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System and method for analyzing HBV DNA integration events from in-vitro serum

An event and serum technology, applied in the field of analysis of HBV DNA integration events, can solve the problems of lack of systematic methods for HBV DNA capture and sequencing results, and achieve good practicability and practical application effects

Pending Publication Date: 2021-07-09
CHONGQING MEDICAL UNIVERSITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

How to carry out effective bioinformatics processing of HBV DNA capture sequencing results still lacks a systematic method, we have established a bioinformatics method that can accurately and sensitively process HBV DNA capture sequencing data

Method used

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  • System and method for analyzing HBV DNA integration events from in-vitro serum
  • System and method for analyzing HBV DNA integration events from in-vitro serum
  • System and method for analyzing HBV DNA integration events from in-vitro serum

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0070] Detection of HBV DNA integration events using simulated data.

[0071] 1. Sample preparation and data acquisition

[0072] Establishment of Human Reference Genome and HBV Reference Genome Database

[0073] There are multiple versions of the human reference genome. We believe that the decoy sequence can help improve the accuracy of the alignment, so we choose the hs37d5 version as our human genome reference sequence (decoy sequence bait sequence, from HuRef, BAC or plasmid clone and NA12878) . And download the annotation file of the corresponding version.

[0074] There are many types of HBV. We downloaded the reference genomes of HBV A / B / C / D / E / F / G / H types from the NCBI database and combined them to construct a reference sequence comparison index library.

[0075] Artificially synthesize the integration sequence of 32 kinds of HBV DNA integrated into the human genome; mix the remaining human cells at a certain concentration to obtain the sample to be tested. Using ca...

Embodiment 2

[0099] Thirty-two HBV DNA integration events were artificially synthesized, and the sequence information is shown in Table 1 below.

[0100] Table 1 Record table of 32 kinds of HBV DNA integration events

[0101]

[0102]

[0103] The specific synthetic sequence is SEQ ID NO:1-SEQ ID NO:32.

[0104]After performing illumina sequencing on 30 samples, calculate the normalized number of support integration event sequence fragments (Normalized Number of Support Segments, nnss) of the above 32 integration events in the sample. When the nnss of any of the integration events is ≥ 1, the integration The event is judged as positive, that is, an integration event occurred in the sample. See Table 2 for detailed results

[0105] Table 2 Test results of 30 samples

[0106]

[0107]

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Abstract

The invention belongs to the technical field of biology and relates to a system and method for analyzing HBV DNA integration events from an in-vitro serum sample. The system comprises a data filtering module, a high-quality sequence splicing module, a sequence comparison module, an integration event identification module and an integration event annotation analysis module; and the integration event identification module is used for analyzing the HBV DNA integration events according to a preliminary comparison result. According to the system and the method for analyzing the HBV DNA integration events from the in-vitro serum sample, provided by the invention, the integration event information is effectively obtained, the HBV DNA integration condition in the sample can be efficiently answered; and the system and the method have better practicability and are more beneficial to practical application.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a system and method for analyzing HBV DNA integration events from isolated serum. Background technique [0002] Viral hepatitis has always been an important public health problem plaguing the world. The World Health Organization proposed a global viral hepatitis strategy in 2016: the incidence rate was reduced by 65%, and this strategy is of great significance to China. my country is a big country with hepatitis B. According to statistics, the number of people infected with HBV in my country in 2016 was 86 million, and the number of people who needed treatment was 32 million. In addition, viral hepatitis can also lead to end-stage liver diseases such as cirrhosis, liver failure and liver cancer. Therefore, domestic hepatitis B prevention and control The situation is still very serious. [0003] For the treatment of hepatitis B, there are currently two types of drugs, nucleotide anal...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B20/30
CPCG16B30/10G16B20/30Y02A90/10
Inventor 黄爱龙陈娟龙泉鑫邓海君
Owner CHONGQING MEDICAL UNIVERSITY
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