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Copy number variation detection method and device

A copy number variation and detection method technology, applied in the fields of instrumentation, genomics, proteomics, etc., can solve the problem of low sensitivity of mutation detection, and achieve the effect of improving sensitivity, high coverage, and accurate resolution

Active Publication Date: 2020-08-28
北京橡鑫生物科技有限公司 +2
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0006] The main purpose of the present invention is to provide a method and device for detecting copy number variation to solve the problem of low sensitivity of mutation detection in the prior art

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  • Copy number variation detection method and device
  • Copy number variation detection method and device

Examples

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Embodiment 1

[0033] In this embodiment, a method for detecting copy number variation is provided, such as figure 1 As shown, the detection method includes:

[0034]Step S101, obtaining the sequencing comparison data of the sample to be tested;

[0035] Step S103, calculating the sequencing depth of each base site in the sequencing alignment data;

[0036] Step S104, divide the reference genome into multiple bins, and calculate the copy number of each bin of the sample to be tested by using the sequencing depth of each base site;

[0037] Step S107, merging the bins whose copy number is different from the ploidy of the specified contig to obtain the region where the germline copy number variation occurs.

[0038] The detection method of the above-mentioned copy number variation obtains the ploidy (ie copy number) of each bin by using a bin-based method, and then compares it with the ploidy of the specified contig to be divided into a plurality of different bins, However, the differential...

Embodiment 2

[0052] This embodiment provides a specific detection method for copy number variation, such as figure 2 shown, including the following steps:

[0053] 1. Data preprocessing

[0054] Input the result file of NGS data in fastq format, and generate the sequence alignment result in bam format.

[0055] 1) Preprocess the original off-machine data to remove reads containing adapters and low quality.

[0056] 2) Compare the processed raw data with the reference genome to obtain a comparison result file in bam format;

[0057] 3) Remove the sequence alignment results outside the range of the capture chip;

[0058] 4) remove the repeated reads in the comparison result file, and obtain a bam file that does not contain the repeated comparison result;

[0059] 2. Calculate the sequencing depth of each base site

[0060] Calculate the sequencing depth of each base site in the specified region in the bam file, and obtain a file in tsv format.

[0061] 3. Determine the CNV region acco...

Embodiment 3

[0069] Using the method of Example 2, the positive samples with known copy number variation were detected, and the results were as follows: image 3 As shown, the horizontal axis is the sample, the vertical axis is the copy number, the dark gray indicates the positive sample result, and the light gray indicates the detection result. It can be seen from the detection results that the detection results are consistent with the known results. It can be seen that the detection method of the present application can not only detect all the mutation sites, but also has high detection accuracy.

[0070] It should be noted that for the foregoing method embodiments, for the sake of simple description, they are expressed as a series of action combinations, but those skilled in the art should know that the present invention is not limited by the described action sequence. Because of the present invention, certain steps may be performed in other orders or simultaneously. Secondly, those sk...

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Abstract

The invention provides a copy number variation detection method and device. The detection method comprises the following steps: acquiring sequencing comparison data of a to-be-detected sample; calculating the sequencing depth of each base site in the sequencing comparison data; dividing a reference genome into a plurality of bins, and calculating the copy number of each bin of the to-be-detected sample by utilizing the sequencing depth of each basic group site; and combining bins of which the copy number is different from the ploidy of the specified contig to obtain an area in which the embryonic system copy number varies. In the aspect, deletion or repetition of a gene exon in the length more than 1000bp can be detected; compared with a chip method in the prior art, the method of the invention has higher coverage and resolution and more accurate copy number evaluation for detecting the CNV, not only can the copy number variation condition of some known sites be detected, but also theunknown copy number variation condition can be detected, and the detection sensitivity is improved.

Description

technical field [0001] The present invention relates to the field of biological information analysis, in particular to a method and device for detecting copy number variation. Background technique [0002] CNV refers to a copy number polymorphism with a length greater than 1 kb, which is a type of genome structural variation (SV), including deletion, insertion, duplication and complex multi-site variation (complexmuti- site variants). One of the mechanisms of CNV generation is DNA recombination, including nonallelic homologous recombination (NAHR) and nonhomologous end-joining (Nohomologous end-joining, NHEJ). CNV caused by DNA recombination can affect gene expression in the following aspects: (1) gene dosage; (2) gene break; (3) gene fusion; (4) position effect; (5) recessive allele dominance etc. [0003] The detection of CNV has the following methods commonly used at present: [0004] Multiplex ligation dependent probe amplification (MLPA), two adjacent probes are des...

Claims

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Application Information

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IPC IPC(8): G16B20/10G16B20/30
CPCG16B20/10G16B20/30
Inventor 曹善柏王文平张萌萌郭璟楼峰
Owner 北京橡鑫生物科技有限公司
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