CN106407748A - Method and device for acquiring mutation sites of genes corresponding to endocrine and metabolism system - Google Patents
Method and device for acquiring mutation sites of genes corresponding to endocrine and metabolism system Download PDFInfo
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Abstract
The invention provides a method and a device for acquiring mutational sites of genes corresponding to an endocrine and metabolism system, and relates to the technical field of biological information. The method comprises the following steps: carrying out data comparison on a plurality of short sequence and reference genome of genes to be tested to obtain the initial mutational site information of the genes to be tested; according to the initial mutational site information, deleting mutational sites which do not meet a preset reservation condition in a plurality of initial mutational sites to obtain sites to be tested; comparing the sites to be tested with a plurality of mutational sites of the genes corresponding to the endocrine and metabolism system in an endocrine and metabolism system gene bank; and when the mutational site of which the position and mutation basic group are the same as the site to be tested exists in the endocrine and metabolism system gene bank, obtaining the site mutation condition of the genes corresponding to the endocrine and metabolism system in the genes to be tested. According to the method and the device, the mutation condition of a plurality of mutational sites relevant to the endocrine and metabolism system in the mutational sites in the genes to be tested can be obtained.
Description
Technical field
The application is related to technical field of biological information, in particular to a kind of corresponding base of Endocrine and metabolism system
Acquisition methods and device because of mutational site.
Background technology
Development with medical science, genomics and high throughput sequencing technologies and maturation, precisely medical (Precision
Medicine) also apply in countries in the world, become new medical model.Precisely medical treatment is by individual people's gene, environment and life
The disease prevention that custom difference is taken into account and the therapy disposed, according to everyone hereditary information, personalized, precision
Go formulate medical treatment and health management scheme.
And everyone genetic background is distinguishing, in the process it is necessary to determine everyone genome or
The catastrophe of some genes being associated with corresponding organ or position, further according to this base mutation situation to allow to
Analysis contrast, determines final ill probability, to specify medical treatment and health management scheme accordingly.
Hormonal system and metabolic system are the important systems of organism, if Endocrine and metabolism system occurs pathological changes, meeting
Produce extremely serious impact.Then, Endocrine and metabolic system disease do certain preventive measure, to reduce incidence probability,
Of crucial importance.
Incidence due to Endocrine and metabolism disease has certain contacting, Endocrine and metabolism system with gene
Unite corresponding gene site base mutation situation different, the different Endocrine and metabolism diseases of Endocrine and metabolism system may be made
The incidence of disease and incidence probability are different.Thus it is possible to utilize accurate medical model, corresponded to according to Endocrine and metabolism system
The base mutation situation of gene and the combination Endocrine of other information carry out with the incidence of metabolic disease and probability
Prediction, carrying out prevention with Endocrine and metabolic disease is a kind of effective precautionary approach.Endocrine and metabolism disease i.e. interior point
Secrete and metabolic system disease.
Existing Endocrine and the determination of metabolic system gene point mutation situation, obtain typically by chemical mode
The base mutation situation of the gene locis of a certain specified location of testing gene, the quantity in the mutational site that this acquisition modes obtains
Limited, be typically only capable to obtain the catastrophe of some or certain several bases it is impossible to determine simultaneously in testing gene with endocrine
The catastrophe of as much as possible multiple variant sites of gene corresponding with metabolic system, makes subsequently to combine other information internal
Secretion is likely to occur relatively large deviation with the predicting the outcome of disease condition of metabolic disease.
Content of the invention
In view of this, the embodiment of the present application provides a kind of obtaining of corresponding gene mutation site of Endocrine and metabolism system
Take method and device, by by the Endocrine and metabolism in the variant sites of testing gene and Endocrine and metabolism system gene storehouse
Multiple variant sites of the corresponding gene of system are compared, it is hereby achieved that the Endocrine and metabolism system in testing gene
The base mutation situation of multiple variant sites of corresponding gene, to improve the problems referred to above.
To achieve these goals, the technical scheme that the application adopts is as follows：
A kind of acquisition methods of the corresponding gene mutation site of Endocrine and metabolism system, methods described includes：Will be to be measured
The multiple short sequence of gene and reference gene group carry out comparing, obtain the preliminary variant sites information of testing gene, described
Preliminary variant sites information includes the mutating alkali yl of multiple preliminary variant sites and the position letter of each preliminary variant sites
Breath；According to described preliminary variant sites information, the variation of default reserve will be unsatisfactory in the plurality of preliminary variant sites
Site is deleted, and the variant sites in the described testing gene obtaining after deleting are as site to be checked；By described site to be checked with
Multiple variant sites of the corresponding gene of Endocrine and metabolism system in Endocrine and metabolism system gene storehouse are compared, institute
State the mutation that Endocrine and metabolism system gene storehouse includes each variant sites of the corresponding gene of Endocrine and metabolism system
Base and each variant sites position；When presence and described Endocrine and metabolism system gene storehouse in described site to be checked
Middle position is identical and mutating alkali yl identical variant sites, obtains the corresponding base of Endocrine and metabolism system in described testing gene
The site mutation situation of cause.
A kind of acquisition device of the corresponding gene mutation site of Endocrine and metabolism system, described device includes：Compare mould
Block, for the multiple short sequence of testing gene and reference gene group are carried out comparing, obtains the preliminary variation of testing gene
Site information, described preliminary variant sites information includes the mutating alkali yl of multiple preliminary variant sites and each tentatively makes a variation
The positional information in site；Filtering module, for according to described preliminary variant sites information, by the plurality of preliminary variant sites
The variant sites being unsatisfactory for default reserve are deleted, and the variant sites in the described testing gene that will obtain after deleting are as treating
Inspection site；Comparison module, for by the Endocrine and metabolism system in described site to be checked and Endocrine and metabolism system gene storehouse
The multiple variant sites of corresponding gene of uniting are compared, and described Endocrine and metabolism system gene storehouse includes endocrine and generation
The mutating alkali yl of each variant sites of the corresponding gene of system of thanking and each variant sites position；Mutation obtains mould
Block, when presence and mutating alkali yl identical identical with position in described Endocrine and metabolism system gene storehouse in described site to be checked
Variant sites, for obtaining the site mutation situation of the corresponding gene of Endocrine and metabolism system in described testing gene.
