Methods and systems for acquiring nucleic acid information of parasites and classifying parasites by sequencing

A parasite and sequencing technology, applied in the field of high-throughput sequencing

Pending Publication Date: 2019-09-24
SHENZHEN HUADA GENE INST
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, this process first requires certain prior knowledge, and it also has high requirements for the clinical knowledge and experience of clinicians, and these confirmatory assumptions are not necessarily accurate, and even some rare parasitic infections may be carried out multiple times. Verification may not be able to do accurate classification and identification

Method used

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  • Methods and systems for acquiring nucleic acid information of parasites and classifying parasites by sequencing
  • Methods and systems for acquiring nucleic acid information of parasites and classifying parasites by sequencing
  • Methods and systems for acquiring nucleic acid information of parasites and classifying parasites by sequencing

Examples

Experimental program
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Effect test

Embodiment 1

[0101] Cell-free DNA was isolated from human peripheral blood and subjected to high-throughput sequencing as follows.

[0102] 1. Select experimental samples, which come from peripheral blood samples collected by cooperative hospitals.

[0103] Including 25 samples clinically identified as echinococcosis infection and 12 negative control samples. The negative control sample is a sample not infected by echinococcosis. Among them, echinococcosis is a chronic parasitic disease caused by human infection with the larvae (echinococcus) of Echinococcus.

[0104] 2. Extraction of free DNA (cfDNA) from peripheral blood plasma.

[0105] 3. Use Agilent 2100 Bioanalyzer (Agilent) to detect the concentration and quality of the extracted DNA.

[0106] 4. Fragment 2 μg of DNA with Covaris E210 (Covaris):

[0107] Fragmentation processing uses Covaris E210 interrupter, the target length is 150bp-200bp, and the relevant parameters are as follows: Duty / cycle: 20, Intensity: 5, Cycle / burst: 20...

Embodiment 2

[0111] In this embodiment, biological analysis is performed on the sequencing data obtained by sequencing according to the following method, so as to determine the type of parasite.

[0112] 1. Construction of parasite reference database. At present, the known parasites that infect humans mainly include protozoa (Protozoa) and worm (Helminths), so the database is constructed based on these two categories. The protozoa reference sequences are from the protozoa database in NCBI refseq, and the worms are from the WormBase ParaSite database. The reference sequences of the two types of data were then pooled together to construct a parasite reference sequence database.

[0113] 2. Use SOAPnuke (-l 15-q 0.2-n 0.05) to perform quality control on the data obtained by high-throughput sequencing in Example 1, and remove the sequencing reads with low quality values ​​and those containing more N.

[0114] Among them, the parameters shown in the brackets of SOAPnuke are the various parame...

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Abstract

The invention relates to the field of high-throughput sequencing and particularly relates to methods and systems for acquiring nucleic acid information of parasites on a host and classifying parasites by high-throughput sequencing. The method for acquiring nucleic acid information of parasites comprises the following steps: acquiring sequence data of free DNA in host blood based on high-throughput sequencing; filtering off host nucleic acid data in the sequence data of free DNA in the host blood by taking the nucleic acid sequence of the host as a reference; filtering off repeated sequence data in the sequence data of free DNA in the host blood; and acquiring the nucleic acid data of parasites to acquire the nucleic acid information of parasites on the host. Based on the method, the invention further provides the system for acquiring the nucleic acid information of parasites, and a method and system for identifying the species of a parasite on a host. The methods and systems are not limited to prior knowledge, can improve the universality of detection methods, have high sensitivity and are rapid.

Description

technical field [0001] The invention relates to the field of high-throughput sequencing, in particular to a method and system for obtaining nucleic acid information of parasites on a host through high-throughput sequencing, and a method and system for identifying the type of parasites on a host through high-throughput sequencing. Background technique [0002] Parasites are a class of microorganisms that depend on their hosts for nutrients to survive. The parasites known to cause human diseases mainly include Protozoa and Helminths. There are many kinds of parasites, and different parasite infections can cause various clinical phenotypes. For different parasite infections, clinicians often need to judge the possibility of infection with a certain parasite based on their clinical phenotype assumptions, and then Do corresponding confirmatory classification and identification, such as etiological microscope classification and identification, immunological classification and iden...

Claims

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Application Information

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IPC IPC(8): C12Q1/6869C12M1/34
CPCC12Q1/6869G16B30/00C12Q2535/122
Inventor 姬敬开麻锦敏
Owner SHENZHEN HUADA GENE INST
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