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A method for screening SNP sites used for detecting sample contamination in high-throughput sequencing and a sample contamination detecting method

A screening method and high-throughput technology, which can be used in biochemical equipment and methods, and the determination/inspection of microorganisms.

Inactive Publication Date: 2018-12-18
天津诺禾致源生物信息科技有限公司
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Problems solved by technology

[0004] The present invention aims to provide a screening method for detecting SNP sites of sample contamination in high-throughput sequencing and a method for detecting sample contamination, so as to solve the problem in the prior art that sample contamination cannot be accurately identified without adding reference products question

Method used

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  • A method for screening SNP sites used for detecting sample contamination in high-throughput sequencing and a sample contamination detecting method
  • A method for screening SNP sites used for detecting sample contamination in high-throughput sequencing and a sample contamination detecting method
  • A method for screening SNP sites used for detecting sample contamination in high-throughput sequencing and a sample contamination detecting method

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Embodiment approach

[0030] According to a typical implementation of the present invention, it is mainly divided into two parts:

[0031] Part 1: Sample Processing

[0032] It mainly includes: breaking DNA, adding adapters, hybridization capture, elution, enrichment, and sequencing.

[0033] Part II: Data processing, such as figure 1 The flow shown includes two parts: completion outside the detection procedure and completion within the detection procedure. Among them, the completion of the detection program mainly includes: use the BWA-mem comparison software to compare the high-throughput sequencing sequence to the human reference gene on the off-machine data, and the unmatched sequence forms a soft truncation; and then according to the position of the comparison. Sorting, and using samtools software to create an index; using VarScan software to input the compared files for mutation detection. The completion of the detection program mainly includes: extracting the screened sites, determining t...

Embodiment 1

[0036] SNP site screening includes:

[0037] 1) Select the SNP sites in the 1000Genome Project project, which needs to satisfy 40%<population frequency<60%, a total of 35824769;

[0038] 2) To select the SNP sites in the HapMap project, 40%

[0039] 3) Select the SNP sites shared by the 1000Genome Project and the HapMap project, a total of 1,086,179;

[0040] 4) Screen the consensus sites covered by the probes used to capture the target region during the sequencing process, a total of 7554;

[0041] 5) Design probes for the above sites and perform sequence alignment with the Hg19 human reference genome, remove sites with more than 1 compared position, and the remaining 7328;

[0042] 6) The 7328 sites are sorted according to the absolute position of the chromosome, and extracted with a step size of 2;

[0043] 7) Finally, 3664 SNP sites evenly distributed in the Panel were obtained for subsequent evaluation. ...

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Abstract

A method for screening SNP sites used for detecting sample contamination in high-throughput sequencing and a sample contamination detecting method are disclosed. The method for screening the SNP sitesincludes S1) selecting SNP sites of N groups of population genomes, with the frequency of occurrence of the SNP sites being 40-60%; S2) selecting SNP sites common in the N groups of population genomes to obtain a first group of common SNP sites; S3) screening common SNP sites covered by a target region from the first group of common SNP sites to form a second group of common SNP sites; and S4) designing probes for the second group of common SNP sites and performing sequence alignment with a reference genome to obtain a third group of SNP sites which are SNP sites used for detecting sample contamination in high-throughput sequencing. Sample contamination recognition can be accurately performed without positive and negative reference materials.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a screening method for SNP (Single Nucleotide Polymorphisms, SNP) sites used for detecting sample contamination in high-throughput sequencing and a method for detecting sample contamination. Background technique [0002] In high-throughput sequencing testing, samples are often contaminated due to negligence in manual operations, resulting in incorrect test results. Therefore, it is very important to identify sample contamination accurately and in a timely manner. [0003] According to the general technical guidelines of next-generation sequencing, a positive reference product and a negative reference product will be designed in each batch, which is also a commonly used method for determining sample contamination. However, in real clinical practice, due to the consideration of cost priority, the purchase and setting of reference products are often ignored, resulting in the risk that ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6876C12Q1/6869
CPCC12Q1/6869C12Q1/6876C12Q2600/156C12Q2535/122C12Q2537/165
Inventor 李雷刘睿赵琳胡杨枝荣成岗蒋智
Owner 天津诺禾致源生物信息科技有限公司
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