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Pretreatment method and device for fetal concentration calculation and application thereof

A preprocessing device and preprocessing technology, applied in the field of high-throughput sequencing, can solve problems such as inaccurate calculation of fetal concentration, and achieve the effect of improving accuracy

Active Publication Date: 2020-04-07
BEIJING USCI MEDICAL DEVICES CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] The main purpose of the present invention is to provide a preprocessing method for fetal concentration calculation, a preprocessing device and its application, so as to solve the problem of inaccurate fetal concentration calculation in the prior art

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  • Pretreatment method and device for fetal concentration calculation and application thereof
  • Pretreatment method and device for fetal concentration calculation and application thereof
  • Pretreatment method and device for fetal concentration calculation and application thereof

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Embodiment 1

[0044] In a preferred embodiment, a preprocessing method for fetal concentration calculation is provided. figure 1 A preprocessing method for fetal concentration calculation in this embodiment is shown. Such as figure 1 As shown, the preprocessing method includes:

[0045] Step S101, obtaining sequencing data of multiple samples;

[0046] Step S102, using the sequencing data to calculate the fetal concentration of each sample under different analysis strategies, wherein different analysis strategies include different lengths of sequencing reads and different amounts of total sequencing data;

[0047] Step S103, performing multi-factor analysis of variance on the fetal concentration of multiple samples under different analysis strategies to obtain the analysis strategy with the highest correlation with the fetal concentration.

[0048] In the above preprocessing method of the present application, by using the fetal concentration calculated under different sequencing strategi...

Embodiment 2

[0063] This embodiment provides a more specific preprocessing method for fetal concentration calculation, and the specific steps are as follows:

[0064] 1. Randomly select 20 NIPS samples, and obtain the whole genome sequence with a length of 150 base sequences through high-throughput sequencing, and remove adapters and low-quality base sequences (fastq files);

[0065] 2. Cut the base sequence with a read length of 150bp into base sequences with a read length of 35bp, 50bp, 75bp, 100bp, 125bp, and 150bp;

[0066] 3. Then randomly extract reads from the fastq files with different lengths of reads obtained above to obtain fastq files containing different data volumes (6M, 8M, 10M, 12M), and finally each sample will get 24 different fragment lengths and Fastq files with different data volumes;

[0067] 4. Use a unified analysis process to compare the obtained fastq files with the human genome hg19 respectively. The comparison results remove the sequences that are not accurately ...

Embodiment 3

[0074] In an optional embodiment, a calculation method for fetal concentration is also provided, the calculation method includes: obtaining the optimal analysis strategy according to any of the above preprocessing methods; analyzing the sequencing data to be analyzed according to the optimal analysis strategy Calculated to obtain the fetal concentration.

[0075] Through the description of the above embodiments, those skilled in the art can clearly understand that the method according to the above embodiments can be implemented by means of software plus a necessary general-purpose hardware platform, and of course also by hardware, but in many cases the former is better implementation. Based on such an understanding, the essence of the technical solution of the present invention or the part that contributes to the prior art can be embodied in the form of software products, and the computer software products are stored in a storage medium (such as ROM / RAM, disk, CD) contains se...

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Abstract

The invention provides a preprocessing method and device for fetal concentration calculation and an application thereof. The preprocessing method comprises the following steps: acquiring sequencing data of a plurality of samples; calculating the fetal concentration of each sample under different analysis strategies by utilizing the sequencing data, wherein the different analysis strategies comprise different sequencing reads lengths and different sequencing total data volumes; and performing multi-factor variance analysis on the fetal concentrations obtained by calculating the plurality of samples under different analysis strategies to obtain an analysis strategy with the highest correlation with the fetal concentrations. According to the invention, through the multi-factor variance analysis on fetal concentrations obtained under different sequencing strategies, different sequencing reads lengths, different sequencing total data volumes and the correlation between the interaction of the sequencing reads lengths and the sequencing total data volumes and fetal concentration calculation are obtained, and then the analysis strategy with the highest correlation is obtained, so that theanalysis strategy with the highest correlation is conveniently adopted for analysis and calculation during subsequent fetal concentration calculation, and the calculation accuracy is improved.

Description

technical field [0001] The invention relates to the technical field of high-throughput sequencing, in particular to a preprocessing method for calculating fetal concentration, a preprocessing device and applications thereof. Background technique [0002] Non-invasive prenatal screening technology (NIPS) is a method of sequencing the free DNA fragments (including fetal free DNA) in the mother's peripheral plasma by taking the venous blood of pregnant women and using next-generation DNA sequencing technology, and obtaining the inheritance of the fetus through bioinformatics analysis. Information, so as to detect whether the fetus suffers from chromosomal genetic diseases (including chromosome 21 / 18 / 13 and micro-deletion and micro-duplication diseases). Obtaining accurate fetal concentration is crucial for NIPS, especially for the clinical application of non-invasive single gene disease and microdeletion microduplication syndrome, it is a very important indicator affecting the ...

Claims

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Application Information

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IPC IPC(8): G16B30/00
CPCG16B30/00Y02A90/10
Inventor 吴梦思张静波王伟伟高司航刘文伍启熹王建伟
Owner BEIJING USCI MEDICAL DEVICES CO LTD
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