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A method for accurate detection of dna virus in human genome

A technology for genome and human detection, applied in genomics, biochemical equipment and methods, proteomics, etc., can solve the problems of inability to determine whether HPV is integrated and the detection of integration status, and the detection of HPV types cannot be covered

Active Publication Date: 2021-03-30
THE FIRST AFFILIATED HOSPITAL OF SUN YAT SEN UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

No matter which method is used above, it cannot cover all HPV types, and it cannot avoid cross-reaction between different types of HPV. Most importantly, none of the above methods can determine whether HPV is integrated or not.

Method used

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  • A method for accurate detection of dna virus in human genome
  • A method for accurate detection of dna virus in human genome
  • A method for accurate detection of dna virus in human genome

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0091] An embodiment of the method for accurately detecting DNA viruses in the human genome of the present invention comprises the following steps:

[0092] For patient A with mild cervicitis, part of the cervical tissue was taken for capture sequencing. The data obtained by sequencing were analyzed as follows.

[0093] By filtering the comparison information of the sequencing reads, the reads from the viral DNA are accurately selected, and by removing the repeat offsets that may be caused during the library construction process, the reads of different types of viral DNA The number of segments is counted to indirectly reflect the load of the infected virus type. The specific steps are as follows:

[0094] (1) In the initial comparison process, all types of HPV virus genomes collected from the Papillomavirus Genome Database PaVE, the collected HPV virus genomes are used as pseudochromosomes, and are merged with the chromosomes of the human genome to construct a hybrid Genome;...

Embodiment 2

[0117] In mild cervicitis patient B (see Example 1 for the detection method), it was found that three HPV types (HPV16, HPV 31, HPV56) were infected (such as Figure 4 As shown), but no HPV integration was found, follow-up can be continued to avoid unnecessary colposcopy, which is different from the international guidelines for HPV16 positive recommendation for colposcopy referral.

Embodiment 3

[0119] In the follow-up follow-up of patient C with low-grade cervical lesions (see Example 1 for the detection method), it was found that high-risk HPV16 infection (such as Figure 5 As shown), but no HPV integration was found, follow-up can be continued to avoid unnecessary colposcopy, which is different from the international guidelines for HPV16 positive recommendation for colposcopy referral.

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Abstract

The invention discloses a method capable of accurately detecting DNA viruses in the human genome. The method can accurately evaluate the infection type and load analysis method of double-stranded DNA viruses, and at the same time accurately and flexibly judge the double-strands integrated into the human genome. DNA virus type, integration site and resulting fusion sequence. The method of the present invention can simultaneously detect a variety of different virus infections; the method of the present invention can finely distinguish the classification of reads of different subtypes of the same virus, so as to judge the viral load; the method of the present invention is suitable for different sources of library construction The type of reads, with the versatility of NGS virus pathogen detection.

Description

technical field [0001] The invention relates to the technical field of virus detection, in particular to a method for accurately detecting DNA viruses in human genome. Background technique [0002] Double-stranded DNA virus-associated tumors refer to tumors that are closely related to double-stranded DNA virus infection, and a series of biological effects generated by the interaction between double-stranded DNA virus and host cells trigger carcinogenesis, often accompanied by high-risk carcinogenesis Infection of viral strains, insertion of genomic DNA of high-risk oncogenic viruses into human cell DNA, and co-infection of multiple virus subtypes during tumor progression. For example, double-stranded DNA viruses such as Human papillomavirus (HPV) and cervical cancer, head and neck tumors, etc.; our previous research found that Hepatitis B virus (HBV), Epstein–Barr virus (EBV) has a common phenomenon of DNA integration into the human genome , and the generation of DNA integr...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6869G16B20/30G16B40/00
CPCC12Q1/6869G16B20/30G16B40/00C12Q2531/113C12Q2535/122C12Q2537/165C12Q2545/101
Inventor 胡争崔资凤许微
Owner THE FIRST AFFILIATED HOSPITAL OF SUN YAT SEN UNIV
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