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Microsatellite unstable site screening and analysis model construction method and device

A microsatellite instability and microsatellite locus technology, applied in the field of biological information, can solve the problems of difficulty in covering all types of samples, low detection efficiency, unsatisfactory specificity and sensitivity, etc.

Inactive Publication Date: 2020-02-14
BEIJING GENEPLUS TECH +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0006] Therefore, the technical problem to be solved by the present invention is that there are many MSI sites in the prior art and it is difficult to cover all types of samples, the specificity and sensitivity are not satisfactory, and the detection efficiency is low, thereby providing a microsatellite instability site The construction method and device of the screening and analysis model, and the constructed microsatellite instability site screening model can screen out the MSI sites that can indicate the MSI status of the corresponding type of samples according to the different types of samples, and eliminate the existing unnecessary detection MSI site, improve the detection efficiency, while having high sensitivity and specificity, to meet the clarity of detection

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  • Microsatellite unstable site screening and analysis model construction method and device
  • Microsatellite unstable site screening and analysis model construction method and device
  • Microsatellite unstable site screening and analysis model construction method and device

Examples

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Embodiment 1

[0079] Example 1 Construction of a screening model for microsatellite instability sites

[0080]The present embodiment provides a method for constructing a microsatellite instability site screening model, comprising the steps of:

[0081] (1) Select the reference genome. In this example, select the human reference genome, use the gene capture chip to capture, and then use the microsatellite repeats (Satellite repeats) in the UCSC repeat mask database. The file address is http: / / hgdownload.cse.ucsc .edu / goldenPath / hg19 / database / rmsk.txt.gz, select the single-base repeat region in the gene capture chip region, and use the selected microsatellite sites as candidate MS sites;

[0082] (2) Compare several cancer tissue samples with their paired samples. The type of cancer tissue samples is not limited. In this embodiment, lung cancer tissue samples are selected, and the microsatellite instability (MSI) status of the cancer tissue samples is detected by immunohistochemical method. ...

Embodiment 2

[0092] Example 2 Construction of Microsatellite Instability Analysis Model

[0093] This implementation provides a method for the construction of a microsatellite instability analysis model, including using the model constructed by the microsatellite instability site screening model construction method in Example 1, and performing microsatellite instability analysis on the above basis Model construction:

[0094] Take the lung cancer sample to be tested and calculate the information entropy of the MSI site according to the step (2) in Example 1, and compare the obtained information entropy value with the entropy threshold of the MSI site. When >30% of the sites are MSI-positive, the lung cancer sample to be tested is high-frequency microsatellite instability; when there are ≥10% of all MSI sites in the lung cancer sample to be tested, and ≤30% of the sites are When MSI is positive, the lung cancer sample to be tested is low-frequency microsatellite instability; when <10% of a...

Embodiment 3

[0095] Example 3 Construction and verification of microsatellite instability analysis model

[0096] This embodiment provides a method for building a microsatellite instability analysis model, the flow chart is as follows figure 1 shown, including:

[0097] (1) Take hg19 as the reference genome, use the gene capture chip (1021panel chip of C1021OncoD product) to capture, and then use the scan step of MSIsensor software to scan the microsatellite position in the region of the gene capture chip (1021panel chip of C1021OncoD product) point, and then use bedtools to pick out the microsatellite loci that fall within the region of the gene trap chip (1021panel chip of C1021OncoD product), and select a total of 370 microsatellite loci as candidate MS loci;

[0098] (2) Select PCR technology, compare several colorectal cancer tissue samples with their corresponding paired samples, and detect the microsatellite instability (MSI) status of colorectal cancer tissue samples, and the tes...

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Abstract

The invention provides a microsatellite unstable site screening and analysis model construction method and device. The method comprises the following steps of: S1, taking a microsatellite site of a reference genome as a candidate MS site, S2, selecting a plurality of samples with known microsatellite instability detection state information as training set samples, carrying out mutation detection on candidate MS site areas of the training set samples, respectively recording mutation types and numbers, and calculating information entropy of mutation of each candidate MS site, and S3, correlatingthe microsatellite instability detection state information with the entropy of the information entropy of the mutation of each candidate MS site, selecting an entropy threshold of each candidate MS site for distinguishing the microsatellite instability detection result, and screening out the candidate MS site with a high distinguishing degree as an MSI site. According to the scheme, the problemsof low detection efficiency caused by excessive fixed MSI sites and low detection specificity and sensitivity caused by incapability of covering all types of samples in the prior art are solved.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a method and device for screening and analyzing microsatellite instability sites. Background technique [0002] Microsatellite sequence (Microsatellite, MS), also known as short tandem repeats (Short tandem repeats, STRs) or simple repeat sequence, is composed of 10 to 50 repeat units consisting of 1 to 6 nucleotides in series with a high degree of polymorphism. Sexual simple tandem sequences widely exist in prokaryotic and eukaryotic genomes. Microsatellite instability (MSI) refers to the phenotype of insertion or deletion of base pairs in microsatellite regions caused by replication errors (RER). The main cause of microsatellite instability is that the gene function defect involved in the pairing error repair (mismatch repair, MMR) leads to the production of a defective protein, which cannot normally correct replication errors, thereby causing duplication of mic...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B5/00G16B20/30G16B40/00
CPCG16B5/00G16B20/30G16B40/00
Inventor 黄毅易鑫杨玲刘久成吴玲清
Owner BEIJING GENEPLUS TECH
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