CN106250719A - The genetic explanations integrity degree detection method of biological gene many sites character and system - Google Patents
The genetic explanations integrity degree detection method of biological gene many sites character and system Download PDFInfo
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Abstract
The invention discloses genetic explanations integrity degree detection method and the system of a kind of biological gene many sites character, detection method step includes each related locus and the genotype thereof determining objective trait, calculates the odds ratio OR of each genotype under each related locus；Logarithm is asked to obtain logarithm b with natural logrithm e the end of for the odds ratio OR of each genotype under each related locus；The logarithm b obtained sorted according to absolute value respectively and takes maximum, obtaining gene odds ratio maximum | b | max of each related locus；Gene odds ratio maximum | b | max of all related locus is sued for peace and obtains gene odds ratio maximum summation | b | sum；By gene odds ratio maximum | b | max divided by gene odds ratio maximum summation | b | sum, obtain genetic explanations integrity degree ratio GIIR；System includes odds ratio computing unit, counting unit, maximum is asked for unit, sum unit and genetic explanations integrity degree computing unit.The present invention have can accurate and effective detection biological character understand integrity, advantage that adaptability is good.
Description
Technical field
The present invention relates to biological gene detection technique, the genetic explanations being specifically related to a kind of biological gene many sites character is complete
Whole degree detection method and system.
Background technology
Along with the development of technique of gene detection, detection price exponentially declines, and gene data also gets more and more, and speed is even
Exceed Moore's Law.Mononucleotide polymorphism site (SNP) in genes of individuals data, usually with individual characters (disease-susceptible humans
Property, drug susceptibility, personal feature, other Physiology and biochemistry abilities) it is associated.The most existing a large amount of scientific researches demonstrate " position
Point and the dependency of character ", it was recently reported that substantial amounts of SNP genetic locus.
The dependency of individual gene site and character can pass through the calculating of odds ratio (OR, odds ratio) and obtain, and
The size of odds ratio has also reacted the impact on character of the different typings in this site.The dependency of Single locus and character is relevant
Having a lot of report in scientific documents, these data can obtain by the way of consulting literatures and public database.Various trait
Different with the relatedness degree of strength of gene, some character (such as emotion control ability) may be not strong with gene relationship, and certain
A little genetic diseasess (such as sickle anemia) have only to a gene loci and undergo mutation.More often, same something lost
Transmissibility shape or disease are affected (being called for short " many sites character ") by multiple sites.For many sites character, there is presently no one
The index easily quantified accurately goes the permutation and combination evaluating different loci to be that the hereditary information solution how affecting this character runs through
Whole property.
Summary of the invention
The technical problem to be solved in the present invention: for the problems referred to above of prior art, it is provided that one can accurate and effective inspection
Survey biological character understand integrity, the genetic explanations integrity degree detection method of biological gene many sites character that adaptability is good and
System.
In order to solve above-mentioned technical problem, the technical solution used in the present invention is:
A kind of genetic explanations integrity degree detection method of biological gene many sites character, step includes:
1) determine each related locus and the genotype thereof of objective trait, calculate each genotype under each related locus
Odds ratio OR；
2) logarithm is asked to obtain logarithm with natural logrithm e the end of for the odds ratio OR of each genotype under each related locus
b；
3) the logarithm b obtained sorted according to absolute value respectively and take maximum, obtaining the gene of each related locus
Odds ratio maximum | b | max；
4) gene odds ratio maximum | b | max summation of all related locus is obtained gene odds ratio maximum summation |
b|sum；
5) according to the value of gene odds ratio maximum | b | max, all related locus are ranked up；Obtain from sequence successively
Sequence list in take out first related locus as current site, by gene odds ratio maximum | b | max in current site,
Gene odds ratio maximum | b | max summation in the site that all sequence numbers are less than current site obtains gene odds ratio maximum office
Portion summation | b | sum1, by gene odds ratio maximum local summation | b | sum1 divided by gene odds ratio maximum summation | b |
Sum, obtains the genetic explanations integrity degree ratio GIIR that current site is corresponding.
