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CNV detection method and CNV detection apparatus

A technology for sequencing results and genome sequencing, applied in the field of biological information, which can solve the problems of low-depth sequencing data, low genome coverage, and large fluctuations in sequence alignment

Inactive Publication Date: 2016-10-05
BGI SHENZHEN CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Single-cell sequencing data, especially low-depth sequencing data, has low genome coverage and high amplification bias, and short sequence alignments in different regions of the genome fluctuate greatly. These CNV detection methods are not suitable for single cell copy number Variation detection

Method used

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  • CNV detection method and CNV detection apparatus
  • CNV detection method and CNV detection apparatus

Examples

Experimental program
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Effect test

Embodiment 1

[0038] Example 1: CNV detection method test based on MDA-amplified CG platform low-depth sequencing data

[0039] With the vigorous development of high-throughput sequencing technology, the second-generation sequencing represented by Complete Genomics (CG), IlluminaSolexa and Roche454, as well as the Helicos Genetic Analysis System and single-molecule real-time sequencing technology included in the third-generation sequencing technology (ie, single-molecule sequencing technology) Various sequencing technologies such as (SMRT) and nanopore single-molecule sequencing technology have become important tools for single-cell omics research. As a next-generation sequencing technology focused on the human genome, the CG platform can completely and accurately sequence the entire human genome, and its sequencing throughput is high, which is highly recognized in the industry. The CG platform mainly includes three parts: sequencing platform, high-throughput process automation technology a...

Embodiment 2

[0048] Example 2: CNV detection method test of single-cell low-depth sequencing based on MDA-amplified Proton platform

[0049] Existing single-cell sequencing data are mostly produced by the Illumina sequencing platform. Although the sequencing throughput of the Illumina sequencer is large, its on-machine sequencing time period is long and the sequencing cost is high, which will limit the rapid development of single-cell CNV detection and analysis. However, some studies often have no requirement for sequencing throughput, and relatively have higher requirements for sequencing time and cost. At this time, the Proton sequencing platform will be a better choice. The Proton sequencing platform runs fast, the sequencing cycle only takes a few hours, and the sequencing cost is low. It is more suitable for deployment in hospitals or third-party testing institutions, shortening the testing time, reducing costs, and improving testing efficiency. However, there are few reports on Prot...

Embodiment 3

[0059] Example 3: CNV detection method test of single-cell low-depth sequencing based on MALBAC-amplified Proton platform

[0060] Five human gastric adenocarcinoma cell lines (BGC823) were extracted, and single-cell low-depth sequencing was performed on the Proton platform after routine library construction by MALBAC whole-genome amplification method; at the same time, a group of cells (BGC ) DNA was sequenced on the Proton platform. The obtained off-board data was tested and analyzed for CNV according to our plan, and CNV was found in five samples of BGC823. The results are as follows Figure 4 As shown, where the abscissa represents the chromosome; the ordinate on the right is 5 single-cell samples and cluster cell samples, and the ordinate on the left is the copy number. The black thick line on the figure represents the ratio value of the divided area, and its value is greater than 2 It means that the copy number in this region is increased, if it is less than 2, it means...

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Abstract

The invention provides a CNV detection method which including the steps of: 1) acquiring a genome sequencing result of a target individual; 2) comparing the sequencing result with a reference sequence to obtain a comparison result, wherein the reference sequence comprises a plurality of windows; 3) on the basis of the comparison result, calculating initial comparison ratio of each window, which is the number of reads in the windows on the comparison dividing the average value of the number of the reads in the windows on the comparison, wherein the average value of the number of the reads in the windows on the comparison is the total number of reads in all windows on the comparison dividing the number of the windows; 4) combining a plurality of adjacent windows of which the initial comparison ratios have no significant difference, and defining the combined adjacent windows as a primary zone, and the rest individual windows are respectively called the primary zones; and 5) if the comparison ratio of the primary zone is not equal to a preset comparison ratio, determining existence of CNV in the primary zone.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular, the invention relates to a method and a device for detecting CNV. Background technique [0002] Single-cell sequencing technology is the use of next-generation sequencing technology to sequence the trace nucleic acid of a single cell. This technology mainly includes three parts: single cell isolation, single cell nucleic acid extraction and amplification, and sequencing. As a revolutionary technology, single-cell sequencing has been widely used in scientific research and biomedicine in recent years. For example, sequence tumor single cells to reveal the heterogeneity of tumor single cells and deduce the evolution process of tumors; non-invasive prenatal diagnosis; assembly of microbial genomes that cannot be cultured; trace cell (can be used in forensic medicine, etc.) genome acquisition ; Single-cell technology has also been introduced into preimplantation diagnosis and so on. Sin...

Claims

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Application Information

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IPC IPC(8): C12Q1/68
Inventor 李甫强史旭莲谢国云鲁娜赵至坤蒋润泽梁瀚侯勇吴逵
Owner BGI SHENZHEN CO LTD
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