Supercharge Your Innovation With Domain-Expert AI Agents!

Sequencing data analysis method, device and computer readable medium for microsatellite instability

A technology for sequencing data and instability, applied in the field of gene detection, can solve the problem of low sensitivity to microsatellite instability, and achieve the effect of improving detection sensitivity

Active Publication Date: 2018-08-24
GENESEEQ TECH INC
View PDF3 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0020] At the same time, the present invention can also solve the problem of low sensitivity in the routine process of determining whether a site is microsatellite instability based on MSI sequencing

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Sequencing data analysis method, device and computer readable medium for microsatellite instability
  • Sequencing data analysis method, device and computer readable medium for microsatellite instability
  • Sequencing data analysis method, device and computer readable medium for microsatellite instability

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0122] Example 1 Preliminary screening of sites

[0123] The following examples of the present invention show the application of the analysis process and MSI site screening method. We performed high-throughput sequencing tests on the tumor tissue samples of 2000 Chinese individuals suffering from solid tumors and the corresponding negative control samples of whole blood. The target genomic interval tested was the whole exon region of 422 cancer-related genes, and Intron regions of some common gene fusions. The detection adopts liquid phase capture method to enrich the target DNA. The sequencing process is a common next-generation sequencing method, and its brief description is as follows: DNA extraction is performed on tissue samples and whole blood samples of each patient to obtain genomic DNA; samples with excessive DNA fragments are broken by ultrasound to mechanically force the samples Break to 200-350 base pairs; perform end-repair, adenine addition, library adapter connec...

Embodiment 2

[0130] Example 2 Data analysis of unstable state of microsatellite sites

[0131] Using the whole blood samples of 100 healthy people in Example 1, and 163 clinical samples of colorectal cancer that have received Promega PCR microsatellite detection, the microsatellite loci were sequenced and analyzed. The sequencing process was performed on the Illumina Next Generation Sequencer Carried on.

[0132] First, after processing the off-machine sequencing data of normal population and patient samples, the reads that can cover 22 MSI sites are found, and then these reads are classified according to the number of single-base repeats in the microsatellite sites. Type and number accumulation. Count the main repeating unit types at each site corresponding to normal samples and patient samples, and count the population-dominant repeating unit types on all normal samples. Then calculate the average and standard deviation of the main repeating unit types at 22 MSI sites (the results are shown...

Embodiment 3

[0142] Example 3 Analysis of microsatellite instability of site combination

[0143] In order to demonstrate the superiority of the 22 microsatellite unstable loci combined with biological indicators proposed in the present invention, the 22 microsatellite loci obtained by screening were compared with 22 randomly selected from the remaining 96 candidate loci. Each site was compared in terms of the accuracy of defining the patient’s microsatellite instability.

[0144] Controlled test 1: Image 6 Shows 22 randomly selected microsatellite unstable points (the numbers in Table 2 are 39, 88, 43, 34, 25, 56, 63, 69, 42, 32, 28, 45, 59, 98, 44) , 50, 85, 99, 67, 53, 52, 66 MSI sites), using only the analysis results obtained from the "number of main repeat unit types". The classification of MSS, MSI-L, and MSI-H in the figure is based on the judgment result of Promagre kit. Each data point is 163 clinical samples that received Promagre microsatellite detection kit, including MSS sample...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

The invention provides a microsatellite instability sequencing data analysis method, device and computer readable medium. NGS sequencing results can be used to determine whether there is microsatellite instability. This analysis and calculation method can significantly improve detection sensitivity without reducing specificity. It can be fast, automated, high-throughput, high-sensitivity, and high-specificity The stable or unstable status of each MSI site can be accurately assessed, and then combined with the status of all MSI sites in each sample, the comprehensive evaluation sample is MSS, MSI‑L, or MSI‑H.

Description

Technical field [0001] The present invention relates to the field of gene detection. Specifically, the present invention relates to a method for analyzing the detection results of microsatellite instability (MSI) indicator sites based on next-generation sequencing technology (NGS). This method is suitable for analyzing one or more microsatellite sites that indicate MSI status at the same time, accurately assessing the patient's MSI status, and providing theoretical basis and guidance for tumor diagnosis, prognosis, and clinical treatment plan formulation. Background technique [0002] Micro-Satellite Instability (or MSI) is a molecular phenotype, which is embodied in the presence of insertion or deletion mutations in the repetitive sequence of the microsatellite locus in the human genome, which in turn leads to non-existent human standard genomes. Alleles. These insertions or deletions have not been corrected by the DNA mismatch repair mechanism (MMR) for various reasons. MSI p...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/22
CPCG16B30/00G16B20/20G16B20/40G16B40/30
Inventor 邵阳朱明赴常志力汪笑男闫重光吴舒雨包华童晓玲
Owner GENESEEQ TECH INC
Features
  • R&D
  • Intellectual Property
  • Life Sciences
  • Materials
  • Tech Scout
Why Patsnap Eureka
  • Unparalleled Data Quality
  • Higher Quality Content
  • 60% Fewer Hallucinations
Social media
Patsnap Eureka Blog
Learn More

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic, Popular Technical Reports.

© 2025 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com