The acquisition methods of the corresponding gene mutation site of Endocrine and metabolism system and device that the embodiment of the present application provides,
Obtain testing gene variant sites in the case of, by the variant sites of testing gene with Endocrine and metabolism system gene
In storehouse, multiple variant sites of the corresponding gene of Endocrine and metabolism system are compared, in Endocrine and metabolism system gene storehouse
Mutating alkali yl including each variant sites of the corresponding gene of Endocrine and metabolism system and each variant sites institute are in place
Put.When in testing gene, presence is identical with position in Endocrine and metabolism system gene storehouse and mutating alkali yl identical becomes dystopy
It may be determined that there is the corresponding gene mutation of Endocrine and metabolism system in this testing gene in point.
Because Endocrine and metabolism system gene storehouse includes the multiple variant sites related to Endocrine and metabolism system,
Then this programme can determine related to Endocrine and metabolism system multiple variant sites in testing gene, and the plurality of variation
The concrete base mutation situation in site.
For enabling the above-mentioned purpose of the application, feature and advantage to become apparent, preferred embodiment cited below particularly, and coordinate
Appended accompanying drawing, is described in detail below.
Brief description
Purpose, technical scheme and advantage for making the embodiment of the present application are clearer, below in conjunction with the embodiment of the present application
In accompanying drawing, the technical scheme in the embodiment of the present application is clearly and completely described it is clear that described embodiment is
Some embodiments of the present application, rather than whole embodiments.Based on the embodiment in the application, those of ordinary skill in the art
The every other embodiment being obtained under the premise of not making creative work, broadly falls into the scope of the application protection.
Fig. 1 shows the structural representation of the computer that the embodiment of the present application provides；
Fig. 2 shows obtaining of the corresponding gene mutation site of Endocrine and metabolism system that the application first embodiment provides
Take a kind of flow chart of method；
Fig. 3 shows obtaining of the corresponding gene mutation site of Endocrine and metabolism system that the application first embodiment provides
The flow chart taking the part steps of method；
Fig. 4 shows obtaining of the corresponding gene mutation site of Endocrine and metabolism system that the application second embodiment provides
Take the functional block diagram of device；
Fig. 5 shows obtaining of the corresponding gene mutation site of Endocrine and metabolism system that the application second embodiment provides
The gene bank taking device sets up the functional block diagram of module；
Fig. 6 shows obtaining of the corresponding gene mutation site of Endocrine and metabolism system that the application second embodiment provides
Take the functional block diagram of the filtering module of device；
Fig. 7 shows obtaining of the corresponding gene mutation site of Endocrine and metabolism system that the application second embodiment provides
Take the functional block diagram of the comparing module of device.
Specific embodiment
Below in conjunction with accompanying drawing in the embodiment of the present application, the technical scheme in the embodiment of the present application is carried out clear, complete
Ground description is it is clear that described embodiment is only some embodiments of the present application, rather than whole embodiments.Generally exist
The assembly of the embodiment of the present application described and illustrated in accompanying drawing can be arranged with various different configurations and design herein.Cause
This, be not intended to limit claimed the application's to the detailed description of the embodiments herein providing in the accompanying drawings below
Scope, but it is merely representative of the selected embodiment of the application.Based on embodiments herein, those skilled in the art are not doing
The every other embodiment being obtained on the premise of going out creative work, broadly falls into the scope of the application protection.
It should be noted that：Similar label and letter represent similar terms in following accompanying drawing, therefore, once a certain Xiang Yi
It is defined in individual accompanying drawing, then do not need it to be defined further and explains in subsequent accompanying drawing.Meanwhile, the application's
In description, term " first ", " second " etc. are only used for distinguishing description, and it is not intended that indicating or hint relative importance.
As shown in figure 1, being the block diagram of the application computer 100.Described computer 100 includes Endocrine and metabolism
The acquisition device 200 of the corresponding gene mutation site of system, memorizer 101, storage control 102, processor 103, peripheral hardware connect
Mouthfuls 104, input-output unit 105 and other.
Described memorizer 101, storage control 102, processor 103, Peripheral Interface 104 and input-output unit 105
Each element is directly or indirectly electrically connected with each other, to realize transmission or the interaction of data.For example, these elements mutually it
Between can realize being electrically connected with by one or more communication bus or holding wire.The corresponding gene of described Endocrine and metabolism system
The acquisition device 200 in mutational site includes at least one and can be stored in described storage in the form of software or firmware (firmware)
In device 101 or be solidificated in the software function module in the operating system (operating system, OS) of described computer 100.
Described processor 103 is used for executing the executable module of storage in memorizer 101, and for example described Endocrine and metabolism system corresponds to
The software function module that includes of acquisition device 200 of gene mutation site or computer program.
Wherein, memorizer 101 may be, but not limited to, random access memory (Random Access Memory,
RAM), read only memory (Read Only Memory, ROM), programmable read only memory (Programmable Read-Only
Memory, PROM), erasable read-only memory (Erasable Programmable Read-Only Memory, EPROM),
Electricallyerasable ROM (EEROM) (Electric Erasable Programmable Read-Only Memory, EEPROM) etc..
Wherein, memorizer 101 is used for storage program, and described processor 103, after receiving execute instruction, executes described program, aforementioned
The method performed by computer 100 of the stream process definition that the embodiment of the present application any embodiment discloses can apply to processor
In 103, or realized by processor 103.
