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A method and electronic device for prioritizing genes based on phenotype

A technology of prioritization and phenotyping, applied in the field of biological information, can solve the problems of low accuracy and low performance of WES data, and achieve the effect of good sorting effect.

Active Publication Date: 2022-02-11
北京易奇科技有限公司
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] However, the existing ranking tools have the problem of low performance when ranking genes. For example, when using the existing ranking tools in the process of diagnosing Mendelian genetic diseases through WES, the interpretation of WES data less accurate

Method used

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  • A method and electronic device for prioritizing genes based on phenotype
  • A method and electronic device for prioritizing genes based on phenotype
  • A method and electronic device for prioritizing genes based on phenotype

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0154] Validation of the performance evaluation of Example 1 in the expected collection of case report test sets

[0155] The inclusion criteria for case reports are: Inclusion criteria: 1) Case reports published in the following five scientific journals: American Journal of Medical Genetics Part A, BMC Medical Genetics, BMC Pediatrics, Frontiers in Genetics, Molecular Genetics & Genomic Medicine; 2) Case reports The report was published between November 25, 2018 and May 25, 2019; 3) the case report described the phenotype of at least one HPO record; 4) the case report identified the causative gene with the corresponding Entrez ID. The exclusion criteria for case reports were: 1) the case report identified multiple disease-causing genes in a single individual; 2) the case report described chromosomal abnormalities.

[0156]In this verification example, 243 case reports were expected to be collected first, 58 case reports were excluded according to the exclusion criteria, and t...

Embodiment 2

[0160] Verify the performance evaluation of Example 2 on the real patient test set

[0161] We investigated the performance of our method using real patient data, cohort 1 of the real patient test set consisted of 784 singleton patients diagnosed according to Baylor Genetics. We evaluate the performance of our method, Phenolyzer, Phenomizer, Phrank and HANRD on this real patient test set. Figure 11 A schematic diagram of the evaluation results of this verification example is shown, Figure 11 Including three graphs A, B and C, graph A shows the performance of this method, Phrank, Phenomizer, HANRD and Phenolyzer on the prioritization of disease-causing genes, as can be seen from graph A, in this evaluation, this method The probability of ranking the disease-causing gene in the Top 10 in the test set of real patients is 11.7%, and the probability of ranking the disease-causing gene in the Top 10 by Phrank, Phenomizer, HANRD and Phenolyzer are respectively: 9.6%, 5.2%, 7.1% an...

Embodiment 3

[0163] Verification Example 3 Increasing the weight of precise phenotypes can significantly improve the performance of this method in the comprehensive test set

[0164] Such as Figure 12 As shown, the linear regression between the number of input phenotypes and the grade of the disease-causing gene showed that there was no significant relationship between the number of phenotypes and the grade of the disease-causing gene (P = 0.513). However, the percentages of accurate and imprecise phenotypes were positively correlated with the detection performance of the software (P = 2.20e-16 and P = 3.79e-8, respectively). In contrast, the percentage of noisy phenotypes was negatively correlated with the detection performance of the software (P = 2.20e-16). This result strongly suggests that increasing the weight of precise or imprecise phenotypes can improve the performance of the method.

[0165] We first constructed a comprehensive test set containing different combinations of pre...

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Abstract

The invention discloses a phenotype-based gene prioritization method, an electronic device and a computer-readable storage medium. The method includes: receiving an input phenotype group, the input phenotype group including at least one phenotype; obtaining the The vector representation of the input phenotype group; obtain the vector representation of each gene to be sorted; and obtain the vector representation of each gene to be sorted and the vector representation of the input phenotype group according to the vector representation of each gene to be sorted and the vector representation of the input phenotype group respectively. Correlation scores between the input phenotype groups; and sorting all the genes to be sorted according to the correlation scores, and the sorting results are used as the priority ranking of the genes to be sorted relative to the input phenotype groups. The gene prioritization method based on phenotype in the present invention has better ranking performance for genes.

Description

technical field [0001] The present invention relates to the technical field of biological information, and more specifically, relates to a gene prioritization method based on phenotype, electronic equipment and a computer-readable storage medium. Background technique [0002] Genetic diseases can be divided into single gene diseases, polygenic diseases, mitochondrial diseases and chromosomal diseases according to the way of inheritance. Single gene disease, also known as Mendelian inheritance disease, is a disease controlled by a pair of alleles. [0003] Mendelian disorders affect millions of live births each year and account for approximately 17.0% of pediatric hospitalizations. Since 2005, second-generation genome sequencing technology has become the main way to detect Mendelian genetic diseases in modern times. The second-generation genome sequencing technology includes whole genome sequencing (whole genome sequencing, WGS), whole exome sequencing (whole exomesequencing...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/00
CPCG16B30/00
Inventor 吴南郑羽陈泽夫杨永鑫赵森吴志宏范燃郑思思陈泽根
Owner 北京易奇科技有限公司