymatics (USA) related kit, mainly including two steps of end repair (5X ER / A-Tailing Enzyme Mix) and adapter (WGSLigase) , the adapter sequence is suitable for the IlluminaNovaSeq 6000 sequencing platform. The adapters were ligated and purified using XP magnetic beads (Agencourt AMPure XP beads, Beckman Coulter). The concentration value of WGS library was determined by qPCR (KAPALibrary Quant Kit, Roche), and the library size was determined by Fragment Analyzer (Agilent, USA). Afterwards, paired-end 150bp sequencing was performed on the IlluminaNovaSeq 6000 sequencing platform, and the average data volume of a single sample was 2X that of the whole genome.

[0085] (2) Data quality control: Use Fastp softwar...

Embodiment 3

[0087] The sequencing data of tumor patients and healthy people were divided into independent training set (510 cases), validation set (98 cases) and test set (349 cases). The training set is used to screen the characteristic single base substitution type, the validation set is used to determine the optimal threshold of the model, and the test set is used to evaluate the model performance.

[0088] Based on the sequencing data obtained in Example 2, calculate the proportion of each type of single-base substitution in each training set sample: use Varscan software to output all sites with single-base substitution mutations in the whole genome, and select the mutation support number (that is, the same base substitution support number) is greater than or equal to 2 sites, remove the high-frequency mutation sites included in the dbSNP database, so as to reduce the impact of background mutations as much as possible, and reduce the systematic error to a certain extent. influences. ...

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Abstract

The invention discloses a screening method of tumor markers or a combination thereof. The screening method meets the following conditions: 1) screening tumor-related markers by using one or more indexes including a single base substitution feature; and / or 2) comprising a step of detecting a single base substitution feature. The invention also provides a tumor risk prediction, screening and / or diagnosis model construction method based on the screening method, a cancer risk prediction, screening and / or diagnosis method, and a related tumor marker combination, a kit, a system, a device, a computer readable storage medium and equipment.

Description

technical field [0001] The present invention belongs to the field of sequencing technology, and in particular relates to a method for screening tumor markers based on single-base substitution characteristics and related tumor risk prediction, screening and / or diagnostic model building methods and diagnostic methods, devices, systems, and computer-based methods. Read storage media, equipment, and related single-base substitution feature quantification methods. Background technique [0002] Cancer is one of the major diseases that endanger human health. According to the latest global cancer statistics in 2018, there were 18.19 million new cancer cases and 9.6 million cancer deaths worldwide, while the cancer prevalence rate in my country is at the upper-middle level in the world. Compared with late-stage cancers, early-stage cancers have not metastasized and are easier to remove through surgery, radiotherapy, chemotherapy, etc. Treatment interventions in the early stages of ca...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B5/00G16B20/20G16B20/30G16B20/50G16B40/00C12Q1/6886C12N15/11
CPCG16B20/30G16B20/20G16B40/00G16B20/50G16B5/00C12Q1/6886C12Q2600/156
Inventor 张清政白健吴琳
Owner BERRY ONCOLOGY CO LTD
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