A kind of genetic explanations integrity degree detecting system of biological gene many sites character, including:
Odds ratio computing unit, for determining each related locus and the genotype thereof of objective trait, calculates each phase
Close the odds ratio OR of each genotype under site；
To counting unit, for the odds ratio OR of each genotype under each related locus was asked with natural logrithm e the end of for
Logarithm obtains logarithm b；
Maximum asks for unit, for being sorted according to absolute value respectively by the logarithm b obtained and taking maximum, obtains each
Gene odds ratio maximum | b | max of individual related locus；
Sum unit, obtains gene odds ratio for being sued for peace by gene odds ratio maximum | b | max of all related locus
Maximum summation | b | sum；
Genetic explanations integrity degree computing unit, for the value according to gene odds ratio maximum | b | max to all relevant bits
Point is ranked up；From the sequence list that sequence obtains, first related locus of taking-up is as current site successively, by current site
Gene odds ratio maximum | b | max, gene odds ratio maximum | b | max in site that all sequence numbers are less than current site ask
With obtain gene odds ratio maximum local summation | b | sum1, by gene odds ratio maximum local summation | b | sum1 divided by base
Because of odds ratio maximum summation | b | sum, obtain the genetic explanations integrity degree ratio GIIR that current site is corresponding.
The genetic explanations integrity degree detection method of biological gene many sites of the present invention character has an advantage that
1, the present invention is by calculating the odds ratio OR of each genotype under each related locus, by each related locus
The odds ratio OR of each genotype lower asks logarithm to obtain logarithm b with natural logrithm e the end of for, by the logarithm b that obtains respectively according to absolutely
Value sorted and takes maximum, obtaining gene odds ratio maximum | b | max of each related locus, by all related locus
Gene odds ratio maximum | b | max summation obtain gene odds ratio maximum summation | b | sum, maximum according to gene odds ratio
All related locus are ranked up by the value of value | b | max；First related locus is taken out successively from the sequence list that sequence obtains
As current site, by gene odds ratio maximum | b | max in current site, site that all sequence numbers are less than current site
Gene odds ratio maximum | b | max summation obtains gene odds ratio maximum local summation | b | sum1, by gene odds ratio
Big value local summation | b | sum1, divided by gene odds ratio maximum summation | b | sum, obtains the genetic explanations that current site is corresponding
Integrity degree ratio GIIR, can be reflected by genetic explanations integrity degree ratio GIIR and be currently known the related locus of odds ratio
The inside, choosing which group related locus can reaction site and the relation of character to greatest extent, it is possible to accurate and effective detection is raw
The deciphering integrity of physical property shape, specifies the gene loci of character to select have directive significance for certain.
2, the genetic explanations integrity degree that the present invention obtains based on the odds ratio OR of each genotype under each related locus
Ratio GIIR is the parameter of a mobilism, is the propelling real-time change according to correlational study in the world, because when an individual character
Under any one related locus of shape, the odds ratio OR of each genotype changes or have updated, then genetic explanations integrity degree ratio
GIIR also can change, and this change can preferably be reacted under As-Is, has the advantage that adaptability is good.
The genetic explanations integrity degree detecting system of biological gene many sites of the present invention character is biological gene multidigit of the present invention
The system of the genetic explanations integrity degree detection method of some character correspondence completely, the most also has above-mentioned advantage, at this no longer
Repeat.
Accompanying drawing explanation
Fig. 1 is the basic procedure schematic diagram of embodiment of the present invention method.
Detailed description of the invention
As it is shown in figure 1, the step bag of the genetic explanations integrity degree detection method of the present embodiment biological gene many sites character
Include:
1) determine each related locus and the genotype thereof of objective trait, calculate each genotype under each related locus
Odds ratio OR；
2) logarithm is asked to obtain logarithm with natural logrithm e the end of for the odds ratio OR of each genotype under each related locus
B, i.e. b=ln (OR)；It is known that the branch that odds ratio OR is in real number presents the trend of a kind of logistic regression, so contrast
The value value than OR seeks logarithm with natural logrithm e the end of for, such that it is able to react the impact on character of this site more intuitively；
3) the logarithm b obtained sorted according to absolute value respectively and take maximum, obtaining the gene of each related locus
Odds ratio maximum | b | max；In view of reduced value than OR ask with natural logrithm e the end of for logarithm obtain logarithm b be one from negative nothing
Poor to the most infinite distribution, its deviation zero point is the most remote, then the effect in this site is the most notable；So, absolute value | b | energy of logarithm b
Enough reflect the impact of a certain related locus.And in three genotype of same related locus, absolute value | b | maximum of logarithm b
Impact is the active effects that this related locus may bring, therefore by the logarithm b of all for related locus genotype according to definitely
Value sorts and takes maximum and obtains maximum | b | max；
4) gene odds ratio maximum | b | max summation of all related locus is obtained gene odds ratio maximum summation |
b|sum；On biological significance, the relation of multiple odds ratio OR and character be the product taking odds ratio OR to represent impact, by
It is the impact having reacted each odds ratio OR in absolute value | b | of logarithm b, so, by the maximum of all for site genotype |
B | max summation obtains maximum summation | b | sum of current character；
5) according to the value of gene odds ratio maximum | b | max, all related locus are ranked up；Obtain from sequence successively
Sequence list in take out first related locus as current site, by gene odds ratio maximum | b | max in current site,
Gene odds ratio maximum | b | max summation in the site that all sequence numbers are less than current site obtains gene odds ratio maximum office
Portion summation | b | sum1, by gene odds ratio maximum local summation | b | sum1 divided by gene odds ratio maximum summation | b |
Sum, obtains the genetic explanations integrity degree ratio GIIR that current site is corresponding.
