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System and method for detecting copy number variation of cell free tumor genes

A technology of copy number variation and gene copy number, which is applied in the fields of electrical digital data processing, special data processing applications, instruments, etc., can solve problems such as inappropriateness, and achieve the effect of reducing the false positive rate

Active Publication Date: 2018-11-23
广州漫瑞生物信息技术有限公司
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Problems solved by technology

Therefore, existing tools are not suitable for capturing ctDNA sequencing data with low-concentration copy number variation and focusing on hotspot variation regions.

Method used

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Embodiment Construction

[0020] In order to better illustrate the purpose, technical solutions and advantages of the present invention, the present invention will be further described below in conjunction with specific examples.

[0021] At present, due to the low concentration of ctDNA with gene copy number variation in plasma, targeted capture sequencing based on second-generation DNA sequencing technology is usually used to perform deep sequencing of multiple DNA mutation hotspots in tumors. Due to the differences in the GC content and capture probe concentration of each capture region, the capture efficiency of the sequencing fragments in each capture interval is different, so a large number of normal control samples are required to construct the baseline value of each interval.

[0022] First: through deep sequencing of the cfDNA of a large number of normal people (for example, the incidence of copy number increase of FGFR1 and MET genes in lung cancer patients is 20% and 2-4%, respectively), to c...

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Abstract

The invention provides a system and a method for detecting copy number variation of cell free tumor genes. The average depth of each capture interval is normalized through the average sequencing depthof an overall capture area, so that the influence of change of capture efficiency caused by experiment operation errors on gene copy number identification is eliminated. In a traditional normalization method, a ratio of interval reads to all sequencing reads is adopted as a normalized value of each interval, and the influence on a result caused by inconsistent capture efficiency among different experiments is not eliminated in the traditional method. Through a method for constructing a normal training set, the problem of inconsistent capture efficiency among the capture intervals in samples due to reasons of GC content, probe concentration and the like can be eliminated, so that the false positive rate is reduced.

Description

technical field [0001] The present invention relates to a system and method for detecting the variation of the copy number of cell-free tumor genes. Background technique [0002] Cell DNA enters the blood circulation system through various mechanisms such as apoptosis, secretion or phagocytosis, and this DNA fragment is called plasma free DNA (cell free DNA, cfDNA). For cancer patients, in addition to normal cells, part of the cfDNA in plasma comes from tumor cells, and this part of DNA carrying tumor cell-specific information is called circulating tumor DNA (ctDNA). The proportion of ctDNA in cfDNA is generally 0.1%-10%, and it varies greatly with the stage of the disease. [0003] The size of ctDNA fragments is usually 160-180bp, carrying mutation information such as single nucleotide variants (SNV), insertion and deletion (INDEL), copy number variation (CNV), and gene fusion (Fusion). Studies have found that most gene copy number variations (CNVs) are closely related to...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18G06F19/20G06F19/24
Inventor 方鹏车健为
Owner 广州漫瑞生物信息技术有限公司
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