CN108509767B - Method and device for processing genetic mutation - Google Patents
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Abstract
The invention discloses a genetic mutation processing method, which comprises the following steps: determining a genetic mutation characteristic of an individual, the genetic mutation characteristic comprising: whether the mutation affects the gene to produce protein deterioration, the known pathogenicity of the mutation, and the frequency of the mutation; performing mutation screening according to the characteristics of the genetic mutation; and sequencing the screened genetic mutations through the destructiveness of the preset genetic mutations and the relationship between the genes where the preset genetic mutations are located and the individual characteristics. Thereby, subsequent molecular diagnosis and treatment costs are reduced.
Description
Technical Field
The invention relates to the technical field of mutation or genetic engineering, in particular to a method and a device for processing genetic mutation.
Background
A gene (genetic element) is a DNA fragment having a genetic effect. Genes support the basic architecture and performance of life. All information of the processes of race, blood type, inoculation, growth, apoptosis and the like of life is stored. All life phenomena of living body such as growth, aging, disease, aging and death are related to genes. It is also an intrinsic factor in determining life health.
Genetic diseases typically occur in a "vertical fashion". Parents are passed to children, children are passed to their children, and generations are passed. The pathogenic gene carried by the patient will continue to be inherited through the reproduction of the offspring, and the family members (such as couples) without relationship have no mutual influence.
Mutation (Mutation), which means the biological meaning of a gene Mutation, refers to an alteration in a genetic gene in a cell, usually to deoxyribonucleic acid present in the nucleus of the cell. It includes point mutations caused by single base changes, or deletions, duplications and insertions of multiple bases. The cause may be errors in the replication of the genetic genes during cell division, or the influence of chemicals, radiation or viruses.
Mutations often result in cells that function improperly or die, and can even cause cancer in higher organisms. At the same time, however, mutations are also considered as "impetus" for the evolution of species. Undesirable mutations are eliminated by the process of selection, while mutations that are beneficial to the species are accumulated.
On 3.5.2007, james hichitz published a "method of assessing genetic disorders" article in which methods of assessing genetic diseases are involved, and correlations between copy number variations in diseased individuals and the diseases were determined by comparing copy number variations in individuals with genetic diseases to copy number variations in at least 100 healthy normal individuals.
However, this approach does not allow for the differential treatment of rare patients whose genetic mutations vary among individuals. At the same time, this method also fails to take into account the role of known gene mutations in different diseases. Finally, in the case of multiple possible disease-causing gene mutations, this approach does not allow for ranking based on the relationship between each mutation and the patient's characterization. Thus, this method of assessing genetic diseases greatly increases the cost of subsequent molecular diagnosis and treatment.
Disclosure of Invention
The invention aims to provide a method for processing genetic mutation, which is used for solving the problems of insufficient diagnosis and high diagnosis cost in the method for evaluating the genetic diseases in the prior art.
In order to achieve the above object, in a first aspect, the present invention provides a method for treating a genetic mutation, the method comprising:
determining a genetic mutation characteristic of an individual, the genetic mutation characteristic comprising: whether the mutation affects the gene to produce protein deterioration, the known pathogenicity of the mutation, and the frequency of the mutation;
screening for genetic mutations based on whether the mutation affects protein deterioration of the gene, known pathogenicity of the mutation, and frequency of the mutation;
and sequencing the screened genetic mutations through the destructiveness of the preset genetic mutations and the relationship between the genes where the preset genetic mutations are located and the individual characteristics.
In one possible implementation, the determining the genetic mutation characteristic of the individual specifically comprises:
annotating the genetically mutated gene with mutation annotation software to determine whether the mutation of the genetically mutated gene affects the gene to produce protein deterioration;
and comparing the genetically mutated gene with a genome aggregation database, a human gene mutation big database gnomAD and a human gene mutation genetic disease big database HGMD to determine the known pathogenicity and mutation frequency of the mutation of the genetically mutated gene.
In one possible implementation, said screening for genetic mutations depending on whether said mutations affect the protein deterioration of the gene, the pathogenicity of the mutations known and the rarity of the mutations specifically comprises:
and comparing the mutation frequency with a preset mutation frequency threshold, and when the occurrence frequency of the mutation in a normal population is less than the mutation frequency threshold and the genetic mutation can influence the function of the generated protein, reserving the genetic mutation for the next analysis.
