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Individual single nucleotide polymorphism site typing method and device

A technology of single nucleotide polymorphism and typing method, applied in the field of individual single nucleotide polymorphism locus typing, can solve the problems of high error rate and cumbersomeness, and achieve the effect of improving accuracy

Active Publication Date: 2021-07-27
SHENZHEN HUADA GENE INST
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

These software are relatively accurate in lower depth sequencing data, but it is cumbersome to apply to the SNP typing project of specific individual fixed-point PCR (Polymerase Chain Reaction, polymerase chain reaction) amplification sequencing data, and the error rate is relatively high. higher

Method used

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  • Individual single nucleotide polymorphism site typing method and device
  • Individual single nucleotide polymorphism site typing method and device
  • Individual single nucleotide polymorphism site typing method and device

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Embodiment Construction

[0013] The present invention will be further described in detail below through specific embodiments in conjunction with the accompanying drawings.

[0014] The present invention is conceived as: counting the number of bases at a certain SNP site (hereinafter referred to as fixed point) in a read segment sequence set (reads) containing SNP site information, and then selecting an appropriate threshold, and realizing A high-accuracy individual SNP site typing result is achieved. This typing method is suitable for all related items of individual fixed-point SNP detection, such as detection of individual disease sites, identification of individuals, and detection of individual functional genes.

[0015] Definitions of terms used in this application:

[0016] (1) Main base, the base with the largest number of SNPs in the individual read sequence set; the number of second bases is second; the number of third bases is second than the number of second bases.

[0017] (2) Tolerance, a...

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Abstract

Provided is a method and device for typing individual single nucleotide polymorphism SNP sites, including: obtaining read sequences containing SNP site information; performing data removal of external adapters in a target library containing amplified target sequences Sequence alignment, obtaining the aligned read sequence set; extracting the base information of all the aligned read sequences at the site to be tested; based on the extracted base information of the site to be tested, the genotype of the site Type it. Because the genotype of the site to be tested is based on the more specific base information extracted, rather than based on the inherent characteristics of the sequence and the statistical probability model, it can be implemented simply, effectively and more accurately. Individual fixed-point typing.

Description

technical field [0001] The invention relates to the technical fields of genomics and bioinformatics, in particular to an individual SNP (Single Nucleotide Polymorphisms, SNP) site typing method and device. Background technique [0002] At present, determining the genotype of an individual at a certain site on the sequencing sequence (that is, single nucleotide polymorphism site typing, referred to as SNP typing) is already a necessary step and a basic prerequisite for many tasks, such as gene function Research, disease-causing gene identification, genotype identification, etc. The quality of typing results directly affects the effectiveness and accuracy of follow-up work. [0003] With the continuous development of genomics and bioinformatics, a variety of SNP typing methods and software are emerging on the second-generation platform, but these software are generally de novo typing based on sequence intrinsic characteristics and statistical probability models method. Thes...

Claims

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Application Information

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IPC IPC(8): G16B30/00C12Q1/6883G16B30/10
CPCC12Q1/68G16B30/00G16B30/10
Inventor 芦静将浩君陈芳蒋慧康熊斌谢伟伟
Owner SHENZHEN HUADA GENE INST