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Detection method of whole genome copy number variation and application of the method

A copy number variation and genome-wide technology, applied in the field of cancer diagnosis devices, can solve the problems of inability to fully reflect the degree of genome disorder, difficulty in effectively diagnosing tumors, and single parameters

Pending Publication Date: 2020-04-17
BERRYGENOMICS CO LTD +1
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  • Abstract
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  • Claims
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Problems solved by technology

[0007] However, at present, in the process of diagnosing tumors through NGS results of CNVs, the risk of tumors is mainly detected by detecting the presence or absence of certain specific CNV markers.
However, tumor is a highly heterogeneous disease, and it is actually difficult to effectively diagnose tumors simply by using a few CNVs as markers
Moreover, the current parameters considered for the analysis of genome-wide CNVs are relatively single, and generally only the length of CNVs is considered, which makes the analysis results of CNVs unable to fully reflect the degree of genome disorder of the sample.

Method used

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  • Detection method of whole genome copy number variation and application of the method
  • Detection method of whole genome copy number variation and application of the method
  • Detection method of whole genome copy number variation and application of the method

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0074] Example 1 Determination of the genome-wide CNV score of the sample according to the detection method of the present invention

[0075] 1. Sample collection

[0076] Between January 2017 and March 2018, tumor tissue samples were obtained from patients through surgery at Beijing Hospital and the Affiliated Hospital of Zhengzhou University. The patients were pathologically diagnosed lung cancer patients and were not treated for lung cancer. Specifically, the patient had the following lung cancers: lung cancer in situ (AIS), minimally invasive lung cancer (MIA), invasive lung cancer (IA), malignant pleural effusion (MPE) and metastatic nodule (MN). Among them, AIS and MIA belong to low-invasive lung cancer, and IA belongs to high-invasive lung cancer. A total of 71 patients' tumor tissue samples and 15 patients' paracancerous samples (ie, non-cancerous samples) were obtained. Tumor tissue samples and paracancerous samples obtained from patients through surgery were fixed...

Embodiment 2

[0093] Example 2: Diagnosis of lung cancer, its invasiveness and cancer grade based on the whole genome CNV detection method of the present invention

[0094] 1. draw the ROC curve according to the CNV score of 71 tumor tissue samples obtained in embodiment 1 and 15 paracancerous samples, to determine the threshold (see figure 2 A-2B). Such as figure 2 As shown in A, when the threshold of CNV score was set at 0.015, it had the highest accuracy in distinguishing cancer samples from normal samples, with a sensitivity and specificity of 93.3% and 97.2%, respectively. Such as figure 2 As shown in B, when the threshold of CNV score was set at 1.940, it had the highest accuracy in distinguishing low-invasive cancer samples from high-invasive cancer samples, with a sensitivity and specificity of 82.6% and 92.9%, respectively. Such as figure 2 As shown in C, when the threshold of CNV score is set at 2.550, it has the highest accuracy in distinguishing low-grade (grade I, II) a...

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Abstract

The invention relates to a detection method for whole genome copy number variation (CNV). The method comprises the following steps: (1) obtaining a sequencing result sequence of whole genome sequencing of a DNA sample; (2) comparing the sequencing result sequence with a human reference genome, and calculating the coordinate position of the CNV in a chromosome section and the copy number CN<detection> of the CNV in the section; and (3) calculating the comprehensive CNV<score> of the DNA sample through corresponding formula in which the CNV<length> represents the length of the CNV calculated according to the coordinate position of the CNV in the chromosome segment, the CN<reference> represents the chromosome copy number in a normal sample, and the CNV<score> represents the whole genome copynumber variation of the DNA sample. The invention also relates to the use of said detection method in the diagnosis of cancer as well as a device for diagnosing cancer conditions.

Description

technical field [0001] The invention relates to a method for detecting the variation of the copy number of the whole genome. The present invention also relates to the use of the detection method in cancer diagnosis, and a device for diagnosing cancer based on the detection method. Background technique [0002] Genome copy number variation (Copy Number Variation, CNV) refers to the complex sequence derived from the insertion, deletion, inversion, translocation and / or duplication of DNA fragments greater than or equal to 1 kb in the genome compared with the genome reference sequence. Chromosomal structural variation, which has the characteristics of wide distribution, heritability, relative stability and high heterogeneity. [0003] Studies have shown that CNV is an important factor in the occurrence and development of tumors, which can induce tumors by affecting the activity of proto-oncogenes and tumor suppressor genes. Multiple studies have shown that CNV detection has th...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00G16H50/20
CPCG16H50/20
Inventor 刘弼李小雨宫玉艳武旺张钰王征刘东戈
Owner BERRYGENOMICS CO LTD
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