In one possible implementation, the screening for genetic mutations based on whether the mutation affects protein deterioration of the gene, known pathogenicity of the mutation, and frequency of the mutation specifically comprises:
when it is determined that the genetic mutation causes disease, the genetic mutation is retained for further analysis.
In a possible implementation manner, the sorting the screened genetic mutations according to the destructiveness of the preset genetic mutations and the relationship between the gene where the preset genetic mutations are located and the individual characteristics specifically includes:
the sorting of the screened genetic mutations according to the destructiveness of the preset genetic mutations and the relationship between the gene where the preset genetic mutations are located and the individual characteristics specifically comprises:
scoring the information carried by the mutation itself, including its destructiveness and whether it is a known causative mutation, to determine a first score;
scoring the relationship between the gene in which the genetic mutation is located and the individual characterization to determine a second score;
weighting the first score and the second score to obtain a third score;
ranking the screened genetic mutations according to the third score. In a second aspect, there is provided a genetic mutation processing apparatus comprising: the device comprises a first determining unit, a second determining unit and a sorting unit;
the first determination unit is used for determining the genetic mutation characteristics of the individual, and the genetic mutation characteristics comprise: whether the mutation affects the gene to produce protein deterioration, the known pathogenicity of the mutation, and the frequency of the mutation;
the second determination unit is used for screening genetic mutation according to whether the mutation affects protein deterioration of the gene, known pathogenicity of the mutation and frequency of the mutation;
and the sequencing unit is used for sequencing the screened genetic mutation through the destructiveness of the preset genetic mutation and the relationship between the gene where the preset genetic mutation is located and the individual representation.
In a possible implementation manner, the first determining unit is specifically configured to:
annotating the genetically mutated gene with mutation annotation software to determine whether the mutation of the genetically mutated gene affects the gene to produce protein deterioration;
and comparing the genetically mutated gene with a genome aggregation database, a human gene mutation big database gnomAD and a human gene mutation genetic disease big database HGMD to determine the known pathogenicity and mutation frequency of the mutation of the genetically mutated gene.
In a possible implementation manner, the second determining unit is specifically configured to:
and comparing the mutation frequency with a preset mutation frequency threshold, and when the occurrence frequency of the mutation in a normal population is less than the mutation frequency threshold and the genetic mutation can influence the function of the generated protein, reserving the genetic mutation for the next analysis.
In a possible implementation manner, the second determining unit is specifically configured to:
when it is determined that the genetic mutation causes disease, the genetic mutation is retained for further analysis.
In a possible implementation manner, the sorting unit is specifically configured to:
scoring the information carried by the mutation itself, including its destructiveness and whether it is a known causative mutation, to determine a first score;
scoring the relationship between the gene in which the genetic mutation is located and the individual characterization to determine a second score;
weighting the first score and the second score to obtain a third score;
according to the third score, the method for sorting the screened genetic mutations has the following advantages: the subsequent diagnosis and treatment costs are reduced.
Drawings
FIG. 1 is a flow chart of a method for processing genetic mutations provided in an embodiment of the present invention;
FIG. 2 is a flowchart illustrating the step 110 according to an embodiment of the present invention;
FIG. 3 is a flowchart illustrating a step 120 according to an embodiment of the present invention;
FIG. 4 is a flowchart illustrating a detailed procedure of step 130 according to an embodiment of the present invention;
FIG. 5 is a schematic representation of the relationship between a gene in which a genetic mutation is located and a representation of an individual provided by an embodiment of the present invention;
FIG. 6 is a schematic structural diagram of a genetic mutation processing apparatus according to an embodiment of the present invention.
Detailed Description
The following examples are intended to illustrate the invention but are not intended to limit the scope of the invention.