Processor 103 is probably a kind of IC chip, has the disposal ability of signal.Above-mentioned processor 103 can
To be general processor, including central processing unit (Central Processing Unit, abbreviation CPU), network processing unit
(Network Processor, abbreviation NP) etc.；Can also be digital signal processor (DSP), special IC (ASIC),
Ready-made programmable gate array (FPGA) or other PLDs, discrete gate or transistor logic, discrete hard
Part assembly.Can realize or execute disclosed each method in the embodiment of the present application, step and logic diagram.General processor
Can be microprocessor or this processor 103 can also be any conventional processor etc..
Various input/output devices are coupled to processor 103 and memorizer 101 by described Peripheral Interface 104.At some
In embodiment, Peripheral Interface 104, processor 103 and storage control 102 can be realized in one single chip.Other one
In a little examples, they can be realized by independent chip respectively.
Input-output unit 105 is used for being supplied to user input data realizes interacting of user and described computer.Described
Input-output unit may be, but not limited to, digital independent device, mouse and keyboard etc..
It should be understood that the structure shown in Fig. 1 be only illustrate, computer 100 can also include more more than shown in Fig. 1 or
Less assembly, or there are the configurations different from shown in Fig. 1.Each assembly shown in Fig. 1 can using hardware, software or its
Combination is realized.
First embodiment
The embodiment of the present application provides a kind of acquisition methods of the corresponding gene mutation site of Endocrine and metabolism system, uses
Base mutation situation in the variant sites obtaining related to Endocrine and metabolism system gene in testing gene.Refer to figure
2, the method includes：
Step S110：The multiple short sequence of testing gene and reference gene group are carried out comparing, obtains testing gene
Preliminary variant sites information, described preliminary variant sites information includes the mutating alkali yl of multiple preliminary variant sites and every
The positional information of individual preliminary variant sites.
First, obtain the multiple short sequence of testing gene, this short sequence can be exported by second filial generation microarray dataset.Will
The short sequence of testing gene and reference gene group are compared.As if testing gene is human gene, this reference gene group is then
Mankind's reference gene group.
Certainly, this comparison process can include repeatedly comparing and the process such as duplicate removal, the multiple change of the inclusion after being compared
The preliminary variant sites information of ectopic sites.
Specifically, as shown in figure 3, in the present embodiment, the comparing in this step is to obtain preliminary variant sites letter
The process of breath can include：
Step S111：The multiple short sequence of described testing gene and reference gene group are compared first, is obtained SAM lattice
The comparison result of formula.
The short sequence of testing gene and reference gene group are carried out comparing, this comparison process can utilize existing ratio
Software is carried out, such as Bowtie2, it is possible to obtain the comparison result of SAM form, be stored with the comparison result of this SAM form ratio
Comparison information to rear acquisition.It should be understood that in the comparison result of this SAM form, including each alkali in testing gene
The information of base, such as positional information.
Certainly, the representation of specifically used comparison software and comparison result is not intended as limiting in the present embodiment
System, can compare the multiple short sequence of testing gene and reference gene group and obtain the comparison information representing comparison result
It is advisable.
Step S112：Duplicate removal is carried out to described comparison result, makes contrast arrive the short sequence of a position of reference gene group
Number is less than or equal to 1.
In the comparison result that step S111 obtains, there are a certain proportion of repetitive sequence and result, for example, contrast with reference to base
Same position because of group may have multiple short sequences, then, in this step, comparison result is carried out duplicate removal.
In the present embodiment, it is possible to use software Picard carries out duplicate removal work.Specifically, using can be Picard
MarkDuplicate instrument duplicate removal, obtain bam form duplicate removal result.
Step S113：Comparing result after duplicate removal is carried out with local anharmonic ratio to (local multiple alignment).
The short sequence compared to reference gene group due to obtaining is difficult to accurately compare highly similar repetition
Region, then the repeat region in genome be readily available false-positive variant sites, such as false-positive SNPs.It is appreciated that
, false-positive variant sites are the variant sites of comparison result mistake.In order to reduce false positive variant sites quantity and
Ratio, in the present embodiment, carries out local anharmonic ratio pair to the comparing result after duplicate removal.
Specifically, this local anharmonic ratio can be using in GATK to (local multiple alignment)
IndelRealigner is carried out, obtain bam form anharmonic ratio to after comparison result.This comparison process typically has three steps,
A. detect suspicious, need to carry out the region of anharmonic ratio pair；B. anharmonic ratio pair is carried out to these suspicious regions；C. repair in anharmonic ratio
To during lose mate pairing information.
Step S114：Recalculate local anharmonic ratio to after comparison result in base mass fraction.
In step S111 during aforementioned processing, each single base can be endowed in data processing
One mass fraction (Quality scores), for reflecting the credibility of nucleotide that corresponding base is observed.
Mass fraction due to obtaining during aforementioned processing does not have preferably to contact with wrong genotyping result probability
Get up, simultaneously the mass fraction of single base, do not contact with other specification phase example, different surveys such as in same sample
Sequence platform, different sequencing circulations, different libraries etc. are contacted.
Therefore, in this step in S114, the mass fraction of each base is connected with each factor in sequencing procedure
System, recalculates to the mass fraction of each base, generates new mass fraction, for judging that each base whether may be used
Letter.
Specifically, in the present embodiment, it is possible to use GATK carries out empirical quality score
Recalibration, obtains the result of bam form.
Step S115：According to described base mass fraction, to local anharmonic ratio to after comparing result carry out SNP and indel
Analysis, obtains preliminary variant sites information.
According to the base mass fraction recalculating acquisition, local anharmonic ratio is carried out to the comparison result obtaining SNP and
The preliminary interpretation of indel, carries out SNP and indel typing to it, to obtain the variant sites information including multiple variant sites,
, as preliminary variant sites information, multiple variant sites that this includes are as preliminary variant sites for this variant sites information.Permissible
Understand, in this preliminary variant sites information, include the mutating alkali yl of multiple preliminary variant sites, and each becomes dystopy
Point position.In the present embodiment, for SNP and indel it is preferred that in the present embodiment, variant sites are only variant sites
SNP.
