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Detection methods and devices of copy number variations (CNVs) and computer-readable medium

A technology for copy number variation and detection method, applied in the field of copy number variation detection based on high-throughput sequencing data, can solve problems such as unstable calculation results, and achieve the effect of avoiding large fluctuation of copy number

Active Publication Date: 2018-08-21
GENESEEQ TECH INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The present invention aims to solve the problem that the calculation result of the copy number of a specific gene is unstable during the detection process of a panel composed of multiple detection regions

Method used

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  • Detection methods and devices of copy number variations (CNVs) and computer-readable medium
  • Detection methods and devices of copy number variations (CNVs) and computer-readable medium
  • Detection methods and devices of copy number variations (CNVs) and computer-readable medium

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0096] Example 1 Detection of MYCN gene copy number

[0097] The target region detected in this embodiment is to detect the copy number of the MYCN gene containing 2 exon regions, and the main information of the target region is shown in the following table:

[0098] Table 1 Two exons of MYCN gene

[0099]

[0100] There are a total of 349 normal people here. The mean value of the z-distribution curve composed of their MYCN gene OR values ​​is 1.08, and the sd is 0.075. The patient samples here use the HD786 standard provided by https: / / www.horizondiscovery.com product, which contains MYCN amplification, the official copy number OR is 4.75, we use the NGS method and the algorithm described above to get the copy number OR of the gene is about 3.95. The control sample used here is the NA18535 standard cell.

[0101] The panel for detection also includes the exon regions of some other sensitive genes. Different numbers of regions are taken to form the panel together with the...

Embodiment 2

[0125] Example 2 Detection of MET gene copy number

[0126] The target region detected in this embodiment is to detect the copy number of the MET gene containing 20 exon regions, and the main information of the target region is shown in the following table:

[0127] table 5

[0128]

[0129] There are a total of 349 normal people here. The mean value of the z-distribution curve composed of the MET gene OR value is 1.01, and the sd is 0.039. The patient samples here use the HD786 standard provided by https: / / www.horizondiscovery.com product, which contains MET amplification, the official copy number OR is 2.25, we use the NGS method and the algorithm described above to get the OR of the gene is 1.72. The control sample used here is the NA18535 standard cell.

[0130] The panel for detection also includes the exon regions of some other sensitive genes. Different numbers of regions and 20 exons of the MET gene are selected to form a panel. A total of 4666 other candidate reg...

Embodiment 3

[0141] Example 3 Detection of CDKN2A gene copy number

[0142] The target region detected in this embodiment is to detect the copy number of the CDKN2A gene containing 5 exon regions, and the main information of the target region is shown in the following table:

[0143] Table 8

[0144]

[0145] There are a total of 349 normal people here. The mean value of the z-distribution curve composed of their CDKN2A gene OR value is 1.01, and the sd is 0.054. The patient samples here use the HD786 standard provided by https: / / www.horizondiscovery.com The official did not provide the copy number variation of this gene, but the OR of this gene obtained by using the NGS method and the algorithm described above is about 0.62.

[0146]The panel for detection also includes the exon regions of some other sensitive genes. Different numbers of regions are taken to form the panel together with the 5 exons of the CDKN2A gene. A total of 4681 other candidate regions are selected, for example, ...

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Abstract

The invention relates to detection methods and devices of gene fragment copy number variations (CNVs) and a computer-readable medium, and particularly to technology of detecting the gene fragment copynumber variations on the basis of high-throughput sequencing (next generation sequencing, NGS) data, and belongs to the field of bioinformatics technology. When one of the detection methods of the gene fragment copy number variations provided by the invention is applied to an NGS process of a group of genes (panel) formed by a plurality of detection regions, average sequencing depth is obtained through adopting T distribution fitting, then a copy number baseline is calculated, and an existing abnormal gene fragment is obtained by analysis. According to the analysis method, impacts of fluctuation, which is of sequencing depth of all the detection regions and is caused due to NGS test methods, on detection results are effectively eliminated, and problems of high copy numerical-value fluctuation caused by sequencing depth increasing / decreasing which is of other regions and is caused by the copy number variations, and inconsistent results of detection in different panels are avoided.

Description

technical field [0001] The invention relates to a detection method, device and computer-readable medium of copy number variation, in particular to a technology for detecting copy number variation based on high-throughput sequencing data, which belongs to the technical field of bioinformatics. Background technique [0002] There is a large amount of variation in the human genome. According to the number of mutated bases, the genetic variation on the genome is divided into single nucleotide variation (Single Nucleotide Variants, SNVs) and structural variation (StructuralVariations, SVs). Copy number variation (Copy Number Variations, CNVs) is a form of structural variation, which refers to the deletion, insertion, duplication and complex multi-site variation of DNA fragments ranging in size from 50 bp to several Mb compared with the reference genome. Studies in recent years have shown that CNVs of genome fragments affect gene expression by changing gene dosage or chromosome...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18G06F19/26G16B45/00
CPCG16B20/00G16B45/00G16B20/10
Inventor 邵阳汪笑男吴雪常志力刘思思那成龙
Owner GENESEEQ TECH INC
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