Metagenome or macrotranscriptome sequencing data automatic analysis method and system

An automated analysis and macro-transcriptome technology, applied in the field of automatic analysis of metagenomic or macro-transcriptome sequencing data, can solve problems such as slow interpretation speed affecting the ultimate delivery of pathogen detection, and it is difficult to quickly go back to historical samples

Active Publication Date: 2020-02-04
广州微远医疗器械有限公司 +4
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  • Abstract
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  • Claims
  • Application Information

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Problems solved by technology

[0003] However, the current screening of pathogenic bacteria relies heavily on manual interpretation, which leads to the following limitations: the slow interpretation speed of a sample affects the ultimate delivery of pathogen d

Method used

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  • Metagenome or macrotranscriptome sequencing data automatic analysis method and system
  • Metagenome or macrotranscriptome sequencing data automatic analysis method and system
  • Metagenome or macrotranscriptome sequencing data automatic analysis method and system

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0077] A method for automatic analysis of metagenomic or metatranscriptome sequencing data, which operates in a linux environment, and operates according to the following steps at the computer level:

[0078] (1) Prepare the required programs: auto_report.pl (for automatic interpretation), auto_report.R (for generating automatic interpretation reports).

[0079] (2) Prepare the required databases: CRP database, CCRP database, background database corresponding to each sample type, detection process, and strain type, etc.

[0080] Specifically, the CRP database (database of clinically reportable pathogens) is established by the following methods: according to the research progress or case reports of suspected pathogens in the literature, to confirm the pathogenic bacteria to establish a database of clinically reportable pathogens; for example, it can be found in NCBI Investigate the published literature in NCBI pubmed in the database, query the research progress or case reports ...

Embodiment 2

[0090] A method for automatic analysis of metagenomic or metatranscriptome sequencing data, the logic flow of which is as follows Figure 1-4 shown, including the following steps:

[0091] 1. Obtain sequencing data.

[0092] Obtain the off-machine data of the metagenomic or metatranscriptome sequencing of the sample to be analyzed, match the microbial type with the gene sequence information, and obtain the initial bacterial species list.

[0093] For example, obtain a clinical sample to be analyzed ("test1", alveolar lavage fluid), match the microbial type with the gene sequence information, and obtain the result annotation file of the information analysis: bacteria result: "test1.bac.anno", virus result: " test1.virus.anno", fungi result: "test1.fungi.anno", parasite result: "test1.parasite.anno".

[0094] According to different background library types, select the corresponding background library for comparison. Specifically, such as:

[0095] Among them, 57 results were...

Embodiment 3

[0165] The automatic analysis system is established according to the method of the above-mentioned Examples 1-3. Before the automatic analysis system is officially put into use, a systematic evaluation is required to evaluate the degree of consistency between the automatic interpretation and the manual interpretation, and whether the requirements are met.

[0166] Randomly selected 890 historical samples from 6 batches of clinical samples in our company between August 4, 2019 and August 26, 2019, which were manually interpreted, and re-interpreted using the automated analysis system of the present invention. Then, at the result level, the consistency between manual interpretation and automatic interpretation was counted, and the results are as follows:

[0167] Table 7. Consistency evaluation

[0168] consistency Number of cases percentage unanimous 881 98.98％ inconsistent 9 1.02％

[0169] The consistency with manual interpretation is as high a...

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Abstract

The invention relates to a metagenome or macrotranscriptome sequencing data automatic analysis method and system and belongs to the technical field of data gene detection. According to the method, a CRP (clinically reported pathogen) database and a background library are compared with differences of negative control samples to remove redundant information; a report strain is selected through ranking of strains in the genus; and finally, based on a CCRP database, the strains are screened and filtered again to prevent leakage, the report strain is obtained, and a report is automatically generated. According to the method and system, the manual interpretation process is automated, the interpretation speed and accuracy are improved, and meanwhile, backtracking of historical information is brought into the interpretation process, so that the interpretation accuracy and reliability are improved.

Description

technical field [0001] The invention relates to the technical field of gene detection, in particular to a method and system for automatic analysis of metagenomic or metatranscriptome sequencing data. Background technique [0002] At present, metagenomic or metatranscriptome technology has begun to be widely used in the rapid detection of unknown pathogens to assist clinical diagnosis and treatment. However, due to the influence of environment, reagents, human microecology and other factors, the detection of a sample is often accompanied by the detection of hundreds of microorganisms. out the real pathogenic bacteria. [0003] However, the current screening of pathogenic bacteria relies heavily on manual interpretation, which leads to the following limitations: the slow interpretation speed of a sample affects the ultimate delivery of pathogen detection; the accuracy of the interpretation results largely depends on the interpretation of the personnel Professionalism and exp...

Claims

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Application Information

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IPC IPC(8): G16B30/00G16B50/00
CPCG16B30/00G16B50/00
Inventor 许腾刘足苟雪静李永军王小锐苏杭
Owner 广州微远医疗器械有限公司
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