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Method and device for carrying out integration on multi-platform genetic typing result

A genotyping, multi-platform technology, applied in the field of bioinformatics analysis, to achieve the effect of increasing the number of genotyped loci, making full use of it, and comprehensive mutation results

Active Publication Date: 2018-07-03
WUXI QINGLAN BIOLOGICAL SCI & TECH +1
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The above information is not specifically reflected in existing results integration methods
In addition, the existing technology fails to fully consider the quality of the sequencing results of each platform, that is, the issue of reliability. It only filters with a certain threshold, and then analyzes and merges them quantitatively.

Method used

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  • Method and device for carrying out integration on multi-platform genetic typing result
  • Method and device for carrying out integration on multi-platform genetic typing result
  • Method and device for carrying out integration on multi-platform genetic typing result

Examples

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Embodiment 1

[0054] In this case, using the whole genome small fragment library Hiseq sequencing data, the whole genome small fragment library CompleteGenomics (CG) sequencing data, and the fosmid library Hiseq sequencing data, the human sample YH (yanhuang) genome chromosome 22 upper exon and its upstream and downstream regions The genotype is integrated. And compared with the result of the unanimous method.

[0055] 1. Definition of haplotype quality value (AQ). In this embodiment, the haplotype quality value is defined as the likelihood that a certain haplotype does not appear at the site and the haplotype at a given location under the conditions of a given observation value (ie sequencing result). A phred measure of the ratio of the likelihood that the type appears at the site (take the common logarithm and multiply by -10). which is,

[0056]

[0057] In the formula, A represents a haplotype, G represents the genotype of the locus, Obs represents the observed value, and L() represents t...

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Abstract

The invention discloses a method and a device for carrying out integration on a multi-platform genetic typing result. The method comprises the following steps that: obtaining a haplotype quality valueobtained from each genetic typing platform, wherein the haplotype quality value means a numerical value which shows the possibility of a preset haplotype or haplotype arrangement / combination occurrence and / or a determination degree; carrying out integration on the haplotype quality value obtained by each genetic typing platform to obtain an integrated haplotype quality value; and on the basis of the integrated haplotype quality value, deducing the genotype of a preset locus, or deducing whether the preset locus contains a specific haplotype or not, or deducing the occurrence possibility ofthe preset locus genotype or the preset haplotype. By use of the method, the information of the typing result of each gene typing platform is fully utilized, the problems that different platform results are inconsistent and confidence levels are difficult are solved, and therefore, a typing locus number can be obviously improved an a premise that result quality is not sacrificed.

Description

Technical field [0001] The invention relates to the technical field of bioinformatics analysis, and in particular to a method and device for integrating multi-platform genotyping results. Background technique [0002] Genotyping technology is the foundation of scientific research and industrial application of genome information. At present, genotyping technology mainly includes unit point typing technology and DNA fragment sequence typing technology. According to the principle, the unit point typing technology can be divided into the genotyping chip based on base pairing technology and the typing based on mass spectrometry. DNA Fragment sequence typing techniques include first-generation blocking sequencing, second-generation synthetic sequencing, and currently developing third-generation single-molecule sequencing. Due to the different technical principles and implementation schemes of various sequencing methods, there will be a certain degree of inconsistency in the typing res...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18G06F19/22
CPCG16B20/00G16B30/00
Inventor 徐煜高强
Owner WUXI QINGLAN BIOLOGICAL SCI & TECH
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