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Method and device for detecting somatic cell copy number variation in specified genome region

A copy number variation and genome technology, applied in the field of genes, to achieve accurate detection results, reduce false positives, and improve accuracy

Active Publication Date: 2020-11-20
BEIJING GENEPLUS TECH +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0008] The above-mentioned software or statistical values ​​are basically used alone in the detection of sample copy number variation, and in the prior art, the copy number variation information of genes or intervals must be clarified through the variation detection process and annotation process

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  • Method and device for detecting somatic cell copy number variation in specified genome region
  • Method and device for detecting somatic cell copy number variation in specified genome region
  • Method and device for detecting somatic cell copy number variation in specified genome region

Examples

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Embodiment 1

[0054] This embodiment provides a method for detecting somatic copy number variation in a designated genomic region, the flow chart of which is as follows figure 1 shown, including:

[0055] (1) Obtain tumor samples with known copy number variation in specified genomic regions, and use the paired samples as control samples; compare the sequencing data of tumor samples and control samples with the reference genome to obtain comparison result files;

[0056] In this example, 8 tumor tissue samples (non-small cell lung cancer were selected in this example) were selected, and the paired samples (control samples) were white blood cells from the peripheral blood of the same patient, and were performed using the Gene+Seq 2000 sequencing platform Whole exome sequencing. The sequencing data were compared with the human reference genome (GRCh37) by BWA-MEM software, and the comparison result file was obtained. It is known that in the specified genomic region (each sample has a specifi...

Embodiment 2

[0073] In this example, the tumor samples and paired samples with known copy number variation of the specified genomic region are used as the verification set, and the detection process is as follows: image 3 As shown, detect according to the method in embodiment 1, including:

[0074] (1) Compare the sequencing data of the tumor sample to be detected and the control sample with the reference genome to obtain a comparison result file;

[0075] The tumor tissue sample number is 190031660FD (provided by Genega), and its paired control is the peripheral blood leukocyte 190031660BD (provided by Genega) of the same patient. Gene+Seq 2000 sequencing platform was used for whole exome sequencing respectively. The sequencing data were compared with the human reference genome (GRCh37) by BWA-MEM software, and the comparison result file was obtained. Detection of CDKN2A gene (chromosome 9, position information on the genome is 21968174-21975187), PTEN gene (chromosome 10, position info...

Embodiment 3

[0094] This embodiment provides a device for detecting somatic copy number variation in a specified genomic region, comprising:

[0095] The comparison unit is used to compare the sequencing data of the tumor sample and the control sample with the reference genome to obtain a comparison result file; the copy number variation of the specified genomic region of the tumor sample is known, and the paired sample is used as a control sample;

[0096] The difference significance P value calculation unit of the normalized read length coverage is used to divide the window in the target capture area or non-target capture area of ​​the specified genomic region based on the comparison result file, and calculate the difference between the tumor sample and the control sample in each The normalized read-length coverage within the window, and then calculate the significant difference P value of the normalized read-length coverage of the tumor sample and the control sample, corresponding to the...

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Abstract

The invention relates to the field of genes, in particular to a method and a device for detecting somatic cell copy number variation in a specified genome region. According to the method, a pluralityof indexes including a log2 (copy Ratio) value, B allele frequency (BAF) difference significance, difference significance of homogenized read length coverage in a target capture area and difference significance of homogenized read length coverage in a non-target capture area are integrated, and multivariable analysis is applied to synthesize a plurality of index analysis results, so efficient andaccurate copy number variation detection is carried out on a specified gene or interval.

Description

technical field [0001] The invention relates to the field of genes, in particular to a method and device for detecting somatic cell copy number variation in a designated genome region. Background technique [0002] Copy number variation (Copy Number Variations, CNV) is a form of DNA sequence structural variation, including duplication and deletion of specific DNA segments (>1kb), and is an important source of normal and pathogenic variation in the human genome. The development of next-generation sequencing (NGS) technologies has greatly improved the ability to detect all types of genomic variation, from single-nucleotide variants and small indels to CNVs and other forms of structural variation (SV). Using whole genome sequencing data has the strongest ability to detect CNV, but due to its high cost, most of the tools and methods for detecting CNV use whole exome sequencing data. However, compared with whole genome sequencing (WGS), whole exome sequencing (WES) introduces...

Claims

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Application Information

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IPC IPC(8): G16B20/10G06N20/00
CPCG16B20/10G06N20/00
Inventor 黄毅罗梓文吴玲清杨玲易鑫
Owner BEIJING GENEPLUS TECH
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