Non-invasive prenatal detection device

A sample and data correction technology, applied in the field of bioinformatics, can solve the problems of trivial data segmentation and non-provision, and achieve the effects of reducing detection costs, avoiding false negatives or false positives, and shortening the detection cycle

Pending Publication Date: 2021-04-27
BEIJING USCI MEDICAL LAB CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

But there are also several shortcomings: it is too trivial to segment data with large fluctuations; it does not provide information about whether it belongs to CNV; it needs to debug different thresholds for different data

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Experimental program
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Effect test

Embodiment 1

[0050] This embodiment provides a method for detecting chromosomal variation using the non-invasive prenatal detection device of the present invention.

[0051] The device includes: a detection module, a data quality control and preprocessing module, a data correction and processing module, and a judging module. Specific steps are as follows:

[0052] 1. Negative reference set construction

[0053] (1) Sample selection

[0054] A total of 9,000 pregnant women whose gestational age was greater than or equal to 12 weeks and had no chromosomal abnormalities in karyotype analysis were selected, and there was no significant difference in the proportion of males and females. Cell-free DNA was extracted, genome sequencing was performed according to high-throughput methods, 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.

[0055] (2) Data preprocessing

[0056] Th...

Embodiment 2

[0100] In this embodiment, the method shown in Example 1 and the comparative method are used to test the sample to be tested.

[0101] (1) The peripheral blood of 20 pregnant women was selected for testing, numbered S1-S20, and the karyotype results showed that one pregnant woman had a fetus with trisomy 21, and the rest of the samples were negative.

[0102] (2) The 20 samples were tested according to the method of Example 1 of the present invention and the comparative method. The comparison method is the same as the method in Example 1, the only difference is that the construction and use of the dynamic database is not carried out, and the deviation caused by different chromosome baselines is not re-corrected, and all negative reference sets are used. In the comparison method, when the number of samples with |Z| greater than or equal to 3 in the same batch is more than half of the total sample data in this batch, and the Z values ​​of the same chromosome are all too large or...

Embodiment 3

[0113] In this embodiment, the method shown in Embodiment 1 is used to test the sample to be tested.

[0114] (1) The peripheral blood of 30 pregnant women was selected for testing, numbered T1-T30, and the karyotype results showed: 19 cases of trisomy 21, 3 cases of trisomy 18, and 1 case of trisomy 13 Body syndrome, 7 cases of microdeletion and microduplication syndrome.

[0115] (2) Using Example 1 to detect each sample.

[0116] Table 4 shows the detection results of 23 cases of abnormal aneuploidy samples (see the bold data in the table), all of which are consistent with the karyotype results. Table 5 shows the detection results of 7 cases of microdeletion and microduplication syndrome samples, all of which are consistent with the karyotype results, from which it can be seen that the fetal concentration is 0.052, and the region with a fragment size of about 2M can also be accurately detected.

[0117] Table 4 Abnormal results of aneuploidy

[0118] sample numb...

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Abstract

The invention relates to the technical field of bioinformatics, and particularly discloses a non-invasive prenatal detection device. The device comprises a detection module, a data quality control and preprocessing module, a data correction and processing module and a judgment module; a dynamic database is constructed through the data correction and processing module to correct deviations caused by different chromosome baselines again, and subsequent PCA noise reduction, parent source CNV recognition screening, segmentation of a window Z value through a CBS algorithm and other modes are matched, so that influences caused by batch deviations are effectively reduced, and false cathodes or false anodes caused by the batch deviations are avoided; application of to-be-tested batch samples as a reference set is avoided, so that inaccurate results caused by small sample size are avoided; the number of samples in a gray area is reduced, the detection cost is reduced, and the detection period is shortened.

Description

technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a non-invasive prenatal detection device. Background technique [0002] Noninvasive prenatal testing (NIPT for short) is a non-invasive prenatal testing technology during pregnancy. This technology is based on the scientific discovery that there is fetal cell-free DNA in the peripheral blood of pregnant women. It has high detection accuracy and can avoid the risks of miscarriage and intrauterine infection caused by invasive tests such as chorionic villus biopsy, amniocentesis and transabdominal venipuncture. [0003] The principle of NIPT detection technology is to extract the plasma free DNA from the peripheral blood of pregnant women, construct a next-generation sequencing library, and use the next-generation sequencer to obtain the sequence information of the free plasma DNA in pregnant women. The Z test method was used to compare the difference between the content of ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B50/00G06K9/62
CPCG16B30/10G16B50/00G06F18/2135G06F18/23213
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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