Specifically, in this step, can be to be analyzed using the Unified Genotyper of GATK.Because complete
After becoming the typing of SNPs, employ a lot of data filtering parameter logistic according to being filtered again, with further control data quality,
So in this step standard minimum confidence thresholds is both configured to zero.It should be understood that
SNPs represents the plural form of SNP.
Certainly, the preliminary interpretation process of this SNP and indel can also be carried out, in the present embodiment not in other ways
As limit or other, the such as HaplotypeCaller of GATK is carried out.
In this step, it is possible to obtain include the vcf file of preliminary variant sites information, the preliminary change in this vcf file
Ectopic sites information includes each variant sites obtaining in step s 110 and the corresponding positional information of each variant sites,
Certainly, other are also included, here is not added with repeating.
Step S120：According to described preliminary variant sites information, will be unsatisfactory for presetting in the plurality of preliminary variant sites
The variant sites of reserve are deleted, and the variant sites in the described testing gene obtaining after deleting are as site to be checked.
In step s 110, it would still be possible to there is false sun in the preliminary variant sites in the preliminary variant sites information of acquisition
Property variant sites, then, this step is filtered further to preliminary variant sites, delete wherein false positive probability higher
Variant sites, the variant sites in result after to delete as the variant sites in this testing gene, make finally to obtain
Variant sites are more accurate.It should be understood that delete after result in further comprises each variant sites positional information and
Other information, will not be described here.
Specifically, in this step, following one or more can be included and delete the variation being unsatisfactory for default reserve
The mode in site：
Mode one：Remove in the plurality of preliminary variant sites, the number of allele is more than the change dystopy of predetermined threshold value
Point.
Allele is more than the variant sites of predetermined threshold value, is that the probability of false positive variant sites is higher, it is carried out
Remove.In the present embodiment, this predetermined threshold value can value according to actual needs, due to comprising more than more than 1 allele
Site just there is higher gene type mistake it is preferred that this predetermined threshold value value can be 1.
When predetermined threshold value value is 1, that is, in the multiple preliminary variant sites removing acquisition, there is more than 1 allele
Variant sites.
Mode two：Delete in the plurality of preliminary variant sites, positioned at each insertion and deletion (indel) upstream span or
The base number that all variant sites in person's span downstream, described upstream span and span downstream include is predetermined number.
Because the short sequence for comparing is often exported by secondary direction finding platform, and the short sequence of secondary microarray dataset exists
It is more prone to the comparison of mistake near the region of insertion and deletion (indel), and the local anharmonic ratio in above-mentioned processing procedure is not to
This mistake can be completely eliminated.Then, all variant sites in insertion and deletion upstream span or span downstream are deleted, with
Reduce the probability of false positive results.
The base number that this upstream span and span downstream include is predetermined number, this predetermined number can by user according to
Actual demand determines, is not restricted in the present embodiment, and, the predetermined number of upstream span and span downstream can phase
Same or different.
In the present embodiment, the base number that scope includes above is had to be preferably 5, the base number that span downstream includes is excellent
Elect 5 as.That is, all indel in preliminary variant sites are determined, for each indel, by its upstream 5bp (5 bases)
Within all variant sites delete, or all variant sites within 5bp downstream are deleted.
Certainly, in the present embodiment, can only delete in variant sites or the span downstream in the upstream span of indel
Variant sites it is also possible to the variant sites in the upstream span of indel and the variant sites in span downstream are all deleted.
Preferably, in the present embodiment, in the upstream span for insertion and deletion (indel) of deletion or span downstream
All SNPs.
Mode three：By in the plurality of preliminary variant sites, the variant sites being spaced default base number each other are deleted
Remove.
In this step, variant sites close to each other are deleted, will each other distance less than the variation of certain value
Site is deleted.
In the present embodiment, this default base number is not intended as limiting, and can set according to actual needs.
Preferably, this default base number is 4, if there is the variation that the base number being spaced each other is less than 4
Site, is deleted.That is, deleting the variant sites within upstream each other or downstream 5bp.
Preferably, in this step, the SNPs for being spaced default base number each other of deletion.
Mode four：By in the plurality of preliminary variant sites, corresponding GQ (Genotype quality) value is less than default
The variant sites of GQ threshold value are deleted.
GQ (Genotype quality) is a posterior probability (the phred-scaled probabilities) value,
For each site, GQ value is not possible of truth in order to represent this site in the genotypic results of current acquisition
Property, that is, represent obtain in this genotype of this site there is a possibility that.Calculation is：
GQ value=- 10*log10 (P [error]), wherein, P [error] represents that corresponding site is not the general of truth
Rate.
Preferably, in the present embodiment, default GQ threshold value is 20.Empirical tests, when GQ threshold value is 20, theoretic mistake
Rate is 1%.
Mode five：By in the plurality of preliminary variant sites, corresponding MQ (Mapping quality) value is less than default MQ
The variant sites of threshold value are deleted.
MQ represents the specificity (uniqueness) in aligned sequences.When same short sequence can compare same
During genome zones of different, the alignment score of the first best comparison area (the first best alignment)
The alignment score of (alignment's score) and the second best comparison area (the second best alignment), two
Person's difference is bigger, shows that the specificity comparing is better, the value of MQ is higher.
In this embodiment it is believed that it is false sun that MQ value has higher probability less than the variant sites of default MQ threshold value
Property, it is deleted.
Preferably, in the present embodiment, default MQ threshold value value is 30.Empirical tests, when MQ value is 30, P [error]=
0.001, arrive current location with respect to comparing, the probability comparing another position is up to 0.1%.
