CN106446606A - Polyploid individual haplotype reconstructing method based on enumeration strategy - Google Patents
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Abstract
The invention discloses a polyploid individual haplotype reconstructing method based on an enumeration strategy. The method reconstructs polyploid individual haplotypes one by one according to columns. When a given locus is constructed, according to a genotype of the given locus, the method enumerates all possible values of the haplotype on the given locus, then calculates index values of SNP fragments aiming at each of the enumerated values according to an assigned index value calculation function and selects the enumerated value corresponding to the maximum index value as the haplotype value of the given locus. The method, with less time and money, has the advantage of quickly reconstructing the polyploid individual haplotypes with higher reconstruction rate, and the performance of the method is less affected by parameters such as the number of fragments, sequencing error rate and haplotype length. Meanwhile, under a framework of the enumeration method, the index value can be calculated with various distance functions with a more flexible algorithm and a good expansibility.
Description
Technical field
The invention belongs to field of bioinformatics is and in particular to a kind of rebuild polyploid individual haplotype based on enumeration strategy
Method.
Technical background
The fast development of gene sequencing technology creates substantial amounts of gene data, and this makes polyploid bion is carried out
Functional genome research work is possibly realized.Polyploid biology usually have growth vigorous, survival rate is high, premunition is strong, yield
The advantages of height, adaptability and strong stress resistance, the research of polyploid biological genome is to the hereditary feature meaning exploring polyploid species
Justice is great, has important theory value and practical value to the cultivation level improving polyploid species.SNP
(Single Nucleotide Polymorphism, SNP) is modal a kind of genetic polymorphism in genome, and it is by contaminating
Change on single nucleotide acid base yardstick for the colour solid genome and the DNA sequence polymorphism that causes.The research of SNP is many to exploring
The aspect such as the biological hereditary capacity of times body and phenotypic difference plays an important role.Due to linkage disequilibrium phenomenon and shortage
Genetic recombinational events, on chromosome, some region of one group of SNP site tends to coinheritance, and this group is located on item chromosome
Associated SNP positions sequence is haplotype (Haplotype), and on chromosome, coexpress SNP multiplexed sequence out forms
Genotype (Genotype).Research shows, haplotype data as the carrier carrying a large amount of genetic disease information, than single
The research of SNP site and application deeper into extensive, therefore how fast, economical ground obtains individual haplotype and becomes biological information
Learn the hot issue of concern.Due to, under current experimental technique level, directly measuring one by biological experiment means
The time and money high cost of individual haplotype, to determine the haplotype of individuality hence with computing technique, that is, individual single
Build Problems of Reconstruction, has extremely important realistic meaning.Individual haplotype Problems of Reconstruction refers to, gives from homologue
The DNA fragmentation data being measured by DNA sequencing method, according to the SNP site value in fragment, assembles the list on homologue
Build.
Individual haplotype Problems of Reconstruction was proposed first in calendar year 2001, deep grind had been carried out for diplont
Study carefully, and achieve good achievement in research, the research for polyploid haplotype Problems of Reconstruction is less.Li etc. deletes to minimum fragment
Except (Minimum Fragment Removal, MFR) model is studied, for void-free SNP matrix, proposed complicated the time
Spend for O (m2n+mk+1) multinomial algorithm, wherein m represents DNA fragmentation number, and n represents SNP site number, for hole in fragment
Maximum number is less than the SNP matrix of t, and proposition time complexity is O (22tm2n+2(k+1)tm(k+1)) dynamic programming algorithm, should
Algorithm can only apply to the less situation of m value (segment number), and when m value is very big, operational efficiency is very low, is not suitable for actual answering
With in；Wang and Qian et al. is to minimum error correction (Minimum Error Correction, MEC) and band genotype data
Minimum error correction (MEC with Genotype Information, MEC/GI) model studied, propose solved
The genetic algorithm of dliploid problem and particle cluster algorithm are extended can be used to solve K- individuality haplotype Problems of Reconstruction, but this
The performance planting extended method is seriously restricted by segment number, and reconstruction rate is not high；Wu Li etc. proposes to solve three times of MEC model
Body individuality haplotype algorithm for reconstructing GTIHR, the method has constructed less solution by the chromosome coding mode quoting novelty
Space, but the increase with error rate and haplotype length, reconstruction rate is not also high, and the increase with haplotype length, its effect
Rate is not high；Emily is equal to 2014 and proposes bayesian algorithm HapTree, and this algorithm calculates complexity and autgmentability is bad, in reality
With in be subject to a definite limitation；2015, Sepideh etc. propose HapColor algorithm, this algorithm with the increase of error rate,
MEC value is in obvious ascendant trend, rebuilds effect and declines substantially.
