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Method and computer system for detecting copy number variation using a single sample based on next-generation sequencing technology

A next-generation sequencing technology and copy number variation technology, applied in the field of methods and computer systems, can solve the problems of high experiment and analysis cost, cumbersome overall process, limited comparison parameters and analysis algorithm parameter settings, etc. Effectively correct false negatives, simplify experiments and analysis steps, and reduce costs

Active Publication Date: 2021-02-26
GENEIS TECH BEIJING CO LTD
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  • Abstract
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Problems solved by technology

However, these methods must be compared without exception, and rely too much on sequencing depth and GC content, and are also limited by the parameter settings of comparison parameters and analysis algorithms. The overall process is cumbersome and complicated, and the cost of experiments and analysis are also higher

Method used

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  • Method and computer system for detecting copy number variation using a single sample based on next-generation sequencing technology
  • Method and computer system for detecting copy number variation using a single sample based on next-generation sequencing technology
  • Method and computer system for detecting copy number variation using a single sample based on next-generation sequencing technology

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Embodiment

[0027] The whole exome data of 5 known ERBB2 amplification-positive cases and 5 known ERBB2-amplified negative cases were selected to test the analysis method of the present invention. Specifically take 1 example of ERBB2 positive sample embodiment Sample1 as an example (such as flow process figure 1 ), all the other embodiments repeat steps 1-11, as follows:

[0028] 1. Collect the whole exome sequencing data of 272 cases of positive ERBB2 gene amplification, and collect the whole exome sequencing data of 1029 cases of negative ERBB2 gene amplification, and divide the data into two parts: training set and test set; The training set includes 223 positive samples and 817 negative samples, and the test set includes 49 positive samples and 212 negative samples;

[0029] 2. The gene ERBB2 contains 27 full exons, and the 27 amplified or deleted regions Lj (0

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Abstract

The invention discloses a method and a computer system for detecting copy number variation using a single sample based on a next-generation sequencing technology. The present invention can start from the original sequencing data, without relying on factors necessary or required by traditional methods such as comparison, sequencing depth, GC content correction, and paired samples to detect copy number variation CNV on a single sample. This not only simplifies the experimental and analysis steps and reduces the cost, but also the analysis results are highly consistent with the traditional method, and the false positives and false negatives detected by the traditional method are effectively corrected by adding clinical verification results (such as FISH verification) .

Description

technical field [0001] The invention relates to gene detection, in particular to a method and a computer system for detecting copy number variation using a single sample based on next-generation sequencing technology. Background technique [0002] Copy number variation (CNV) is a structural variation caused by genome rearrangement, which can be divided into microscopic and submicroscopic according to its size. Structural variation at the microscopic level mainly refers to chromosomal aberrations visible under the microscope, including euploidy or aneuploidy, insertions, deletions, inversions, and translocations; structural variation at the submicroscopic level mainly refers to DNA fragments with a length of 1Kb The above include mutations such as insertions, deletions, duplications, inversions, and translocations. Copy number variation is one of the important pathogenic factors of human diseases. Current studies have found that CNV is related to the pathogenic mechanism or ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/10G16B20/20G16B20/50G16B40/00
CPCG16B20/10G16B20/20G16B20/50G16B40/00
Inventor 郎继东王博杨家亮田埂
Owner GENEIS TECH BEIJING CO LTD
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