In embodiments of the present invention, mode one is optional executive mode to mode five, that is, in this step, can adopt it
In a certain mode, certain several ways or all of mode.When carrying out being unsatisfactory for the change of reservation conditions using various ways
During the deletion of ectopic sites, the execution sequence between this various ways is not intended as limiting.Certainly, this various ways can also be parallel
Execution.
In addition, in this step 120, when there being various ways to be performed serially, follow-up step can be in preceding step
On the basis of execute.For example, if the number of the plurality of preliminary variant sites allelic of removal of executive mode one is more than in advance
If in the variant sites of threshold value, and mode three, default base will be spaced in the plurality of preliminary variant sites each other
The variant sites of number are deleted, and first carry out mode one, then executive mode three.Then in mode three, deletion can be mode
It is spaced the variant sites of default base number each other in variant sites after one process.
After step S120 carries out to preliminary variant sites deleting and filters, variant sites in the final result of acquisition are as treating
The site to be checked of cls gene, can be represented with vcf formatted file.
Step S130：By the Endocrine and metabolism system pair in described site to be checked and Endocrine and metabolism system gene storehouse
Multiple variant sites of the gene answered are compared, and described Endocrine and metabolism system gene storehouse includes Endocrine and metabolism system
Unite the mutating alkali yl of each variant sites of corresponding gene and each variant sites position.
In embodiments of the present invention, initially set up Endocrine and metabolism system gene storehouse, this Endocrine and metabolism system base
Because storehouse includes mutating alkali yl and each variant sites of each variant sites of the corresponding gene of Endocrine and metabolism system
Position.
This Endocrine and metabolism system gene storehouse step S130 relatively before set up.Specifically, this set up process can
To be, acquisition COSMIC gene database, the clivar data base of NCBI, other international and domestic each big authority's academic journals are miscellaneous
In the gene database that will, gene test company and relevant government department announce, the base related to Endocrine and metabolism system
Because of site information.Mainly obtain is the base mutation of each variant sites including the corresponding gene of Endocrine and metabolism system
Situation and the described gene locis information of each variant sites position.
Certainly, the Data Source obtaining gene locis information can also be other, is not intended as in the present embodiment limiting.
Further, the every of the corresponding gene of Endocrine and metabolism system can also be included in the gene locis information of acquisition
The impact to protein function for the every kind of mutating alkali yl of individual variant sites, that is, the base getting certain variant sites is by normal alkali
Base is mutated current mutating alkali yl, and the function of corresponding protein can be produced with which kind of impact.
Certainly, in the present embodiment, can also include in the gene locis information of acquisition：The corresponding base in each mutational site
Write a Chinese character in simplified form because of name, gene name full name, coordinate in human genome for this site, corresponding histoorgan type, gene are dashed forward
Become type, the normal gene base in this site, whether this kind of mutation in this site of clinical research causes a disease, original mutation finds
Crowd, the sex of original mutation carrier patient, the age of original mutation carrier patient, in the source of original mutation record
One or more.
Again by described gene locis information with a low credibility in preset standard and mistake gene locis information deletion,
The gene locis information obtaining forms described Endocrine and metabolism system gene storehouse.
In the present embodiment, include following at least one less than the gene locis information of preset standard：
1) the gene locis information getting from the very poor periodical of non-SCI periodical or reputation in the field of business, reputation is very in the industry for this
The periodical of difference can be that factor of influence is less than the periodical being unsatisfactory under the periodical of certain value or other judgment criteria requiring；2) record
In the original of this gene locis information, sample size used is less than certain value so that being not enough to draw the conclusion of science
's；3) in the original recording this gene loci, this gene loci is not the most important gene locis finding in document,
This most important gene loci can be in the result getting front 10% site.
The gene locis information of mistake includes following at least one：1) this gene locis information described in the data base obtaining
Original substantially do not have been reported that this site；2) record in the original of this gene loci, this gene loci
Result is statistically non-significant.
Certainly, the criterion of preset standard and gene locis information errors, is not intended as limiting in the present embodiment,
Can be determined according to practical situation.
Further, because the Endocrine gene studiess related to metabolic system are constantly carried out, with Endocrine and metabolism
The catastrophe of the related variant sites of gene of system can be in renewal, and in current Endocrine and metabolism system gene
Might not there is the variant sites catastrophe of the related gene of all Endocrine and metabolism systems, then, at this in storehouse
In bright embodiment, also include every preset time period, described Endocrine and metabolism system database being updated.
Specific renewal process can be, every preset time period, acquisition is up-to-date to be published in internal authority scholarly journal, such as
The research paper related to Endocrine and metabolism system delivered on Nature, Nature Genetics etc., the research that will obtain
The up-to-date gene locis information related to Endocrine and metabolism system in paper, delete wherein with a low credibility in preset standard
And the gene locis information of mistake, it is added in Endocrine and metabolism system database to realize updating.
After obtaining Endocrine and metabolism system gene storehouse, in site to be checked and Endocrine and metabolism system database
The multiple variant sites secreting gene corresponding with metabolic system are compared.
In the present embodiment, this comparison procedure can directly be carried out behind the acquisition site to be checked of step S120, also may be used
To be to be carried out by user's triggering.I.e. after the inquiry request receiving user's triggering, execute the comparison in this step S130.
Alternatively, it is also possible to be, one or more of site to be checked obtaining in user input step S120, step S130
The middle site to be checked by user input and the corresponding gene of Endocrine and metabolism system in Endocrine and metabolism system gene storehouse
Multiple variant sites be compared.
Alternatively, it is also possible to be, user directly obtains Endocrine and metabolism system from Endocrine and metabolism system gene storehouse
Related variant sites.Specifically, user by input-output unit input gene name, site genome the letter such as coordinate
Breath.After receiving the information of user input, the information according to user input is carried out in Endocrine and metabolism system gene storehouse
Search, by lookup result, the such as various information such as gene name, site coordinate, base mutation type are shown.If endocrine with
Find the information of user input in metabolic system gene bank, then prove the corresponding gene locis of this input information and endocrine with
Metabolic system is related, and there is base mutation.It should be understood that the position in the coordinate as site in genome for the site.
