Copy number variation detection apparatus

A copy number variation and detection device technology, which is applied in the fields of electrical digital data processing, special data processing applications, instruments, etc., can solve the problems of difficult to guarantee the accuracy of CNV and the need to improve the detection sensitivity

Active Publication Date: 2018-07-06
ZHEJIANG ANNOROAD BIO TECH CO LTD +2
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  • Abstract
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  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, due to the fundamental difference between the whole genome sequencing data and the target region capture sequencing data, the current CNV detection method of the traditional N

Method used

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Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0139] The copy number variation detection device of Example 1 includes the following modules.

[0140]Sequencing data acquisition module:

[0141] The 2.1G Base sequencing data obtained by using the cancer target region capture chip to capture and sequence the genomic DNA to be detected was obtained.

[0142] Data quality inspection module:

[0143] Perform data quality inspection on the sequencing data, filter out short sequences with an average quality value lower than 15, filter out short sequences with an N content higher than 5%, filter out short sequences related to Adapter, and finally leave 2.0G Base sequencing data C .

[0144] Sequence Alignment Module:

[0145] Use the filtered 2.0G Base sequencing data C to perform a short sequence alignment with the human reference genome HG19, and obtain the alignment result A. According to the comparison result A, the depth value of each site on the genome is calculated, and the result D is obtained.

[0146] Pre-data proc...

Embodiment 2

[0183] Example 2 is CNV detection for multiple target genes (determined genes) of breast cancer. The test sample was a blood sample from a female breast cancer patient. The copy number variation detection device in Example 2 includes: a sequencing data acquisition module, a data quality inspection module, a sequence comparison module, a pre-data processing module, a normalization module, a background library screening module, a data fluctuation elimination module, and an output module.

[0184] Test results such as image 3 shown. Each dot in the figure is the Zpg value of a window. Among them, the PDGFRA and KIT genes were the copy number increase corresponding to the low-purity subtype; the ERBB2 gene was the copy number increase corresponding to the normal-purity subtype.

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Abstract

The invention relates to a copy number variation detection apparatus, which is high in detection sensitivity. The copy number variation detection apparatus comprises a sequence comparison module, an early stage data processing module, a normalization module, a background library screening module, a data fluctuation elimination module, a GC correction module, a CNV region prejudgment module, a CNVregion breakpoint determination module, a CNV region screening module and an output module.

Description

technical field [0001] The invention belongs to the field of molecular biology detection, and in particular relates to a copy number variation detection device and a detection method. Background technique [0002] Gene copy number variation (Copy Number Variation, CNV) is a very important structural variation in clinical practice, which is related to the prognosis of various tumors and the sensitivity of targeted drugs. Reliable CNV detection results can provide a very important basis for clinical medication and disease assessment. [0003] Most of the CNV detection techniques currently used clinically are experimental methods based on PCR or immunohistochemistry (such as FISH, IHC, etc.). This type of method can only detect CNV of common known genes, and the sensitivity of the detection results is low. It can only detect high-fold (generally more than 8 times) amplification variation, and a single detection can only cover one gene. [0004] The CNV detection based on the ...

Claims

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Application Information

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IPC IPC(8): G06F19/18G06F19/22
CPCG16B20/00G16B30/00
Inventor 荆瑞琳张萌萌王晓雯李雪峰玄兆伶李大为梁峻彬陈重建
Owner ZHEJIANG ANNOROAD BIO TECH CO LTD
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