Method for detecting copy number variation by means of single sample based on second-generation sequencing technology, and computer system

A second-generation sequencing technology and copy number variation technology, applied in the field of methods and computer systems, can solve problems such as high cost of experiments and analysis, cumbersome and complicated overall processes, and achieve effective correction of false positives and false negatives, simplifying experiments and analysis steps, high consistency effect

Active Publication Date: 2019-09-17
GENEIS TECH BEIJING CO LTD
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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

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  • Method for detecting copy number variation by means of single sample based on second-generation sequencing technology, and computer system
  • Method for detecting copy number variation by means of single sample based on second-generation sequencing technology, and computer system
  • Method for detecting copy number variation by means of single sample based on second-generation sequencing technology, and computer system

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[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. The 27 amplified or deleted regions Lj (0

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Abstract

The invention discloses a method for detecting copy number variation by means of a single sample based on second-generation sequencing technology, and a computer system. The method and the system can realize copy number variation (CNV) detection on the single sample according to sequencing original data without necessary or required factors in traditional methods such as comparison, sequencing depth, GC content correction and sample paring, thereby simplifying experiment and analysis steps, reducing cost, realizing high consistence between an analysis result and a traditional method, and performing effective correction on false positive and false negative results which are detected according to the traditional method through 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 ...

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Application Information

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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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