Step S140：When in described site to be checked exist identical with position in described Endocrine and metabolism system gene storehouse and
Mutating alkali yl identical variant sites, obtain the site mutation of the corresponding gene of Endocrine and metabolism system in described testing gene
Situation.
When comparative result is, exist in site to be checked and identical variant sites in Endocrine and metabolism system database,
Then can be determined according to this identical variant sites in Endocrine and metabolism system database have in this testing gene endocrine with
The site mutation of the corresponding gene of metabolic system, and catastrophe and this identical variation in Endocrine and metabolism system database
Site is consistent.Thus it is possible to there be the variant sites of which gene related to Endocrine and metabolism system in acquisition testing gene
And the concrete catastrophe of each variant sites related to Endocrine and metabolism system, which position this catastrophe included in
Which base mutation put is which base.
It should be understood that the position that identical variant sites refer to variant sites is identical and base mutation situation is identical, that is, exist
Same position there is identical mutating alkali yl it is believed that be in site to be checked with identical in Endocrine and metabolism system database
Variant sites.I.e. related to the Endocrine and metabolism system gene of the corresponding gene of Endocrine and metabolism system.
Then, related personnel can be according to the site of the corresponding gene of Endocrine and metabolism system in the testing gene obtaining
Possible ill feelings under catastrophe, and other information, such as every kind of catastrophe of Endocrine and metabolism system related genes
Condition, determines the Endocrine and metabolism system disease condition of the corresponding object of this testing gene.
Further, in the present embodiment, can also be corresponding according to Endocrine and metabolism system in described testing gene
The site mutation situation of gene, and in Endocrine and metabolism system database the corresponding gene of Endocrine and metabolism system every
The impact to protein function for the every kind of mutating alkali yl of individual variant sites, determines the prominent of each variant sites in described testing gene
Become the impact to protein function, may thereby determine which and the endocrine of the corresponding object of testing gene (as corresponding people)
The protein function related to metabolic system is affected, and receives which impact.So that skilled addressee can basis
The impact of protein function, in conjunction with other information, such as protein function changes interactively with organ concrete function etc., judges
The Endocrine and metabolism systemic disease illness probability and may be suffered from which Endocrine and metabolism of the corresponding object of this testing gene
Disease.
Certainly, include the catastrophe Endocrine of every kind of variant sites in embodiments of the present invention or directly
With the pathogenic situation of metabolic system disease, the impact such as to thyroiditiss potentially include pathogenic, may cause a disease, risk factor, no
Determine, have the result of study of conflict, optimum, the wherein pathogenic situation of certain certain mutating alkali yl of position is risk factor, shows
The probability that the object that there is this kind of mutating alkali yl this position suffers from thyroiditiss is very high, should be noted to prevent.
Second embodiment
Present embodiments provide a kind of acquisition device 200 of the corresponding gene mutation site of Endocrine and metabolism system, please
Referring to Fig. 4, this device 200 includes：
Comparing module 210, for the multiple short sequence of testing gene and reference gene group are carried out comparing, acquisition is treated
The preliminary variant sites information of cls gene, described preliminary variant sites information includes the mutating alkali yl of multiple preliminary variant sites
And the positional information of each preliminary variant sites.
Filtering module 220, for according to described preliminary variant sites information, pre- by being unsatisfactory in multiple preliminary variant sites
If the variant sites of reserve are deleted, the variant sites in the described testing gene obtaining after deleting are as site to be checked.
Comparison module 230, for by the endocrine in described site to be checked and Endocrine and metabolism system gene storehouse and generation
Multiple variant sites of the corresponding gene of system of thanking are compared, and described Endocrine and metabolism system gene storehouse includes endocrine
The mutating alkali yl of each variant sites of gene corresponding with metabolic system and each variant sites position.
Mutation acquisition module 240, when presence and described Endocrine and metabolism system gene storehouse middle position in described site to be checked
Put identical and mutating alkali yl identical variant sites, for obtaining the corresponding base of Endocrine and metabolism system in described testing gene
The site mutation situation of cause.
Further, also include the every of the corresponding gene of Endocrine and metabolism system in Endocrine and metabolism system gene storehouse
The impact to protein function for the every kind of mutating alkali yl of individual variant sites, the mutation acquisition module 240 in the present embodiment is additionally operable to
According to the site mutation situation of the corresponding gene of Endocrine and metabolism system in described testing gene, determine in described testing gene
The impact of the mutations on protein function of each variant sites.
Further, in the present embodiment, as shown in figure 4, also including gene bank to set up module 250, it is used for setting up endocrine
With metabolic system gene bank, described gene bank sets up module 250 and includes：Data capture unit 251, for obtaining COSMIC gene
The gene locis information related to Endocrine and metabolism system, described gene locis in data base, the clivar data base of NCBI
Information includes the mutating alkali yl of each variant sites and each variant sites of the corresponding gene of Endocrine and metabolism system
Position.Data deletion unit 252, for by described gene locis information with a low credibility in preset standard and mistake
Gene locis information deletion, the gene locis information of acquisition forms described Endocrine and metabolism system gene storehouse.
Further, as shown in figure 5, this gene bank sets up module 250 also includes updating block 253, for every default
Time period is updated to described Endocrine and metabolism system gene storehouse.
Further, as shown in fig. 6, in the present embodiment, filtering module 220 includes one or more of：First deletes
Except unit 221, for removing in the plurality of preliminary variant sites, the number of allele is more than the change dystopy of predetermined threshold value
Point.Second deletion unit 222, for deleting in the plurality of preliminary variant sites, positioned at the upstream span of each insertion and deletion
Or the base number that all variant sites in span downstream, described upstream span and span downstream include is predetermined number.
