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Microsatellite loci for detecting msi, screening method and application thereof

A technology of microsatellite sites and screening methods, which is applied in the field of detecting MSI microsatellite sites, can solve the problems of low accuracy of test results, and achieve high sensitivity and specificity, high sensitivity and high specificity

Active Publication Date: 2021-06-15
臻和(北京)生物科技有限公司 +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The main purpose of the present invention is to provide a microsatellite site for detecting MSI, its screening method and application, to solve the problem of low accuracy of detection results in the prior art

Method used

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  • Microsatellite loci for detecting msi, screening method and application thereof
  • Microsatellite loci for detecting msi, screening method and application thereof
  • Microsatellite loci for detecting msi, screening method and application thereof

Examples

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Embodiment 1

[0079] In this embodiment, a screening method for detecting microsatellite sites of MSI is provided, the screening method comprising:

[0080] S101, select the microsatellite loci that meet the first condition, and record it as the first locus set. The first condition includes: a. a single-base repeat sequence ≤ 15 bp; b. the single-base repeat sequence is a repeat of A or T sequence; c. The similarity value to the flanking sequence of the single-base repeat sequence is lower than the similarity threshold;

[0081] S103, acquiring the sequencing data of multiple microsatellite stable samples, and screening the first locus set from the sequencing data of each microsatellite stable sample, and counting the number of repeat units of each microsatellite locus in the first locus set type and frequency of type for each repeat unit;

[0082] S105, selecting microsatellite loci satisfying the second condition from the first locus set as the second locus set, the second condition incl...

Embodiment 2

[0101] This embodiment provides a method for constructing a baseline for detecting MSI, the construction method comprising:

[0102] Obtain the sequencing data of multiple known MSS samples, and downsample the sequencing data of each known MSS sample (downsampled) to obtain MSS samples with different data volumes, and count the spanning of each microsatellite locus for each sample The type frequency of coverage, duplicate ratio and repeating unit, wherein, the microsatellite locus is the microsatellite locus (part of the 37 loci shown in Table 1) that is screened for the detection of MSI by the above screening method or all sites);

[0103] Under the condition that the spanning coverage reaches the saturation value (100~200, the value of different sites is different), according to the duplicate ratio and the type frequency of the repeating unit of each microsatellite site in each sample, construct microsatellites at different duplicateratio levels The baseline of the deletion...

Embodiment 3

[0121] This embodiment provides a detection method for microsatellite status, the detection method comprising: obtaining the sequencing data of the sample to be tested and calculating the spanning coverage, duplicate ratio (d) and deletion ratio of each microsatellite site in the sample to be tested ;

[0122] Compare the sample to be tested with the baseline at the same duplicate ratio level, the baseline is the baseline constructed by the above construction method; if the spanning coverage of the microsatellite site reaches the saturation value (100~200, different sites have different saturation values), And the duplicate ratio is greater than or equal to the lowest duplicate ratio of the baseline of the site, then the site passes the quality control; if the site k deletion ratio(k)(d)> mean(k)(d)+n* of the sample to be tested Mean(k)(d), preferably, n is 3 or 4, then it is determined that the microsatellite site to which it belongs is unstable;

[0123] Determine the micro...

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Abstract

The invention provides a microsatellite site for detecting MSI, its screening method and application. The screening method includes: selecting microsatellite loci with A or T single-base repeat sequences of ≤15 bp and whose flanking sequence similarity value is lower than the similarity threshold, and recording them as the first locus set; obtaining sequencing data of multiple MSS samples and Screen and count the type of repeating unit and the frequency of each repeating unit in the first locus set; select the locus that satisfies the second condition as the second locus set, and the second condition includes: 1) the highest frequency The type of repeating unit is consistent with the reference sequence; 2) The capture efficiency in the process of library construction and sequencing is higher than the capture threshold; 3) The polymorphism in the population is less than 5%; count and retain every Sites where there is a significant difference in the deletion ratio between the negative sample group and the positive sample group. The screened sites can improve the sensitivity and specificity of detection.

Description

technical field [0001] The invention relates to the field of high-throughput sequencing data analysis, in particular to a microsatellite site for detecting MSI, its screening method and application. Background technique [0002] Microsatellite instability (MSI) is a phenotypic manifestation of mismatch repair (MMR) deficiency and is increasingly used as a biomarker in clinical tumor diagnosis and treatment. Compared with PCR-based MSI detection, NGS-based MSI detection has several clinical advantages: MSI detection and other detections, such as SNV, can be performed simultaneously in a customized targeted panel. In addition, MSI detection based on PCR detection requires high tumor purity (>20%), and MSI detection based on NGS can reduce the requirement of tumor content due to the optimization of the algorithm. [0003] NGS-based MSI detection methods are developing rapidly. The current conventional deduplication strategy is "based on the highest sum of base quality value...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/00G16B30/10
CPCG16B20/00G16B30/10
Inventor 赵利利谢泓禹于佳宁王小庆洪媛媛陈维之何骥杜波
Owner 臻和(北京)生物科技有限公司
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