Content of the invention
The purpose of the present invention is to overcome the deficiencies in the prior art and provide and a kind of rebuild polyploid individual based on enumeration strategy
The method of haplotype, the time and money low cost that the method needs, autgmentability preferably, can be suitably used for polyploid individual haplotype
Problems of Reconstruction, reconstruction rate is high, and its performance be subject to segment number, sequencing error rate and haplotype length isoparametric affect less.
The method of the present invention is a kind of method of solution MEC/GI Model Reconstruction polyploid individual haplotype, is given below one
A little symbol definitions and explanation.
K genome (k is times body number), its chromatid the preceding paragraph continuum is contained in polyploid biological cell
Interior related SNP sequence just constitutes a haplotype, that is, constitute k bar haplotype.SNP site typically has dimorphism, that is,
Each SNP site only has two kinds of base compositions, so to represent haplotype and genotype number using the sequence in character set { 0,1 }
According to, and without using real base character.If chromosome is identical in the base value of certain SNP site, on this site
Genotype be referred to as homozygote, otherwise referred to as heterozygote.Assume that m bar SNP fragment is the haplotype by k bar length in k times of body for n
Sequencing produces, and thus defines SNP fragment matrix Mm×n, the row M of matrixi-Represent SNP fragment, matrix column M-jRepresent SNP site,
Element mij∈ 0,1 ,-(i=1,2 ..., m, j=1,2 ..., n) (- represent that fragment i does not cover j-th SNP site, or piece
The section value in j-th site for the i is unknown).Make g=g1,g2,...,gnRepresent genotype matrix, gj=(gj1,gj2,...,gjk)T
Represent the genotype of j-th SNP site, gji(i=1 ..., k, j=1,2 ..., n), k represents a times body number to ∈ { 0,1 }.
Given x, y ∈ 0,1 ,-, definition
Given two SNP fragments Mu-=(mu1,mu2,…,mun) and Mv-=(mv1,mv2,…,mvn), definition HD is fragment Mu-
With fragment Mv-The different digit summation of corresponding position value, i.e. Hamming distances, such as shown in formula (2)：
HD can be used for solving the distance between the distance between two SNP fragments, SNP fragment and haplotype and two lists
The distance between build.When HD represents the distance between two SNP fragments, if HD is more than 0, represent fragment Mu-And Mv-Conflict,
Otherwise represent that they are compatible.Fragment conflict means them to be derived from different monomers type or fragment data to exist that sequencing is wrong
By mistake.If all fragments are not all sequenced, mistake or mistake are corrected, and in matrix M, row is divided into k (k and times body number
Corresponding) the individual subset mutually disjointing and all comprising compatible fragment, each subset deduces one by the overlapping part of fragment
Bar haplotype, at this moment claims fragment matrix M feasible or free from error.Given k bar haplotype h=h1,h2,...,hk(hi=hi1,
hi2,...,hin, i=1 ..., k) and genotype matrix g=g1,g2,...,gn, gj=(gj1,gj2,...,gjk)T(gji∈{0,
1 }, i=1 ..., k, j=1,2 ..., n), whenWhen, claim haplotype h compatible with genotype g.