3rd deletion unit 223, for by the plurality of preliminary variant sites, being spaced the change dystopy of default base number each other
Point deletion.4th deletion unit 224, for by the plurality of preliminary variant sites, corresponding GQ value is less than default GQ threshold value
Variant sites delete.5th deletion unit 225, for by the plurality of preliminary variant sites, corresponding MQ value is less than pre-
If the variant sites of MQ threshold value are deleted.
In this example, refer to Fig. 7, comparing module 210 can include：Comparing unit 211, for by described base to be measured
The multiple short sequence of cause and reference gene group are compared first, obtain the comparison result of SAM form；Duplicate removal unit 212, is used for
Duplicate removal is carried out to described comparison result, makes the short sequence number that a position of reference gene group is arrived in contrast be less than or equal to 1；Weight
Comparing unit 213, for carrying out local anharmonic ratio pair to the comparing result after duplicate removal；Computing unit 214, is used for recalculating locally
Anharmonic ratio to after comparison result in base mass fraction；Just sentence unit 215, for according to described base mass fraction, to this
Ground anharmonic ratio to after comparing result carry out SNP and indel analysis, obtain preliminary variant sites information.
In sum, the acquisition side of the corresponding gene mutation site of Endocrine and metabolism system provided in an embodiment of the present invention
Method and device are behind the site to be measured obtaining testing gene, corresponding with Endocrine and metabolism system gene storehouse by site to be measured
Multiple variant sites of gene be compared, it is hereby achieved that in the variant sites in this testing gene with endocrine and generation
Thank to the catastrophe of the related multiple variant sites of system, for the possible illness feelings of auxiliary Endocrine and metabolism systemic disease
The judgement of condition.
It should be noted that each embodiment in this specification is all described by the way of going forward one by one, each embodiment weight
Point explanation is all difference with other embodiment, between each embodiment identical similar partly mutually referring to.
For device class embodiment, due to itself and embodiment of the method basic simlarity, so description is fairly simple, related part ginseng
See that the part of embodiment of the method illustrates.
It should be understood that disclosed apparatus and method are it is also possible to pass through in several embodiments provided herein
Other modes are realized.Device embodiment described above is only schematically, for example, the flow chart in accompanying drawing and block diagram
Show the device of multiple embodiments according to the application, the architectural framework in the cards of method and computer program product,
Function and operation.At this point, each square frame in flow chart or block diagram can represent the one of a module, program segment or code
Part, a part for described module, program segment or code comprises holding of one or more logic function for realizing regulation
Row instruction.It should also be noted that at some as in the implementation replaced, the function of being marked in square frame can also be to be different from
The order being marked in accompanying drawing occurs.For example, two continuous square frames can essentially execute substantially in parallel, and they are sometimes
Can execute in the opposite order, this is depending on involved function.It is also noted that it is every in block diagram and/or flow chart
The combination of the square frame in individual square frame and block diagram and/or flow chart, can be with the special base of the function of execution regulation or action
System in hardware to be realized, or can be realized with combining of computer instruction with specialized hardware.
In addition, each functional module in each embodiment of the application can integrate one independent portion of formation
Divide or modules individualism is it is also possible to two or more modules are integrated to form an independent part.
If described function realized using in the form of software function module and as independent production marketing or use when, permissible
It is stored in a computer read/write memory medium.Based on such understanding, the technical scheme of the application is substantially in other words
Partly being embodied in the form of software product of part that prior art is contributed or this technical scheme, this meter
Calculation machine software product is stored in a storage medium, including some instructions with so that a computer equipment (can be individual
People's computer, server 100, or network equipment etc.) execution each embodiment methods described of the application all or part step
Suddenly.And aforesaid storage medium includes：USB flash disk, portable hard drive, read only memory (ROM, Read-Only Memory), deposit at random
Access to memory (RAM, Random Access Memory), magnetic disc or CD etc. are various can be with the medium of store program codes.
It should be noted that herein, such as first and second, another or the like relational terms be used merely to an entity or
Person's operation is made a distinction with another entity or operation, and not necessarily requires or imply that between these entities or operation, presence is appointed
What this actual relation or order.And, term " inclusion ", "comprising" or its any other variant are intended to non-row
The comprising of his property, so that including a series of process of key elements, method, article or equipment not only include those key elements, and
And also include other key elements of being not expressly set out, or also include intrinsic for this process, method, article or equipment institute
Key element.In the absence of more restrictions, the key element being limited by sentence "including a ..." is it is not excluded that including institute
Also there is other identical element in process, method, article or the equipment of stating key element.
The foregoing is only the preferred embodiment of the application, be not limited to the application, for the skill of this area
For art personnel, the application can have various modifications and variations.All within spirit herein and principle, made any repair
Change, equivalent, improvement etc., should be included within the protection domain of the application.It should be noted that：Similar label and letter exist
Representing similar terms in figure below, therefore, once being defined in a certain Xiang Yi accompanying drawing, being then not required in subsequent accompanying drawing
It is defined further and to be explained.
The above, the only specific embodiment of the application, but the protection domain of the application is not limited thereto, and any
Those familiar with the art, in the technical scope that the application discloses, can readily occur in change or replacement, all should contain
Cover within the protection domain of the application.Therefore, the protection domain of the application should described be defined by scope of the claims.
Claims (10)
1. a kind of acquisition methods of the corresponding gene mutation site of Endocrine and metabolism system are it is characterised in that methods described bag
Include：
The multiple short sequence of testing gene and reference gene group are carried out comparing, obtains the preliminary variant sites of testing gene
Information, described preliminary variant sites information includes mutating alkali yl and each preliminary variant sites of multiple preliminary variant sites
Positional information；
According to described preliminary variant sites information, the variant sites of default reserve will be unsatisfactory in multiple preliminary variant sites
Delete, the variant sites in the described testing gene obtaining after deleting are as site to be checked；
Described site to be checked and the corresponding gene of Endocrine and metabolism system in Endocrine and metabolism system gene storehouse is many
Individual variant sites are compared, and described Endocrine and metabolism system gene storehouse includes the corresponding gene of Endocrine and metabolism system
The mutating alkali yl of each variant sites and each variant sites position；
When existing in described site to be checked, identical with position in described Endocrine and metabolism system gene storehouse and mutating alkali yl is identical
Variant sites, obtain described testing gene in the corresponding gene of Endocrine and metabolism system site mutation situation.