Example 1
FIG. 1 is a flow chart of a method for processing genetic mutations provided in an embodiment of the present invention. As shown in fig. 1, the execution subject of the method may be a client, such as a Personal Computer (PC), a desktop, etc. The method comprises the following steps:
Further, the determining the genetic mutation characteristics of the individual specifically comprises: annotating the genetically mutated gene with mutation annotation software, such as SnpEff, to determine whether the mutation of the genetically mutated gene affects the gene to produce protein deterioration; and comparing the genetically mutated gene with a genome aggregation database, a human gene mutation big database gnomAD and a human gene mutation big database HGMD to determine the known pathogenicity and rareness of mutation of the genetically mutated gene.
Specifically, as shown in fig. 2, the location where the gene mutation occurs, such as which gene is mutated, on which exon the mutated gene is located, and the transcription of transcript, which conforms to the Human Genome Variation Society (HGVS) description, whether the mutation affects the protein deterioration of the gene, etc., are determined using open source software such as SnpEff. Subsequently, these several characteristics can be used as the basis for the subsequent screening of genetic mutations. In the present application, whether mutation affects protein deterioration of a gene is taken as a main feature, and it is understood that any other feature may be taken as a basis for determining genetic mutation screening as needed, and the present application is not limited thereto.
Thereafter, the known pathogenicity of mutations of the genetically mutated genes found in the patient individuals and the frequency of mutations in the respective healthy population were further annotated by comparing gnomAD and HGMD.
As shown in fig. 3, screening and filtering are performed according to three characteristics of each genetic mutation, and specifically, in one example, the screening of genetic mutations according to whether the mutation affects protein deterioration of a gene, pathogenicity of a mutation known, and frequency of mutation specifically includes:
the mutation frequency may be compared with a preset mutation frequency threshold, and when the mutation frequency is smaller than the mutation frequency threshold and the genetic mutation affects the function of generating protein, the genetic mutation is screened out, and the deleted genetic mutation may form a gene list according to the gene where the genetic mutation is located, so as to be analyzed in the next step 130. At this time, a mutation frequency threshold value, for example, 0.5% can be set as a mutation frequency threshold value in healthy people as needed (the threshold value required for rare genetic disease analysis is generally low). Mutations that may cause protein deterioration include the following:
splice region variants splice _ region _ variant
Stop reservation stop _ retained
Initiator _ codon start codon
Nonsense mutation stop _ gated
Loss stop _ loss
Start _ lost
Frame shift with frame shift mutation
Intra-frame miss inframe _ deletion
Intra-frame insertion
Missense mutation missense
If a gene is mutated and appears at a very low frequency in a healthy individual and affects the protein deterioration of the gene, the genetically mutated gene can be retained and added to the list of genetically mutated genes.
The genetic mutation may also be retained for further analysis when it is determined that the genetic mutation will cause disease.
In another example, the screening for genetic mutations based on whether the mutation affects protein deterioration of the gene, known pathogenicity of the mutation, and frequency of the mutation specifically includes:
when it is determined that the genetic mutation causes disease, the genetic mutation is retained for further analysis.
And step 130, sequencing the screened genetic mutations through the destructiveness of the preset genetic mutations and the relationship between the genes where the preset genetic mutations are located and the individual characteristics.
Specifically, as shown in fig. 4, the sorting of the screened genetic mutations according to the destructiveness of the preset genetic mutations and the relationship between the gene in which the preset genetic mutation is located and the individual characteristics specifically includes:
scoring the information carried by the mutation itself, including its destructiveness and whether it is a known causative mutation, to determine a first score;
scoring the relationship between the gene in which the genetic mutation is located and the individual characterization to determine a second score;
weighting the first score and the second score to obtain a third score;
ranking the screened genetic mutations according to the third score. Among them, the destructive effect of genetic mutation is mainly reflected in the influence on the production of proteins by genes. The application takes the splice _ denor and the splice _ adaptor as the most destructive, and the next level is other splice _ region _ variant, frame shift, stop _ gain, start _ loss and stop _ loss; inframe and missense are the least destructive. Another feature is the relationship between the gene in which the genetic mutation is located and the individual's characteristics, as shown in FIG. 5. According to the method, individual characteristics correspond to a Human characteristic tree (Human Phenotype Ontology), an individualized tree diagram is generated on the basis of the characteristic tree, genes related to any node in the tree diagram are extracted, and an individual gene list is formed. After that, common genes in the gene list of the individual and the gene list carrying the filtered mutations are found and ordered according to an algorithm based on network topology. Finally, the application calculates the respective weights of the two characteristics through a large amount of clinical data and a gradient parameter algorithm, and forms a uniform score for each filtered genetic mutation. This score represents the likelihood that the mutation is a causative gene in the individual. The application finally returns a list of gene mutations ordered by this score. Thereby, subsequent molecular diagnosis and treatment costs are reduced.
