Unlock instant, AI-driven research and patent intelligence for your innovation.

Method for identifying chromosome outer circular DNA composition gene of tumor cell

An extrachromosomal and tumor cell technology, applied in the field of identification of extrachromosomal circular DNA constituent genes of tumor cells, can solve the problems of low resolution, unrealizable detection, limitations, etc., and achieve the effect of ensuring accuracy

Active Publication Date: 2021-11-30
HARBIN MEDICAL UNIVERSITY
View PDF6 Cites 2 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] Extrachromosomal circular DNA was first discovered by HOTTA Y in 1965 by analyzing the karyotype of tumor cells, but due to the limitation of molecular technology at that time, it failed to receive widespread attention. Later, due to FISH (Fluorescence insitu hybridization, fluorescence in situ hybridization With the rise of technology, people have further understood the molecular structure of extrachromosomal circular DNA
However, FISH technology has the following disadvantages: 1) FISH experimental methods are very cumbersome and expensive; 2) its resolution is very low, and it can only detect an area of ​​about 1M; cells, which is impossible for the detection of clinical tissue samples
However, the software needs to provide a specified bed (a file type that can indicate the location of the target gene in targeted sequencing) region when using it, and the software currently does not have any tools that can predict the bed region. In addition, because of the gene amplification of tumor cells is abnormal and the software is not effectively corrected for the copy number of tumor cells
[0005] Therefore, the existing technology still lacks extensive and in-depth research on the structure and composition of extrachromosomal circular DNA, and a method that can predict and verify the extrachromosomal circular structure of chromosomes is needed

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Method for identifying chromosome outer circular DNA composition gene of tumor cell
  • Method for identifying chromosome outer circular DNA composition gene of tumor cell
  • Method for identifying chromosome outer circular DNA composition gene of tumor cell

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0060] figure 1 It is a flowchart of an embodiment of the present invention, such as figure 1 As shown, this embodiment provides a method for identifying genes constituting extrachromosomal circular DNA of tumor cells, which includes the following steps:

[0061] Step 1: Perform whole-genome next-generation sequencing on the sample to be analyzed through the illumina platform (the next-generation sequencing platform provided by Illumina), and obtain the filtered fastq format (a text format that stores biological sequences and corresponding quality evaluations) Next-generation sequencing results of files and quality control;

[0062] In this embodiment, among them, step 1 specifically is:

[0063] Step 11: Use barcode (DNA barcode) + NGS (Next Generation Sequencing, next-generation sequencing technology, that is, high-throughput sequencing) to perform sequencing. Specifically, perform whole-genome next-generation sequencing on the sample to be analyzed through the illumina pl...

Embodiment 2

[0102] In this example, the human ovarian cancer cell line UACC-1598 is used as the material, and the method for identifying the genes constituting extrachromosomal circular DNA of tumor cells is as follows:

[0103] Step 1: The fastq file is obtained through next-generation sequencing, and the quality is qualified after performing quality control according to the standard of removing reads with a ratio of N greater than 10%. figure 2 It is a schematic diagram of part of the results obtained by performing step 1 in an embodiment of the present invention, such as figure 2 Partial quality control qualified reads are shown. Then, the extracted fastq file was compared with the hg19 reference genome by BWA software, and the first bam format file after comparison was obtained.

[0104] Step 2: Use CNVkit to filter out the regions with Copynumber>3 and Length(kb)>100, as shown in the partially screened examples shown in Table 1.

[0105] Table 1

[0106]

[0107] Step 3: Use ...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

The invention discloses a method for identifying exochromosome circular DNA composition genes of tumor cells, and the method comprises the following steps: adding umi in next-generation sequencing to correct errors caused by PCR, designing a filtering algorithm according to next-generation sequencing data of a tumor sample, and providing a new quality control standard which is more suitable for analyzing exochromosome DNA; and finally, correcting the linker sequence by combining three-generation sequencing, so that the prediction accuracy is ensured.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a method for identifying genes constituting extrachromosomal circular DNA of tumor cells. Background technique [0002] Extrachromosomal circular DNAs (eccDNAs) are sequences produced on chromosomes and have high heterogeneity in origin, which can affect the life activities of cells and promote the evolution and adaptive evolution of tumor cells. important genomic features. [0003] Extrachromosomal circular DNA was first discovered by HOTTA Y in 1965 by analyzing the karyotype of tumor cells, but due to the limitation of molecular technology at that time, it failed to receive widespread attention. Later, due to FISH (Fluorescence insitu hybridization, fluorescence in situ hybridization With the rise of technology, people have further understood the molecular structure of extrachromosomal circular DNA. However, FISH technology has the following disadvantages: 1) ...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00G16B40/00G16B20/50G16B20/20
CPCG16B30/00G16B40/00G16B20/50G16B20/20Y02A90/10
Inventor 张莹董科显贾学渊王冬于景翠白静傅松滨
Owner HARBIN MEDICAL UNIVERSITY