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Processing method and processing apparatus for sequencing data

A processing method and technology of a processing device, which are applied in the fields of electrical digital data processing, special data processing applications, sequence analysis, etc., can solve the problems of large demand for samples, convenient constraints, high throughput, and long time consumption, so as to speed up the analysis. effect of speed, elimination of dependencies, avoidance of data fluctuations

Active Publication Date: 2016-08-10
GUANGZHOU RIBOBIO
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the existing genome sequencing detection method needs to compare and analyze the sample to be tested with multiple samples or standard normal samples, which takes a long time and requires a large number of samples (such as the Chinese patent application with application number CN200880108377.1), and There are strict requirements on the consistency of experimental conditions for each batch of samples, which restricts its convenient and high-throughput application

Method used

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  • Processing method and processing apparatus for sequencing data
  • Processing method and processing apparatus for sequencing data
  • Processing method and processing apparatus for sequencing data

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0061] Example 1 Processing method of sequencing data of samples to be tested

[0062] (1) High-throughput sequencing of cell-free DNA fragments in the peripheral blood of pregnant women to be tested

[0063] (1) Collect the whole blood of pregnant women, and obtain plasma after pretreatment;

[0064] After obtaining the consent notice, 5-10ml of blood was collected from a woman at 22 weeks of pregnancy (i.e. sample S001 in the follow-up table 2) by venipuncture, and added to an ethylenediaminetetraacetic acid (EDTA) tube, and the blood sample was centrifuged at a high speed Afterwards, plasma samples were obtained from which blood cells were removed, and the plasma volume of each sample was about 700ul.

[0065] (2) extract plasma DNA;

[0066] The DNA in the plasma was extracted using the DNA extraction kit HiPure Circulating DNA Kits produced by Magen (Product No. D3180-02).

[0067] (3) Prepare the DNA extracted from plasma into a library that can be sequenced by a next...

Embodiment 2

[0095] Example 2 Effectiveness Evaluation

[0096] (1) Evaluation using online data samples

[0097] The steps in the processing method shown in Embodiment 1 can be implemented by a computing device in the form of modules or units. In order to evaluate the effectiveness of the method in Example 1, a test is carried out below using a processing device formed of a module or unit capable of performing the above steps. The processing unit includes:

[0098] The sequencing module is used to obtain the nucleotide sequence information of all chromosomes derived from maternal peripheral blood samples through high-throughput sequencing;

[0099] Optionally, the above modules include Illumina's cBot instrument, Illumina's Genome Analyzer, HiSeq2000 / 2500, Hiseq3000 / 4000, NextseqCN500 and other supporting model sequencers, or Life Technologies' SOLiD and other matching sequencer modules that perform sequencing functions.

[0100] The specific region division module calls the specific r...

Embodiment 3

[0122] Example 3 Stability and data volume research

[0123] (1) Sample stability

[0124] Using the above method, the four samples of s002, s006, s007, and s008 (the corresponding karyotype results are respectively T13 positive, T21 positive, T18 positive and normal) were repeatedly measured 8 times, and the relative chromosome expression was counted (denoted as CR ) and Z test value (denoted as ZV) to study data fluctuations to evaluate the stability of the detection method, and the evaluation results are shown in Table 3.

[0125]

[0126] Table 3. s002, s006, s007, s008 repeatability test data summary table

[0127]

[0128]

[0129] In Table 3 above, Mean represents the mean value, SD represents the standard deviation, and CV represents the dispersion coefficient. It can be seen from Table 3 that the CV (discrete value) of the CR value corresponding to the 4 samples repeated detection 8 times is less than 0.01, and the fluctuation (SD value) of ZV is also withi...

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Abstract

The present invention provides a processing method and processing apparatus for sequencing data. The processing method comprises: acquiring nucleotide sequence information originating from a maternal peripheral blood sample by means of high throughput sequencing; dividing a reference genome into a plurality of specific regions, wherein NRSc values in the specific regions are equal; allocating nucleotide sequence information originating from all chromosomes of the maternal peripheral blood sample to the plurality of specific regions of the reference genome, and collecting statistics of an NRSc value of the sample in each specific region; modifying the NRSc value of the sample in each specific region by using a GC content, and marking a modified NRSc value as an NRSs' value; based on the NRSs' value, separately collecting statistics of mean values of NRSs' values of all specific regions on a target chromosome and a contrast chromosome, and marking the mean values as a first mean value and a second mean value; and performing a difference check on the first mean value and the second mean value, and according to a difference check result, determining whether the chromosome has aneuploidy. The processing method improves accuracy of sequencing data processing.

Description

technical field [0001] The present invention relates to the field of sequencing data processing, in particular to a processing method and device for sequencing data. Background technique [0002] Chromosomal abnormalities may be numerical or structural. Quantitative abnormalities, including trisomy (one extra chromosome), monosomy (loss of one chromosome), and polyploidy (an entire extra set of chromosomes). Structural abnormalities include structural rearrangements such as translocations, inversions, deletions, and insertions caused by chromosomal breaks, etc. [0003] Abnormalities in the number of chromosomes, such as aneuploidy and polyploidy, are associated with a variety of diseases including birth defects and cancer. There are nearly 20 million newborns in my country every year, and about 4% to 6% of them have birth defects. Among them, fetal chromosomal abnormalities are one of the most common types of birth defects in clinical practice. According to statistics, ab...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22
CPCG16B30/00
Inventor 张必良曹亮
Owner GUANGZHOU RIBOBIO
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