2. method according to claim 1 is it is characterised in that also include interior in described Endocrine and metabolism system gene storehouse
The impact to protein function for the every kind of mutating alkali yl of each variant sites of secretion gene corresponding with metabolic system,
Methods described also includes：
According to the site mutation situation of the corresponding gene of Endocrine and metabolism system in described testing gene, determine described base to be measured
The impact of the mutations on protein function of each variant sites in cause.
3. method according to claim 1 is it is characterised in that described by described site to be checked and Endocrine and metabolism system
Before multiple variant sites of the corresponding gene of Endocrine and metabolism system in system gene bank are compared, also include in foundation
Secretion and metabolic system gene bank, described Endocrine and metabolism system gene storehouse of setting up includes：
The gene locis related to Endocrine and metabolism system in acquisition COSMIC gene database, the clivar data base of NCBI
Information, described gene locis information includes the mutating alkali yl of each variant sites of the corresponding gene of Endocrine and metabolism system
And each variant sites position；
By in described gene locis information with a low credibility in preset standard and mistake gene locis information deletion, acquisition
Gene locis information forms described Endocrine and metabolism system gene storehouse.
4. method according to claim 3 is it is characterised in that also include：
Every preset time period, described Endocrine and metabolism system gene storehouse is updated.
5. method according to claim 1 is it is characterised in that described will be unsatisfactory for default guarantor in multiple preliminary variant sites
The variant sites deletion staying condition includes one or more of：
Remove in the plurality of preliminary variant sites, the number of allele is more than the variant sites of predetermined threshold value；
Delete in the plurality of preliminary variant sites, all in the upstream span or span downstream of each insertion and deletion
The base number that variant sites, described upstream span and span downstream include is predetermined number；
By in the plurality of preliminary variant sites, the variant sites being spaced default base number each other are deleted；
By in the plurality of preliminary variant sites, the variant sites that corresponding GQ value is less than default GQ threshold value are deleted；
By in the plurality of preliminary variant sites, the variant sites that corresponding MQ value is less than default MQ threshold value are deleted.
6. method according to claim 1 is it is characterised in that the described multiple short sequence by testing gene and reference gene
Group carries out comparing, and the preliminary variant sites information obtaining testing gene includes：
The multiple short sequence of described testing gene and reference gene group are compared first, is obtained the comparison result of SAM form；
Duplicate removal is carried out to described comparison result, so that the short sequence number of contrast a to position of reference gene group is less than or equal to
1；
Local anharmonic ratio pair is carried out to the comparing result after duplicate removal；
Recalculate local anharmonic ratio to after comparison result in base mass fraction；
According to described base mass fraction, to local anharmonic ratio to after comparing result carry out SNP and indel analysis, obtain preliminary
Variant sites information.
7. method according to claim 1 is it is characterised in that described variant sites are SNP.
8. a kind of acquisition device of the corresponding gene mutation site of Endocrine and metabolism system is it is characterised in that described device bag
Include：
Comparing module, for the multiple short sequence of testing gene and reference gene group are carried out comparing, obtains testing gene
Preliminary variant sites information, described preliminary variant sites information includes the mutating alkali yl of multiple preliminary variant sites and every
The positional information of individual preliminary variant sites；
Filtering module, for according to described preliminary variant sites information, being unsatisfactory for default reservation in multiple preliminary variant sites
The variant sites of condition are deleted, and the variant sites in the described testing gene obtaining after deleting are as site to be checked；
Comparison module, for by the Endocrine and metabolism system pair in described site to be checked and Endocrine and metabolism system gene storehouse
Multiple variant sites of the gene answered are compared, and described Endocrine and metabolism system gene storehouse includes Endocrine and metabolism system
Unite the mutating alkali yl of each variant sites of corresponding gene and each variant sites position；
Mutation acquisition module, when in described site to be checked exist identical with position in described Endocrine and metabolism system gene storehouse and
Mutating alkali yl identical variant sites, for obtaining the site of the corresponding gene of Endocrine and metabolism system in described testing gene
Catastrophe.
9. device according to claim 8 sets up module it is characterised in that also including gene bank, is used for setting up endocrine
With metabolic system gene bank, described gene bank sets up module and includes：
Data capture unit, for obtain in the clivar data base of COSMIC gene database, NCBI with Endocrine and metabolism
The related gene locis information of system, described gene locis information includes each of the corresponding gene of Endocrine and metabolism system
The mutating alkali yl of variant sites and each variant sites position；
Data deletion unit, for by described gene locis information with a low credibility in preset standard and mistake gene position
Point information deletion, the gene locis information of acquisition forms described Endocrine and metabolism system gene storehouse.
10. device according to claim 8 is it is characterised in that described filtering module includes one or more of：
First deletion unit, for removing in the plurality of preliminary variant sites, the number of allele is more than predetermined threshold value
Variant sites；
Second deletion unit, for deleting in the plurality of preliminary variant sites, positioned at each insertion and deletion upstream span or
The base number that all variant sites in person's span downstream, described upstream span and span downstream include is predetermined number；
3rd deletion unit, for by the plurality of preliminary variant sites, being spaced the variation of default base number each other
Site is deleted；
4th deletion unit, for by the plurality of preliminary variant sites, corresponding GQ value is less than the variation of default GQ threshold value
Site is deleted；
5th deletion unit, for by the plurality of preliminary variant sites, corresponding MQ value is less than the variation of default MQ threshold value
Site is deleted.
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