Method and device for integrated detection of CNV, uniparental disomy, triploidy and Roh

A uniparental disomy and triploid technology, applied in the field of genetic testing, can solve the problems of high testing cost and complicated process, and achieve the effect of simplifying the testing process, reducing the testing cost and improving the testing efficiency.

Active Publication Date: 2022-04-15
SUZHOU BASECARE MEDICAL DEVICE CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0004] In summary, there is no effective method for integrated detection in the prior art, and the detection cost is high and the process is complicated. Therefore, it is necessary to develop an effective method for detecting CNV, uniparental disomy, triploidy and ROH, and simplify the detection and analysis process , cost reduction is of great significance to the field of genetic testing technology

Method used

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  • Method and device for integrated detection of CNV, uniparental disomy, triploidy and Roh
  • Method and device for integrated detection of CNV, uniparental disomy, triploidy and Roh
  • Method and device for integrated detection of CNV, uniparental disomy, triploidy and Roh

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Embodiment 1

[0124] In this embodiment, the method of integrated detection of CNV, uniparental disomy, triploidy and ROH of the present invention is used to detect small CNV samples (cell line samples), including the following steps:

[0125] 1. Construction of genome sequencing library;

[0126] 2. Sequencing on the machine to obtain the whole genome sequencing data of the processed sample 1;

[0127] 3. Obtain analysis parameters: coverage depth information and SNP genotype information of each window;

[0128] 4. Based on the sequencing depth information, follow the CNV analysis process to obtain small CNVs of more than 100 kb;

[0129] 5. Based on the SNP genotype information, detect uniparental disomy and polyploidy according to the uniparental disomy / triploid analysis process;

[0130] 6. Based on the SNP genotype information, detect more than 5M ROH according to the ROH analysis process.

[0131] Test results such as figure 2 As shown, the CNV detection result is:

[0132] dup(...

Embodiment 2

[0138] In this embodiment, the method for the integrated detection of CNV, uniparental disomy, triploidy and ROH of the present invention is used to detect uniparental disomy samples (cell line samples), including the following steps:

[0139] 1. Construction of genome sequencing library;

[0140] 2. Sequencing on the machine to obtain the whole genome sequencing data of the processed sample 2;

[0141] 3. Obtain analysis parameters: coverage depth information and SNP genotype information of each window;

[0142] 4. Based on the sequencing depth information, follow the CNV analysis process to obtain small CNVs of more than 100 kb;

[0143] 5. Based on the SNP genotype information, detect uniparental disomy and polyploidy according to the uniparental disomy / triploid analysis process;

[0144] 6. Based on the SNP genotype information, detect more than 5 M ROH according to the ROH analysis process.

[0145] Test results such as image 3 As shown, CNV detection results: no CNV...

Embodiment 3

[0147] In this embodiment, the method of integrated detection of CNV, uniparental disomy, triploid and ROH of the present invention is used to detect triploid samples (cell line samples), including the following steps:

[0148] 1. Construction of genome sequencing library;

[0149] 2. Sequencing on the machine to obtain the whole genome sequencing data of the processed sample 3;

[0150] 3. Obtain analysis parameters: coverage depth information and SNP genotype information of each window;

[0151] 4. Based on the sequencing depth information, follow the CNV analysis process to obtain small CNVs of more than 100 kb;

[0152] 5. Based on the SNP genotype information, detect uniparental disomy and polyploidy according to the uniparental disomy / triploid analysis process;

[0153] 6. Based on the SNP genotype information, detect more than 5 M ROH according to the ROH analysis process.

[0154] Test results such as Figure 4As shown, CNV detection results: +(mosaic)(X); -(mosaic...

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Abstract

The invention discloses a method and a device for integrated detection of CNV, uniparental disomy, triploidy and ROH. The method comprises the following steps: (1) Obtaining coverage depth information and SNP genotype information on the sample genome; (2) Constructing a uniparental disomy and triploid analysis reference database, a CNV analysis reference database and a ROH analysis reference database; (3 ) for uniparental disomy and triploid analysis, CNV analysis and ROH analysis. The method for integrated detection of CNV, uniparental disomy, triploid and ROH of the present invention can detect CNV, uniparental disomy, triploid and ROH regions in an integrated manner based on whole genome sequencing data, which simplifies the detection process and improves Improve detection efficiency and reduce detection cost.

Description

technical field [0001] The invention belongs to the technical field of genetic detection, and relates to a method and a device for integrated detection of CNV, uniparental disomy, triploidy and ROH. Background technique [0002] Copy number variation (CNV), uniparental disomy (UPD), triploidy, and runs of homozygosity (ROH) are large genomic aberrations that contribute to many common genetic disorders, cancer, and other complex diseases. Identifying these aberrations is critical to understanding disease. [0003] To detect CNV and ROH regions, single nucleotide polymorphism (SNP) arrays are heavily used. In recent years, detection of CNVs from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method, which requires very high depth of coverage across the whole genome. Current methods for detecting uniparental disomy and triploid include: 1) Chromosome karyotype analysis: triploid can be detected, but overall uniparental dis...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20G16B20/30G16B50/30
CPCG16B20/20G16B20/30G16B50/30
Inventor 卢娜如张军孔令印梁波
Owner SUZHOU BASECARE MEDICAL DEVICE CO LTD
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