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An automatic classification method, device and electronic device for gene variation

A gene variation and automatic classification technology, applied in genomics, sequence analysis, instruments, etc., can solve the problems of 40-60 minutes of time-consuming, time-consuming, and high-level requirements for interpretation technicians, so as to avoid psychological pressure and save money. Operation time, effect of reducing the proportion of undetermined clinical significance

Active Publication Date: 2022-07-19
PRECISION SCI BIOMEDICINE (SUZHOU) CO LTD +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

In addition, the classification of genetic variants using manual methods involves searching a large number of documents, so the evaluation of the pathogenicity of a variant takes an average of 40-60 minutes, which is not only time-consuming, but also requires the level of interpreting technicians. very high

Method used

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  • An automatic classification method, device and electronic device for gene variation
  • An automatic classification method, device and electronic device for gene variation

Examples

Experimental program
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Embodiment 1

[0074] The embodiment of the present invention takes the BRCA2 gene variation NM_000059.3 (BRCA2):c.4677del (p.Phe1559LeufsTer9) as an example to illustrate the process of using the method of the present invention to interpret it and classify it.

[0075] This variant is an insertion / deletion variant, and the predicted protein consequence is a frameshift, so this variant type is a frameshift variant. The evidence that needs to be judged according to the type of mutation includes at least: PVS1, PM2, PS4, PP5. Evidences PVS1, PM2, PS4, PP5 were searched sequentially in public databases and the literature database. After searching, it was found:

[0076] For PVS1, according to the evidence evaluation rules established in the present invention, it satisfies "when the pathogenic mechanism of a disease is loss of function (LOF), non-functional variants (nonsense mutations, frameshift mutations, classical ± 1 or 2 splicing mutations, Start codon variant, single or multiple exon de...

Embodiment 2

[0085] The embodiment of the present invention takes the BRCA1 gene variation BRCA1:NM_007294.3(BRCA1):c.80+4A>T as an example to illustrate the process of using the method of the present invention to interpret it and classify it. This variant is an intronic variant and cannot be ruled out to have an effect on mRNA splicing. The evidence that needs to be judged according to the type of mutation includes at least: PP3, PM2, PS3. Evidence PP3, PM2, PS3 was searched sequentially in the public database and said literature database. After searching, it is found that: for PP3, according to the evidence evaluation rules established in the present invention, if "when the intron variation satisfies SpliceAI, (anyΔscore≥0.2)", it can be judged that the variation conforms to the evidence of PP3. For PM2, it was retrieved that the mutation was missing in population frequency in gnomAD, which satisfies the judgment rule of the present invention: "PM2_MOD: The occurrence of this mutation w...

Embodiment 3

[0098] The embodiment of the present invention takes the PALB2 gene mutation NM_024675.4 (PALB2): c.1054G>C (p.Glu352Gln) as an example to illustrate the process of using the method of the present invention to interpret it and classify it.

[0099] The variant is a missense variant, and the pathogenic impact of the variant cannot be determined for the time being. The evidence that needs to be judged according to the variant type includes at least: BS1, BP4.

[0100] Evidence BS1, BP4 is searched in turn in the public database and the literature database. After searching, it was found:

[0101] For BS1, according to the evidence judgment rule established by the present invention, it satisfies "In the gnomAD v2.1.1 (non-cancer) database, when the Popmax Filtering AF (95% confidence) corresponding to a certain variation that is qualified for quality control is greater than 0.01% (0.0001 ), then BS1 is satisfied.”

[0102] For BP4, according to the evidence judging rules establi...

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Abstract

The invention discloses an automatic classification method, device and electronic equipment for gene variation. The method includes: obtaining information on gene variation; establishing evidence evaluation rules for gene variation; building a gene variation evidence literature database; according to the gene variation information, based on the gene variation evidence evaluation rules, using public database and literature database to match to obtain gene variation Evidence; classification of genetic variants according to matching evidence or a combination of evidence. By using the method provided by the invention, automatic interpretation, classification and batch processing of variants can be realized, operation time is saved; meanwhile, the proportion of unknown clinical significance is reduced, and the accuracy is improved. Therefore, the method of the present invention can be widely used in the process of precise diagnosis and treatment of patients.

Description

technical field [0001] The invention relates to the technical field of gene variation classification, in particular to an automatic classification method, device and electronic equipment for gene variation. Background technique [0002] Since genes play a very important role in life, some serious diseases may occur when certain genes are mutated, deleted or inactivated. [0003] For example, BRCA1 (Breast cancer susceptibility gene 1, breast cancer susceptibility gene 1), BRCA2 (Breast cancer susceptibility gene 2, breast cancer susceptibility gene 2), PALB2 (partner and localizer of BRCA2, BRCA2 localization and cooperation gene) belong to tumor suppressor Genes, as the core genes involved in the homologous recombination repair pathway, occupy an important proportion in ovarian cancer, prostate cancer, breast cancer, and pancreatic cancer. Individuals who carry germline pathogenic or probable pathogenic variants in these genes are at increased risk of developing breast, ov...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20G16B20/50G16B30/00G16B50/30
CPCG16B20/20G16B20/50G16B30/00G16B50/30
Inventor 季序我胥新芸董宇郭忠玉薛超
Owner PRECISION SCI BIOMEDICINE (SUZHOU) CO LTD
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