According to above-mentioned definition, (the MEC with Genotype of the minimum error correction with genotype data
Information, MEC/GI) it is expressed as follows：Given SNP fragment matrix M and genotype matrix g, minimal number in modification matrix M
Element (0 is changed to 1 or is changed to 0 by 1) so that the SNP fragment matrix changed is feasible, and k reconstruction haplotype and base
Because type g is compatible.
The technical scheme realizing the object of the invention is：
A kind of method rebuilding polyploid individual haplotype based on enumeration strategy, specifically includes following steps：
1) pre-process：Fragment matrix M and genotype matrix g is pre-processed, deletes useless to haplotype reconstruction
Homozygosis SNP site, after pretreatment, the fragment matrix containing only heterozygous sites and genotype matrix are represented with M' and g' respectively；
2) carry out the enumeration strategy stage：For step 1) the fragment matrix M' containing only heterozygous sites that obtains and genotype square
Battle array g', according to SNP site order, enumerates institute on this site for the haplotype according to the genotype of each heterozygosis SNP site successively
It is possible to value, calculate function using desired value and calculate the desired value that SNP fragment is directed to all enumerated values, and choose corresponding maximum
The enumerated value of desired value, as the value in this site, reconstructs, with this, the haplotype h' only containing heterozygous sites；
3) extension phase：By step 1) the middle homozygosis SNP site add-back again deleted, only contain heterozygous sites for rebuild
Haplotype h', if the value that certain has deleted site is designated as 0 or 1, by the corresponding SNP site of haplotype h' insertion 0 or
1, thus being extended to final haplotype h；
Through above-mentioned steps, obtain final haplotype.
Described step 1) in, delete the homozygosis SNP site useless to haplotype reconstruction and delete in genotype matrix g
Meet gj1=gj2=...=gjkThe row of (j=1,2 ..., n, k represent a times body number), and the respective column in fragment matrix M is deleted
Remove, remember that this row value is gj1, through row delete after, some nulls can be produced in matrix M, that is, element value be all-row, by these
Row is also deleted.Fragment matrix M' and the genotype matrix g' containing only heterozygosis SNP site is obtained after pretreatment, similar, in M'
Row M'i-Represent SNP fragment, arrange M'-jRepresent SNP site, element m'ij∈ 0,1 ,-,-represent that fragment i does not cover j-th SNP
Site, or the value in j-th site for fragment i unknown (i=1,2 ..., m', j=1,2 ..., n').Genotype matrix g'
=g'1,g'2,...,g'n', g'j=(g'j1,g'j2,...,g'jk)T,g'ji∈ { 0,1 }, k represent times body number (i=1 ..., k, a j
=1,2 ..., n').
Described step 2) in, h' represents the haplotype only containing heterozygous sites reconstructing, i.e. h'=h'1,h'2,...,h'k,
K is times body number, wherein h'i=h'i1,h'i2,...,h'in',h'ij∈ { 0,1 } (i=1 ..., k, j=1 ..., n'), index
Value calculates function and can rebuild according to SNP site order and only contain heterozygosis using different distance functions, when implementing enumeration strategy
The haplotype in site.It is assumed that front j-1 site rebuilds, then genotype g' according to j-th SNP site to be reconstructedj, enumerate
Go out haplotype all possible r value on j-th site, and function is calculated according to desired value and obtain r corresponding index
Value E1,…,Er, make Em=max { E1,…,Er, then choose the monomer as j-th site for the enumerated value that corresponding desired value is Em
Type value.
The method have technical effect that：Present invention proposition is a kind of to rebuild polyploid individual haplotype based on enumeration strategy
Method, the time and money low cost that the method needs, its performance is subject to segment number, the sequencing ginseng such as error rate and haplotype length
The impact of number is less, can rapidly reconstruct the polyploid individual haplotype with higher reconstruction rate.Meanwhile, in this enumeration methodology
Framework under, desired value can be calculated using different distance functions, and algorithm flexibility is strong, has preferable autgmentability.
