Gene SNP (single nucleotide polymorphism) site detection method based on SOLID (supported oligo ligation detection) sequencing technique

A detection method and site technology, applied in the field of bioengineering, can solve the problems of SNP site detection methods are difficult to meet, high-throughput sequencing technology has a large number, etc., to avoid false positive SNP sites, high anti-noise characteristics, and improve accuracy degree of effect

Inactive Publication Date: 2013-12-18
JIANGSU TODAYSOFT TECH
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Problems solved by technology

[0005] The purpose of the present invention is to provide a SNP detection method based on SOLiD sequencing, which aims to solve the technical problem that the existing SNP site detection method is difficult to meet the requirements of high-throughput sequencing technology and produces a large number of false positive SNP sites

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  • Gene SNP (single nucleotide polymorphism) site detection method based on SOLID (supported oligo ligation detection) sequencing technique
  • Gene SNP (single nucleotide polymorphism) site detection method based on SOLID (supported oligo ligation detection) sequencing technique
  • Gene SNP (single nucleotide polymorphism) site detection method based on SOLID (supported oligo ligation detection) sequencing technique

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Embodiment 1

[0054] The HLA gene is the human leukocyte antigen gene, which is a highly polymorphic complex composed of a series of closely linked gene loci. In order to make the purpose, technical scheme and advantages of the present invention clearer, this paper takes the HLA type I gene HLA-A gene used for bone marrow transplantation matching as an example to perform data analysis:

[0055] 1. The data is downloaded from EBI (http: / / www.ebi.ac.uk / ipd / imgt / hla / dictionary.html). Including GeneBank format data of HLA-A (HLA-A.gbk), and fasta sequence data of each subtype of HLA-A

[0056] (HLA-A_dictionary.fasta).

[0057] 2. Extract the subtype of HLA-A 01:01:01:01 as the standard sequence (HLA-A_01010101.fasta).

[0058] 3. Comparing the sequence with the HLA-A.gbk reference sequence, a total of 45 SNP sites were identified, which were recorded as positive SNP sites

[0059] 4. Perform data simulation on the HLA-A 01:01:01:01 sequence, add 5% noise points randomly, and construct 2824 ...

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Abstract

The invention belongs to field of bioengineering, and particularly relates to an SNP (single nucleotide polymorphism) site detection method based on an SOLID (supported oligo ligation detection) sequencing technique. The method comprises the following steps: (1) obtaining a color sequence of a gene sample to be detected in an SOLID sequencing manner; (2) preparing the color sequence of a reference order; (3) preparing an index table of a color coding reference order to rapidly position a sample order; (4) comparing an SOLID sequencing sample order with the color coding reference order so as to find out the optimal matching position of the sample order in the reference order, comparing the sample order with the reference order so as to obtain color encoding matching information; (5) analyzing base matching information of the SOLID sample order and the color encoding reference order according to the color encoding matching information, and determining uncertain change points; (6) counting the obtained uncertain change points, and removing noise and the uncertain change points caused by a sequencing error, so as to obtain a sample SNP site. By adopting the SNP detection method disclosed by the invention, the characteristic of high positioning accuracy of an SOLID data in a comparison process is kept; the accuracy of the SNP analysis method is also improved.

Description

technical field [0001] The invention belongs to the field of bioengineering, in particular to a method for detecting SNP sites. Background technique [0002] SNP (Single Nucleotide Polymorphism, SNP) refers to the polymorphism of nucleic acid sequence due to the change of a single nucleotide base. In the nucleotide sequences of the same chromosome or the same locus of different individuals, most of the nucleotide sequences are consistent but only one base is different, which is SNP. Due to the large number and high frequency of occurrence of SNP in the human genome, it is considered to be a new generation of genetic markers after microsatellites. It is widely used in medical genetics, pharmacogenetics, disease genetics, disease diagnosis, and human evolution. And other research fields have high research value and application prospects. [0003] The full name of SOLiD is supported oligo ligation detetion. It is unique in that it is based on the continuous ligation synthesis...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68
Inventor 邓彦王月兰倪受庸刘新华
Owner JIANGSU TODAYSOFT TECH
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