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Method for establishing baseline for detecting microsatellite instability, method for establishing model for detecting microsatellite instability, and application

A technology for microsatellite instability and microsatellite loci, applied in character and pattern recognition, instrument, sequence analysis, etc., can solve the problems of low detection sensitivity of microsatellite loci, and achieve the effect of improving utilization efficiency and sensitivity

Active Publication Date: 2019-12-13
北京橡鑫生物科技有限公司
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  • Application Information

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Problems solved by technology

[0004] The main purpose of the present invention is to provide a method and application for establishing a baseline and model for detecting microsatellite instability, so as to solve the problem of low detection sensitivity of microsatellite sites in sequencing data in the prior art

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  • Method for establishing baseline for detecting microsatellite instability, method for establishing model for detecting microsatellite instability, and application
  • Method for establishing baseline for detecting microsatellite instability, method for establishing model for detecting microsatellite instability, and application
  • Method for establishing baseline for detecting microsatellite instability, method for establishing model for detecting microsatellite instability, and application

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Embodiment 1

[0042] In a preferred embodiment of the present application, a method for establishing a baseline for detecting microsatellite instability is provided, figure 2 is a flowchart of a method for establishing a baseline for detecting microsatellite instability according to an embodiment of the present invention. Such as figure 2 As shown, the method includes:

[0043] Step S101, searching for all available microsatellite sites in the region corresponding to the sequence data of the sample to be tested on the human reference genome;

[0044] Step S102, using the sequencing data of multiple control blood cell samples, counting the average coverage depth baseline of each microsatellite site in each control blood cell sample, and retaining the microsatellite sites whose average coverage depth baseline meets the depth threshold as candidate microsatellite sites ;

[0045] Step S103, using each candidate microsatellite site and the average coverage depth baseline, calculating the a...

Embodiment 2

[0054] In a preferred embodiment, the present application also provides a method for establishing a model for detecting microsatellite instability, the method comprising: using any of the aforementioned methods to establish a baseline for detecting microsatellite instability; using a machine learning algorithm The average coverage depth and number of peaks in multiple positive samples and multiple negative samples in the baseline were modeled to obtain a model for detecting microsatellite instability.

[0055] In this preferred embodiment, on the one hand, the baseline for detection is established by maximizing the use of microsatellite site information in the sequencing data; The number of peaks and the number of peaks for each detected microsatellite locus in negative samples established a predictive model for detecting microsatellite instability. The model established by the machine learning method predicts the microsatellite status of the sample, and the machine learning m...

Embodiment 3

[0058] In a preferred embodiment of the present application, a model for detecting microsatellite instability is also provided, and the model is constructed by using the method for establishing a model for detecting microsatellite instability. The model established by machine learning algorithm is used to analyze and judge the microsatellite status of the sample, which has high sensitivity and specificity.

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Abstract

The invention provides a method for establishing a baseline for detecting microsatellite instability, a method for establishing a model for detecting microsatellite instability, and an application. The method for establishing a baseline for detecting microsatellite instability includes: searching all available microsatellite loci in a region corresponding to the sequencing data of a to-be-tested sample on a human reference genome; obtaining and maintaining microsatellite loci with an average coverage depth baseline that meets a depth threshold as candidate microsatellite loci by using the sequencing data of multiple control blood cell samples; calculating and searching out, by using each candidate microsatellite locus and the average coverage depth baseline, the candidate microsatellite loci with a significant difference in the number of peaks among multiple positive samples and multiple negative samples as detection microsatellite loci, such that the average coverage depth and the number of peaks of each detection microsatellite loci in the multiple positive samples and the multiple negative samples form a baseline for detecting the microsatellite instability. The method not onlyimproves the utilization efficiency of the sequencing data, but also improves the detection sensitivity.

Description

technical field [0001] The invention relates to the field of gene sequencing data analysis, in particular to a method and application for establishing a baseline and a model for detecting microsatellite instability. Background technique [0002] Microsatellite instability (Microsatellite Instability, MSI) refers to the decrease or increase of microsatellite repeats, and the emergence of new alleles. A large number of studies have shown that microsatellite instability is caused by defects in mismatch repair genes and is closely related to the occurrence of tumors. Clinically, microsatellite instability has been used as an important molecular marker for the prognosis of colorectal cancer and other solid tumors and the formulation of adjuvant treatment plans, and has been applied to assist in the screening of Lynch syndrome. However, for NGS data, there is no gold standard for discriminating microsatellite instability. [0003] Currently, for NGS data such as figure 1 As sho...

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Application Information

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IPC IPC(8): G16B30/10G16B40/00G06K9/62
CPCG16B30/10G16B40/00G06F18/24323
Inventor 周涛陈利斌郭璟楼峰曹善柏
Owner 北京橡鑫生物科技有限公司
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