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Chromosome copy number variation detection device based on low-depth high-throughput genome sequencing

A chromosome copy number and genome sequencing technology, applied in the field of bioinformatics, can solve problems such as large impact on data quality, sequence-specific deviation, library preparation deviation, etc., and achieve the effect of obvious CNV breakpoints, stable data, and accurate results

Pending Publication Date: 2021-04-16
BEIJING USCI MEDICAL LAB CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, accurate detection of CNVs from NGS data remains challenging, mainly due to the large data nature of NGS data, short read lengths, sequence-specific bias, library preparation bias, and high noise
Existing CNV detection devices have disadvantages such as high false positive rate, which are greatly affected by data quality, and can only accurately detect areas above 1M
In addition, due to the influence of noise, the detection of samples with a chimeric ratio lower than 30% is also inaccurate

Method used

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  • Chromosome copy number variation detection device based on low-depth high-throughput genome sequencing
  • Chromosome copy number variation detection device based on low-depth high-throughput genome sequencing
  • Chromosome copy number variation detection device based on low-depth high-throughput genome sequencing

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0072] This embodiment provides a method for detecting chromosomal variation using the device for detecting chromosomal copy number variation based on low-depth high-throughput genome sequencing of the present invention.

[0073] The device includes: a detection module, a data quality control module, a data preprocessing module, a data correction and processing module and a judging module. Specific steps are as follows:

[0074] 1. Negative reference set construction

[0075] (1) Sample selection

[0076] A total of 300 peripheral blood samples from healthy people with no chromosomal abnormality in karyotype analysis were selected, and there was no significant difference in the proportion of males and females. DNA was extracted, genome sequencing was carried out according to the high-throughput method, and fastq data with a read length of 50 bp was obtained by single-end sequencing. The sequencing platform used was the MGISEQ-2000 gene sequencer manufactured by MGI.

[0077...

Embodiment 2

[0134] In this embodiment, the method shown in Embodiment 1 is used to test the experimental mixed sample data.

[0135] 13 positive samples with chip results and different sizes of abnormal fragments were mixed according to a certain chimerism ratio for library construction, chimerism gradient: 10%, 20%, 40%, 60%, 80%, 100%; positive region information As shown in table 2.

[0136] Table 2

[0137]

[0138] Specifically according to the method of the present invention, when the window is divided into 50kb, the R of the candidate CNV region of the above-mentioned positive sample obtained sample 、mean R reference 、sd R reference , Z value see Table 3. When the window is divided into 100kb, the R of the candidate CNV regions of the above positive samples obtained sample 、mean R reference 、sd R reference , Z value see Table 4. According to the judgment method of the present invention, the judgment results obtained under the two window widths are integrated, and the fin...

Embodiment 3

[0149] In this embodiment, the method shown in Embodiment 1 is used to test the clinical sample data.

[0150] Select 20 clinically positive samples (confirmed by CytoScan 750K SNP-Array chip test), including 8 males and 12 females. The sample types include: embryonic tissue, abortion tissue, villi, and induced fetal tissue. The specific sample types and chip results are shown in Table 5. The above 20 samples were detected by the method of Example 1. The two judgment results obtained after dividing according to the size of the two windows are combined, and the final judgment results obtained are all positive. The test results are shown in Table 6.

[0151] table 5

[0152]

[0153] Table 6

[0154]

[0155] According to the above results, it can be seen that the method of the present invention is used to detect all the small fragment CNVs above 100kb, all the CNVs and aneuploids with a low proportion of mosaicism, and all the regions with multiple abnormal CNVs. The ...

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Abstract

The invention relates to the technical field of bioinformatics, and particularly discloses a chromosome copy number variation detection device based on low-depth high-flux genome sequencing. The device comprises a detection module, a data quality control module, a data preprocessing module, a data correction and processing module and a judgment module. The data correction and processing module is used for correcting deviations caused by different chromosome baselines by a weighted linear regression model through repeated sequence and group CNV elimination, renormalization, sex chromosome diploidy processing, GC correction and mappability correction, PCA noise reduction, CBS algorithm noise reduction, maternal pollution elimination and the like, and other processing modules are combined to provide the chromosome copy number variation detection device with higher detection accuracy.

Description

technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a chromosome copy number variation detection device based on low-depth high-throughput genome sequencing. Background technique [0002] Chromosomal abnormalities are an important cause of spontaneous abortion in the first trimester, with an incidence rate as high as 50%-70%. Among them, the abnormal number of chromosomes accounts for about 96%, and the abnormal structure is only 3-5%. Aneuploidy is the main form of chromosomal abnormality in spontaneous abortion, accounting for more than 86% of chromosomal abnormalities. Examination of chromosomal abnormalities in the miscarriage can not only clarify the cause of the miscarriage, but also guide another pregnancy by combining genetic counseling and assisted reproductive methods. Currently, cell culture and karyotype analysis of flow-through products are important methods for detecting chromosomal abnormalities. However, ...

Claims

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Application Information

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IPC IPC(8): G16B20/20G16B20/10G16B30/00
Inventor 张静波王伟伟李小雨伍启熹王建伟刘倩唐宇
Owner BEIJING USCI MEDICAL LAB CO LTD
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