Example 2
FIG. 6 is a schematic structural diagram of a genetic mutation processing apparatus according to an embodiment of the present invention. As shown in fig. 6, the genetic mutation processing apparatus 600 includes: a first determining unit 601, a second determining unit 602, and a sorting unit 603.
The first determining unit 601 is configured to determine a genetic mutation characteristic of an individual, where the genetic mutation characteristic includes: whether the mutation affects the protein deterioration of the gene, the known pathogenicity of the mutation and the frequency of the mutation.
The second determination unit 602 is used for screening genetic mutations according to whether the mutation affects protein deterioration of the gene, known pathogenicity of the mutation and frequency of the mutation.
The sorting unit 603 is configured to sort the screened genetic mutations according to destructiveness of the preset genetic mutations and a relationship between a gene where the preset genetic mutations are located and an individual characterization.
Further, the first determining unit 601 is specifically configured to:
annotating the genetically mutated gene with mutation annotation software, such as SnpEff, to determine whether the mutation of the genetically mutated gene affects the gene to produce protein deterioration;
and comparing the genetically mutated gene with a genome aggregation database, a human gene mutation big database gnomAD and a human gene mutation genetic disease big database HGMD to determine the known pathogenicity and mutation frequency of the mutation of the genetically mutated gene.
Further, the second determining unit 602 is specifically configured to:
and comparing the mutation frequency with a preset mutation frequency threshold, and when the occurrence frequency of the mutation in a normal population is less than the mutation frequency threshold and the genetic mutation can influence the function of the generated protein, reserving the genetic mutation for the next analysis.
Further, the second determining unit 602 is specifically configured to:
when it is determined that the genetic mutation causes disease, the genetic mutation is retained for further analysis.
Further, the sorting unit 603 is specifically configured to:
scoring the information carried by the mutation itself, including its destructiveness and whether it is a known causative mutation, to determine a first score;
scoring the relationship between the gene in which the genetic mutation is located and the individual characterization to determine a second score;
weighting the first score and the second score to obtain a third score;
ranking of the genetic mutations after screening based on the third score although the present invention has been described in detail above with general description and specific examples, it will be apparent to those skilled in the art that modifications and improvements can be made based on the present invention. Accordingly, such modifications and improvements are intended to be within the scope of the invention as claimed.
Claims (8)
1. A method of genetic mutation management, said method comprising:
determining a genetic mutation characteristic of an individual, the genetic mutation characteristic comprising: whether the mutation affects the gene to produce protein deterioration, the known pathogenicity of the mutation, and the frequency of the mutation;
screening for genetic mutations based on whether the mutation affects protein deterioration of the gene, known pathogenicity of the mutation, and frequency of the mutation;
sequencing the screened genetic mutations through the destructiveness of the preset genetic mutations and the relationship between the genes where the preset genetic mutations are located and individual characteristics;
wherein, the sorting of the screened genetic mutations according to the destructiveness of the preset genetic mutations and the relationship between the gene where the preset genetic mutations are located and the individual characteristics specifically comprises:
scoring the information carried by the mutation itself, including its destructiveness and whether it is a known causative mutation, to determine a first score;
scoring the relationship between the gene in which the genetic mutation is located and the individual characterization to determine a second score;
weighting the first score and the second score to obtain a third score;
ranking the screened genetic mutations according to the third score;
the individual characteristics correspond to a human body characteristic tree, an individualized dendrogram is generated on the basis of the characteristic tree, genes related to any node in the dendrogram are extracted to form an individual gene list, common genes in the individual gene list and the filtered mutation bearing gene list are found, and the common genes are sequenced according to an algorithm based on network topology.
