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Detection method and system for copy number variation in genome

A technology of copy number variation and genome, which is applied in the field of genome research and disease diagnosis and treatment, and can solve problems such as human bias and data error prone

Active Publication Date: 2017-12-01
郝柯 +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, the data used in these methods are relatively error-prone and have problems such as human bias.

Method used

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  • Detection method and system for copy number variation in genome
  • Detection method and system for copy number variation in genome
  • Detection method and system for copy number variation in genome

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0142] Example 1 Obtaining the tester's tissue sample and extracting DNA

[0143] 10 ml of venous blood was drawn from the test subject, collected into a collection tube containing EDTA, and free DNA in serum was extracted using a kit for extracting nucleic acid from blood (Qiagen QIAamp DSP DNA Blood Mini Kit). The operation method of the kit is described in detail at https: / / www.qiagen.com / us / shop / sample-technologies / dna / dna-preparation / qiaamp-dsp-dna-blood-mini-kit#orderinginformation.

[0144] In addition, oral swabs were used to swab back and forth on the inner wall of the oral cavity several times to obtain oral epithelial samples of patients. The DNA of the oral epithelium was extracted using a nucleic acid extraction kit (Promega Maxwell RSC Buffy Coat DNA Kit). The operation method of the kit is at https: / / www.promega.com / products / dna-purification-quantitation / genomic-dna-purification / maxwell-rsc-system-dna-purification-kits / maxwell-rsc-buffy- coat-dna-kit / is detai...

Embodiment 2

[0145] Example 2 Whole-genome sequencing was performed on the tester's DNA, and genotype determination was performed on its SNP site

[0146] 5ug of DNA was fragmented into approximately 200bp fragments by sonication, a library was established using the Illumina Paired-endSequencing Sample Preparation Kit, and the whole genome was sequenced using the Illumina HiSeq platform. The sequences of 40 million to 400 million DNA fragments of 200 to 300 bp were obtained by sequencing.

Embodiment 3

[0147] Example 3 Analysis of DNA sequencing and genotyping results of tissue cells, such as oral epithelial cells

[0148] The method of the present invention can be used to detect cells of various tissues of a test subject or a patient, including epithelial cells, normal white blood cells in blood, and the like.

[0149] Step (a) collect a batch of reference samples (reference samples) of normal population, and carry out sequencing and genetic analysis on the DNA of the reference samples according to the same method of DNA collection, library preparation, sequencer, and sequencing depth as in Example 1 and Example 2. type determination. DNA samples from normal cells do not contain genomic information from cancer cells. Genomic copy number polymorphisms (polymorphisms) detected in normal cellular DNA are inherited by the patient. In the method of the present invention, the sequencing process used for the reference sample and the sequencing process (including DNA collection, ...

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Abstract

The invention provides a method for analyzing copy number variation in a genome of a testee. According to the method, mathematical manipulation is creatively performed on variables extracted from sequencing data, new two-dimensional variables, namely a sequencing depth ratio (SDR) and alternate allele frequency (AAF) or alternate allelic haploid frequency (AHF) are derived, the signal / noise ratio is further increased, detection sensitivity and precision are improved, and information contained in the high-throughput DNA sequencing data is utilized more fully. Besides, the method is used for processing free DNA in a body fluid sample of the testee, wherein when a CNV feature signal of a certain locus of the genome is extracted from the sequencing data, the information close to the locus is introduced, so that signal strength is greatly improved, and the copy number variation in the free DNA in urine or serum can be effectively detected. The invention furthermore provides a system for implementing the method.

Description

technical field [0001] The invention relates to the fields of genome research and disease diagnosis and treatment. Specifically, the present invention provides a method and a related system for analyzing copy number variation in a sample genome of a subject (such as a mammal, especially a human). Background technique [0002] Genomic abnormalities are often associated with various genetic and degenerative diseases, as well as cancer. For example, the loss or gain of gene copies is not uncommon in cancer, as is the loss or amplification of gene fragments or specific regions. Therefore both the study of tumorigenesis and the development of better diagnostic and prognostic methods are of interest to the identification and cloning of specific gene regions associated with cancer and various genetic diseases. [0003] The core feature of cancer is the somatic mutation of the genome. These mutations can be point mutations, chromosome structural mutations, or copy number variation...

Claims

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Application Information

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IPC IPC(8): G06F19/00G06F19/18C12Q1/68
CPCC12Q1/6827C12Q1/6869G16B20/00C12Q2537/16
Inventor 郝柯张仲阳
Owner 郝柯
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