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Method for screening SNP (Single Nucleotide Polymorphism) sites and application thereof

A locus and candidate locus technology, applied in the field of genetic engineering, can solve problems such as small target range, uneven genome distribution, and inability to obtain heterozygous loci.

Pending Publication Date: 2022-05-20
BERRY ONCOLOGY CO LTD +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the target range of target capture sequencing is generally small, and the distribution in the genome is not uniform enough to obtain a sufficient number of uniform heterozygous loci

Method used

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  • Method for screening SNP (Single Nucleotide Polymorphism) sites and application thereof
  • Method for screening SNP (Single Nucleotide Polymorphism) sites and application thereof
  • Method for screening SNP (Single Nucleotide Polymorphism) sites and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0078] A method for screening multi-purpose SNP sites, which includes the following steps.

[0079] (1) Obtain SNP candidate sites:

[0080] Select the sites that appear frequently in databases such as Thousand Genomes, ExAC, and gnomAD, that is, select points with an allele frequency (AF) of 40% to 60% as candidate sites, so that the selected sites can be used in different populations. The utilization rate is large and stable (that is, there are more loci showing heterozygosity in the population cases and the fluctuation between different people is small).

[0081] Then, according to the repetitive sequence information recorded in the human rmsk database, the mutation sites located in the repetitive sequence were removed to form a pre-set of SNP candidate sites.

[0082] (2) Formulate the primary selection panel: design a 120nt probe based on the 60 bp sequence information before and after the above SNP candidate site, remove the probe sequence that can be compared to more t...

Embodiment 2

[0116] Detect the difference in the standard deviation of the mutation abundance of all heterozygous mutation sites in the SNP panel and the whole genome sequencing in 36 samples, the results are as follows figure 1 shown.

[0117] The present invention tests the SNP panel screened out by the present invention, the standard deviation of the heterozygous mutation frequency is 0.05957, the general panel gene region is 0.1247, and the WGS data is 0.0710. combine figure 1 It can be seen that the standard deviation of the mutation frequency of the SNP panel screened by the present invention is significantly lower than that of the whole genome sequencing, reflecting that the method of using the SNP panel can make the mutation frequency of the mutation site more stable.

[0118] figure 2is the distribution of mutation sites in SNP panel and traditional Gene panel, where, figure 2 A is the result of SNPpanel, figure 2 Middle B is the result of the traditional Gene panel. From ...

Embodiment 3

[0120] Use the third-party software Conpair (Bergmann E A, Bo-Juen C, Kanika A, et al. Concordance and contamination estimator for matched tumor–normal pairs [J]. Bioinformatics (20): 3196-3198.) for contamination assessment, The evaluation samples were 88 contaminated samples with contamination levels from 0.6% to 27% and 95 non-contaminated samples. All sample data were target capture sequencing data containing our SNP panel sites.

[0121] Use the conpair software to perform contamination detection on these samples, set the markers parameter as the default or the SNP panel provided in Example 1 of the present invention to generate two sets of evaluation results.

[0122] image 3 is the correlation analysis between two groups of evaluation results and real results of contaminated samples, where, image 3 A is the correlation analysis result of Compair, image 3 Middle B is the correlation analysis result of SNP panel. The result shows that the correlation between the res...

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Abstract

The invention discloses a method for screening SNP loci and application thereof, and relates to the technical field of genetic engineering.The method comprises the steps that according to mutation frequency information of SNP candidate loci in N sample genomes, loci meeting the screening standard serve as multipurpose SNP loci, the multipurpose SNP loci meeting the screening standard are judged, and the mutation frequency information of the SNP candidate loci in the N sample genomes is obtained; the distance between the adjacent multipurpose SNP loci on a single chromosome is more than 250 kb to 350 kb. According to the method, a batch of heterozygosity site sets which are uniformly distributed in a genome and are stable in performance can be rapidly screened out, and the sets have various wide applications, such as detection of sample pollution level, detection of gene heterozygosity deficiency and tumor genome ploidy detection, and have the advantages of being lower in detection cost, high in sensitivity and the like. The detection time is short; the detection effectiveness is higher, and the like.

Description

technical field [0001] The invention relates to the technical field of genetic engineering, in particular to a method for screening SNP sites and its application. Background technique [0002] Cancer is one of the three major diseases that seriously endanger human health in the world. The latest global tumor statistics in 2018 show that there are an estimated 18.19 million new cancer cases and 9.6 million cancer deaths worldwide. Lung cancer is the most frequently diagnosed cancer (11.6% of total cases) and the leading cause of cancer death (18.4% of total cancer deaths). The remaining cancers with higher incidence were breast cancer (11.6%), colorectal cancer (10.2%), prostate cancer (7.1%) and gastric cancer (5.7%). [0003] It is well known that the occurrence of tumors results from the accumulation of a series of gene changes, which lead to errors in signaling pathways and cell division cycles. The process involves a number of key cytokines and receptor proteins. These ...

Claims

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Application Information

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IPC IPC(8): C12Q1/6811C12Q1/6876C12M1/34C12M1/00
CPCC12Q1/6811C12Q1/6876C12Q2600/156C12Q2537/165
Inventor 王瑞如王寅白健屈紫薇吴琳
Owner BERRY ONCOLOGY CO LTD
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