Assume that one has n gene odds ratio maximum | b | max, then with gene odds ratio maximum summation | b | sum be
Denominator, molecule respectively with gene first data (maximum) of odds ratio maximum | b | max, the first two data (maximum and time greatly,
Sum, front 3 data sums below), the most down, until front n-1 data sum, all n data sums
As gene odds ratio maximum local summation | b | sum1, gene odds ratio maximum summation | b | sum is asked business, this business
It is genetic explanations integrity degree ratio GIIR.For the character in many sites, all sites can not be detected if subject to conditions
Time, how certain character is explained by some genetic locus of choosing of science, is the one of puzzlement susceptibility loci detection
Individual difficult point.And introduce genetic explanations integrity degree ratio GIIR and the explanation degree in a certain group of site of quantitative interpretation can account for whole site and solve
The ratio of degree of releasing.As a example by as shown by the data in table 1, for a character gastric cancer, there are eight site quilts in the site being currently known
Report relevant with gastric cancer, absolute value | the b | of the logarithm b that each site is corresponding according to from big to small sequence after from 1.94 to 0.38,
The genetic explanations integrity degree ratio GIIR of the last string of form corresponds respectively to first gene odds ratio maximum | b | max and arrives
Gene odds ratio maximum | b | max sum of these row.Such as, the genetic explanations integrity degree ratio GIIR of serial number 1 is this row
Corresponding gene odds ratio maximum local summation | b | sum1 (1.94) is divided by gene odds ratio maximum summation | b | sum
(6.31), genetic explanations integrity degree ratio GIIR value is 0.307, i.e. 30.7%；And the genetic explanations integrity degree ratio of sequence number 5
GIIR is that gene odds ratio maximum local summation | b | sum1 (1.94+1.09+0.76+0.74+0.52=5.05) is divided by gene
Odds ratio maximum summation | b | sum (i.e. 6.31) genetic explanations integrity degree ratio GIIR value afterwards is 0.801, i.e. 80.1%. heredity
The meaning of explanation integrity degree ratio GIIR is, for a certain group of related locus, to analyze if it is desired to take part related locus,
This part related locus then taken is the ratio of shared explanation degree in all related locus.
Table 1: the detection tables of data of the present embodiment.
The genetic explanations integrity degree detection method of the present embodiment biological gene many sites character be in the specific implementation by terms of
The mode of calculation machine software realizes, the genetic explanations integrity degree detecting system bag of biological gene many sites character of its correspondence
Include:
Odds ratio computing unit, for determining each related locus and the genotype thereof of objective trait, calculates each phase
Close the odds ratio OR of each genotype under site；
To counting unit, for the odds ratio OR of each genotype under each related locus was asked with natural logrithm e the end of for
Logarithm obtains logarithm b；
Maximum asks for unit, for being sorted according to absolute value respectively by the logarithm b obtained and taking maximum, obtains each
Gene odds ratio maximum | b | max of individual related locus；
Sum unit, obtains gene odds ratio for being sued for peace by gene odds ratio maximum | b | max of all related locus
Maximum summation | b | sum；
Genetic explanations integrity degree computing unit, for the value according to gene odds ratio maximum | b | max to all relevant bits
Point is ranked up；From the sequence list that sequence obtains, first related locus of taking-up is as current site successively, by current site
Gene odds ratio maximum | b | max, gene odds ratio maximum | b | max in site that all sequence numbers are less than current site ask
With obtain gene odds ratio maximum local summation | b | sum1, by gene odds ratio maximum local summation | b | sum1 divided by base
Because of odds ratio maximum summation | b | sum, obtain the genetic explanations integrity degree ratio GIIR that current site is corresponding.
The above is only the preferred embodiment of the present invention, and protection scope of the present invention is not limited merely to above-mentioned enforcement
Example, all technical schemes belonged under thinking of the present invention belong to protection scope of the present invention.It should be pointed out that, for the art
Those of ordinary skill for, some improvements and modifications without departing from the principles of the present invention, these improvements and modifications are also
Should be regarded as protection scope of the present invention.
