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Tumor neoantigen prediction method based on HPV integration

A prediction method, antigen technology, applied in the field of bioinformatics, can solve the problems of deletion, chromosome amplification, host cell genome instability, etc.

Pending Publication Date: 2021-09-07
NEOCURA BIO-MEDICAL TECH CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

HPV integration causes strong instability of the host cell genome, resulting in a large number of chromosomal amplifications, deletions, rearrangements, and translocations near the integration site

Method used

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  • Tumor neoantigen prediction method based on HPV integration
  • Tumor neoantigen prediction method based on HPV integration
  • Tumor neoantigen prediction method based on HPV integration

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Experimental program
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Effect test

Embodiment 1

[0039] Such as figure 1 Shown, a kind of neoantigen prediction method based on HPV integration, the method comprises the following steps carried out by processor:

[0040] S01, Assembly of tumor sample transcripts

[0041] Specifically, firstly, the ribosomal chain specific library construction method and the small fragment enrichment screening library construction method were used to construct the library and sequence, and obtain the deep sequencing data of the sample mRNA. The sample data includes multiple overlapping or partially overlapping short-read sequences. The degree of overlap is related to the depth of sequencing. The RNA-Seq sequencing data of a sample of not less than 15G should be obtained.

[0042] Secondly, filter the sequencing data, remove short-read sequences with an average base quality of less than 20 or contain sequencing primer adapters in the sequencing data, and convert the data format into a form that can be accepted by the subsequent assembly softw...

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Abstract

The invention discloses a tumor neoantigen prediction method based on HPV integration, and belongs to the technical field of bioinformatics. The method comprises the following steps: S01, assembling a tumor sample transcript; s02, screening a sample HPV (human papillomavirus) integrated transcript; s03, translating the HPV and integrating the transcript into polypeptide; s04, obtaining polypeptide short sequence fragments, and filtering polypeptides in human normal proteome; s05, performing genetic typing on the human leukocyte antigen of the sample; and S06, predicting the affinity of the peptide fragment, and screening new antigens. The new antigen obtained by the invention is a result of HPV integration and is closely related to a disease progression process. The new antigen obtained by the invention comes from RNA sequencing data, is a result of cell transcription, and has higher probability of translation to produce protein.

Description

technical field [0001] The invention belongs to the technical field of bioinformatics, and in particular relates to a method for predicting new antigens based on HPV insertion fragments in human genome. Background technique [0002] HPV (Human papillomavirus), also known as human papillomavirus, is a DNA virus belonging to the genus Papillomavirus of the family Papillomaviridae, which can infect human epidermis and mucosal tissues. There are more than 100 subtypes of HPV virus found so far, more than 80 of which are closely related to the human body. Studies have confirmed that HPV infection is the pathogenic factor of cervical cancer, and most cervical cancers are caused by persistent infection of high-risk HPV, among which the most representative high-risk HPV subtypes are HPV16 and HPV18. It takes about 15 years from infection with HPV to eventual development of cervical cancer. In the early stage of HPV infection, the HPV genome exists in episomal form outside the huma...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B25/10G16B30/00C12Q1/6869
CPCG16B25/10G16B30/00C12Q1/6869C12Q2535/122C12Q2537/165
Inventor 万季刘鹏沈一鸣潘有东王弈
Owner NEOCURA BIO-MEDICAL TECH CO LTD
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