2. The method according to claim 1, wherein said determining the genetic mutation characteristic of the individual comprises in particular:
annotating the genetically mutated gene with mutation annotation software to determine whether the mutation of the genetically mutated gene affects the gene to produce protein deterioration;
and comparing the genetically mutated gene with a genome aggregation database, namely a human gene mutation big database and a human gene mutation genetic disease big database HGMD, and determining the known pathogenicity and mutation frequency of the mutation of the genetically mutated gene.
3. The method according to claim 1, wherein said screening for genetic mutations based on whether said mutations affect protein deterioration of genes, known pathogenicity of mutations and rarity of mutations comprises:
and comparing the mutation frequency with a preset mutation frequency threshold, and when the occurrence frequency of the mutation in a normal population is less than the mutation frequency threshold and the genetic mutation can influence the function of the generated protein, reserving the genetic mutation for the next analysis.
4. The method according to claim 1, wherein said screening for genetic mutations based on whether said mutations affect protein deterioration of genes, known pathogenicity of mutations and frequency of mutations comprises:
when it is determined that the genetic mutation causes disease, the genetic mutation is retained for further analysis.
5. A genetic mutation processing apparatus, comprising: the device comprises a first determining unit, a second determining unit and a sorting unit;
the first determination unit is used for determining the genetic mutation characteristics of the individual, and the genetic mutation characteristics comprise: whether the mutation affects the gene to produce protein deterioration, the known pathogenicity of the mutation, and the frequency of the mutation;
the second determination unit is used for screening genetic mutation according to whether the mutation affects protein deterioration of the gene, known pathogenicity of the mutation and frequency of the mutation;
the sequencing unit is used for sequencing the screened genetic mutations according to the destructiveness of the preset genetic mutations and the relationship between the genes where the preset genetic mutations are located and the individual characteristics, and is specifically used for:
scoring the information carried by the mutation itself, including its destructiveness and whether it is a known causative mutation, to determine a first score;
scoring the relationship between the gene in which the genetic mutation is located and the individual characterization to determine a second score;
weighting the first score and the second score to obtain a third score;
ranking the screened genetic mutations according to the third score;
the individual characteristics correspond to a human body characteristic tree, an individualized dendrogram is generated on the basis of the characteristic tree, genes related to any node in the dendrogram are extracted to form an individual gene list, common genes in the individual gene list and the filtered mutation bearing gene list are found, and the common genes are sequenced according to an algorithm based on network topology.
6. The apparatus according to claim 5, wherein the first determining unit is specifically configured to:
annotating the genetically mutated gene with mutation annotation software to determine whether the mutation of the genetically mutated gene affects the gene to produce protein deterioration;
and comparing the genetically mutated gene with a genome aggregation database, namely a human gene mutation big database and a human gene mutation genetic disease big database HGMD, and determining the known pathogenicity and mutation frequency of the mutation of the genetically mutated gene.
7. The apparatus according to claim 5, wherein the second determining unit is specifically configured to:
and comparing the mutation frequency with a preset mutation frequency threshold, and when the occurrence frequency of the mutation in a normal population is less than the mutation frequency threshold and the genetic mutation can influence the function of the generated protein, reserving the genetic mutation for the next analysis.
8. The apparatus according to claim 5, wherein the second determining unit is specifically configured to:
when it is determined that the genetic mutation causes disease, the genetic mutation is retained for further analysis.
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| CN106575321A (en) * | 2014-01-14 | 2017-04-19 | 欧米希亚公司 | Methods and systems for genome analysis |
| CN107229841A (en) * | 2017-05-24 | 2017-10-03 | 重庆金域医学检验所有限公司 | A kind of genetic mutation appraisal procedure and system |
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| CN105603062A (en) * | 2006-05-03 | 2016-05-25 | 人口诊断股份有限公司 | Method of evaluating genetic disorders |
| CN106575321A (en) * | 2014-01-14 | 2017-04-19 | 欧米希亚公司 | Methods and systems for genome analysis |
| CN105279369A (en) * | 2015-09-06 | 2016-01-27 | 苏州协云和创生物科技有限公司 | Next generation sequencing based coronary heart disease genetic risk evaluation method |
| CN105678093A (en) * | 2016-02-01 | 2016-06-15 | 北京东方亚美基因科技研究院 | Gene detection method for estimating inheritance risk of disease |
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