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Device for noninvasive prenatal detection of chromosome abnormality

A technology for chromosomal abnormalities and prenatal detection, applied in the field of bioinformatics, can solve the problems of low efficiency, time-consuming, waste of sequencing costs, etc., and achieve the effect of reducing the number, improving the detection rate, and simplifying the function.

Active Publication Date: 2021-03-19
BEIJING USCI MEDICAL LAB CO LTD
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AI Technical Summary

Problems solved by technology

[0005] In order to solve this problem, in the prior art, there are reference set data for training multiple corresponding sequencing depths for samples to be tested with different sequencing depths, that is, retraining the chromosome heterozygosity ratio of the reference set for a specific sequencing sample every time standard deviation parameters, but this scheme has some defects, mainly including the following aspects: (1) For samples with a high depth, if it is necessary to train the reference set data of the corresponding depth samples, a lot of sequencing costs will be wasted; (2) Every time when detecting the chromosome Z value of the sample to be tested, if the corresponding sequencing depth of the sample has not been trained by the corresponding reference set, it is necessary to rebuild a new reference set, which will take a lot of time, and the constructed The reference set is also only used for poor labeling of one test sample, so it is very inefficient

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  • Device for noninvasive prenatal detection of chromosome abnormality
  • Device for noninvasive prenatal detection of chromosome abnormality
  • Device for noninvasive prenatal detection of chromosome abnormality

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0040] Embodiment 1 Fitting function establishment

[0041] In this example, the standard deviation of the number of reads of 22 chromosomes at different sequencing depths is calculated. For the change diagram, see figure 2 , image 3 , Figure 4 .

[0042] Among them, each graph represents a chromosome, and the abscissa in each graph is the number of reads in the reference set sample, and the ordinate is the standard deviation of the chromosome under this number of reads. From Figure 2-Figure 4 It can be seen that the standard deviation of the number of chromosome reads at different sequencing depths changes significantly. As the number of reads increases (that is, the sequencing depth increases), the standard deviation will become smaller. This shows that for a sample, it should be used instead of The standard deviation parameter should be matched to the sequencing depth instead of using the same standard deviation for all samples.

[0043] In each figure, according t...

Embodiment 2

[0058] Embodiment 2 Chromosomal Abnormal Judgment

[0059] This embodiment provides a method for detecting chromosomal abnormalities using the device for non-invasive prenatal detection of chromosomal abnormalities of the present invention. For a schematic diagram of the testing process, see figure 1 . details as follows:

[0060] (1) Use the detection module to perform sequencing on the peripheral blood cell-free DNA data of the pregnant woman to be tested. The sequencing platform used is the MGI2000 platform. The fq file (including the sequencing sequence and the sequencing quality of the sequence) can be obtained through sequencing on the sequencing platform, and the read length is 50bp ;

[0061] (2) Use the data quality control module to perform quality control screening on the fq file: remove PCR repeats, remove low-quality reads containing consecutive N bases (or the average Phred score of 5 consecutive nucleotides is less than 20), if Remove the above-mentioned fra...

Embodiment 3

[0075] In this example, 135 true positive samples and 3 negative samples with chromosomal abnormalities were verified by using the method in Example 2 and the traditional method. The gestational weeks of the 138 samples were all greater than 10 weeks, and their peripheral blood data were taken for verification.

[0076] The detection process of the traditional method and the method of Example 2 of the present invention is only different in the process of calculating the Z value in the last step, and other processing processes including sequencing, calculating the number of reads in each window width, GC correction, baseline correction, etc. are all the same (as in Example 2 process).

[0077] Traditional method:

[0078] The inventive method:

[0079] As can be seen from the method of the Z value calculation of above-mentioned traditional method and the inventive method, the denominator of traditional method uses fixed standard deviation (in the present embodiment, the f...

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Abstract

The invention relates to the technical field of bioinformatics, and particularly discloses a device for noninvasive prenatal detection of chromosome abnormality. The device comprises a detection module, a data quality control module, a data preprocessing module, a calculation module and a judgment module, wherein the calculation module comprises a chromosome heterozygosis ratio calculation unit, achromosome adaptive correction standard deviation calculation unit and a chromosome Z value calculation unit; and the chromosome adaptive correction standard deviation calculation unit is used for carrying out logistic regression according to the relationship between the sequencing depth of a reference set sample and the standard deviation of the chromosome heterozygosis ratio to obtain a fittingfunction, and substituting the sequencing depth of a pregnant woman sample to be detected based on the fitting function to obtain the chromosome adaptive correction standard deviation of the sample to be detected. The device can improve the detection rate of chromosome abnormal true positive samples.

Description

technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a device for non-invasive prenatal detection of chromosomal abnormalities. Background technique [0002] Prenatal screening is an important part of obstetric care. Current methods of prenatal testing include amniocentesis and chorionic villus sampling, both of which carry a certain risk of miscarriage due to invasive fetal sampling. Non-invasive prenatal screening (NIPT) can address the miscarriage risk problem associated with invasive prenatal testing. Usually, non-invasive prenatal screening uses fetal cell-free DNA (cfDNA) in the peripheral blood of pregnant women to detect whether the fetus has chromosomal abnormalities. The rapid development of bioinformatics algorithms and tools has opened up new directions for the detection of fetal chromosomal abnormalities. [0003] When detecting chromosomal abnormalities based on high-throughput sequencing technology, after a...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6883G16B20/20G16B20/30
CPCC12Q1/6883G16B20/30G16B20/20C12Q2600/156
Inventor 张静波曲丽王伟伟徐冰伍启熹王建伟刘倩唐宇
Owner BEIJING USCI MEDICAL LAB CO LTD
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