Claims (2)
1. the genetic explanations integrity degree detection method of biological gene many sites character, it is characterised in that step includes:
1) determine each related locus and the genotype thereof of objective trait, calculate the ratio of each genotype under each related locus
Value compares OR；
2) logarithm is asked to obtain logarithm b with natural logrithm e the end of for the odds ratio OR of each genotype under each related locus；
3) the logarithm b obtained sorted according to absolute value respectively and take maximum, obtaining the gene ratio of each related locus
Than maximum | b | max；
4) gene odds ratio maximum | b | max summation of all related locus is obtained gene odds ratio maximum summation | b |
sum；
5) according to the value of gene odds ratio maximum | b | max, all related locus are ranked up；Obtain from sorting successively is suitable
In sequence table, first related locus of taking-up is as current site, by gene odds ratio maximum | b | max in current site, owns
It is total that gene odds ratio maximum | b | max summation in the site that sequence number is less than current site obtains gene odds ratio maximum local
With | b | sum1, by gene odds ratio maximum local summation | b | sum1 divided by gene odds ratio maximum summation | b | sum, obtain
The genetic explanations integrity degree ratio GIIR corresponding to current site.
2. the genetic explanations integrity degree detecting system of biological gene many sites character, it is characterised in that including:
Odds ratio computing unit, for determining each related locus and the genotype thereof of objective trait, calculates each relevant bits
The odds ratio OR of point each genotype lower；
To counting unit, for the odds ratio OR of each genotype under each related locus is sought logarithm with natural logrithm e the end of for
Obtain logarithm b；
Maximum asks for unit, for being sorted according to absolute value respectively by the logarithm b obtained and taking maximum, obtains each phase
Close gene odds ratio maximum | b | max in site；
Sum unit, obtains gene odds ratio for being sued for peace by gene odds ratio maximum | b | max of all related locus maximum
Value summation | b | sum；
Genetic explanations integrity degree computing unit, for clicking on all relevant bits according to the value of gene odds ratio maximum | b | max
Row sequence；From the sequence list that sequence obtains, first related locus of taking-up is as current site successively, by the base in current site
Because gene odds ratio maximum | b | max of odds ratio maximum | b | max, site that all sequence numbers are less than current site sues for peace
To gene odds ratio maximum local summation | b | sum1, by gene odds ratio maximum local summation | b | sum1 divided by gene ratio
Value ratio maximum summation | b | sum, obtains the genetic explanations integrity degree ratio GIIR that current site is corresponding.
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Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101302563A (en) * | 2008-07-08 | 2008-11-12 | 上海中优医药高科技有限公司 | Comprehensive evaluation method of polygenic diseases genetic risk |
| CN103146821A (en) * | 2013-02-25 | 2013-06-12 | 安徽农业大学 | Method for evaluating inheritance effect of SNP (Single Nucleotide Polymorphism) sites to traits and application thereof |
| US20140359422A1 (en) * | 2011-11-07 | 2014-12-04 | Ingenuity Systems, Inc. | Methods and Systems for Identification of Causal Genomic Variants |
| CN105069322A (en) * | 2015-07-24 | 2015-11-18 | 上海丰核信息科技有限公司 | Disease susceptibility risk prediction method and device |
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- 2016-08-01 CN CN201610623216.2A patent/CN106250719B/en active Active
Patent Citations (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101302563A (en) * | 2008-07-08 | 2008-11-12 | 上海中优医药高科技有限公司 | Comprehensive evaluation method of polygenic diseases genetic risk |
| US20140359422A1 (en) * | 2011-11-07 | 2014-12-04 | Ingenuity Systems, Inc. | Methods and Systems for Identification of Causal Genomic Variants |
| CN103146821A (en) * | 2013-02-25 | 2013-06-12 | 安徽农业大学 | Method for evaluating inheritance effect of SNP (Single Nucleotide Polymorphism) sites to traits and application thereof |
| CN105069322A (en) * | 2015-07-24 | 2015-11-18 | 上海丰核信息科技有限公司 | Disease susceptibility risk prediction method and device |
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Inventor after: Wei Wenjuan Inventor after: Zhou Qinghua Inventor after: Song Zhuo Inventor after: Chen Xiang Inventor after: Chuan Jun Inventor after: Meng Fei Inventor before: Wei Wenjuan Inventor before: Zhou Qinghua Inventor before: Song Zhuo Inventor before: Chen Xiang |