Brief description
Fig. 1：The present embodiment is the schematic diagram of triploid monomer type；
Fig. 2：The present embodiment is the schematic diagram of triploid SNP fragment matrix M' after pretreatment；
Fig. 3：The present embodiment is the schematic diagram of triploid genotype matrix g' after pretreatment；
Fig. 4：A kind of flow chart of the method rebuilding polyploid individual haplotype based on enumeration strategy.
Specific embodiment
With reference to the accompanying drawings and examples present invention is further elaborated, but is not limitation of the invention.
Embodiment：
A kind of method rebuilding polyploid individual haplotype based on enumeration strategy, specifically includes following steps：
1) pre-process：Fragment matrix M and genotype matrix g is pre-processed, deletes useless to haplotype reconstruction
Homozygosis SNP site.After pretreatment containing only heterozygous sites fragment matrix and genotype matrix represented with M' and g' respectively；
2) carry out the enumeration strategy stage：For step 1) the fragment matrix M' containing only heterozygous sites that obtains and genotype square
Battle array g', according to SNP site order, enumerates institute on this site for the haplotype according to the genotype of each heterozygosis SNP site successively
It is possible to value, calculate function using desired value and calculate the desired value that SNP fragment is directed to all enumerated values, and choose Maximum Index
It is worth corresponding enumerated value as the value in this site, the haplotype h' only containing heterozygous sites is reconstructed with this；
3) extension phase：By step 1) the middle homozygosis SNP site add-back again deleted, only contain heterozygous sites for rebuild
Haplotype h', if the value that certain has deleted site is designated as 0 or 1, by the corresponding SNP site of haplotype h' insertion 0 or
1, thus being extended to final haplotype h；
Through above-mentioned steps, obtain final haplotype.
Described step 1) in, delete the homozygosis SNP site useless to haplotype reconstruction and delete in genotype matrix g
Meet gj1=gj2=...=gjkThe row of (j=1,2 ..., n, k represent a times body number), and the respective column in fragment matrix M is deleted
Remove, remember that this row value is gj1.Through row delete after, some nulls can be produced in matrix M, that is, element value be all-row, by these
Row is also deleted.Fragment matrix M' and the genotype matrix g' containing only heterozygosis SNP site is obtained after pretreatment.Similar, in M'
Row M'i-Represent SNP fragment, arrange M'-jRepresent SNP site, element m'ij∈ 0,1 ,-,-represent that fragment i does not cover j-th SNP
Site, or the value in j-th site for fragment i unknown (i=1,2 ..., m', j=1,2 ..., n').Genotype matrix g'
=g'1,g'2,...,g'n', g'j=(g'j1,g'j2,...,g'jk)T,g'ji∈ { 0,1 }, k represent times body number (i=1 ..., k, a j
=1,2 ..., n').
Described step 2) in, h' represents the haplotype only containing heterozygous sites reconstructing, i.e. h'=h1',h'2,...,h'k,
K is times body number, wherein h'i=h'i1,h'i2,...,h'in',h'ij∈ { 0,1 } (i=1 ..., k, j=1 ..., n').Index
Value calculates function can be using different distance functions, two kinds of distance functions described herein：
1) function for support
Wherein,
Formula (3) can calculate the support of certain enumerated value.In formula (3), m' represents the row of fragment matrix M',
J (j=2 ..., n') represents site to be reconstructed, and k represents a times body number, m'ijRepresent the element of fragment matrix M', h'ljOnly represent
Haplotype containing heterozygous sites is in the value in j-th site, c (m'it,m'ij,h'lt,h'lj) represent m'itAnd h'ltAnd m'ijWith
h'ljCompare all equal number two-by-two.
2) diversity factor function
Wherein,
Formula (5) can calculate the diversity factor of certain enumerated value.In formula (5), j (j=2 ..., n') expression is treated
The site rebuilding, r (j) represents the fragment collection covering j-th site, the i-th row element m' in l (i) representing matrix M'ij≠-
Little row number, HD (h'l,M'i-, l (i), j) represent from l (i) site to j-th site, h'lWith the i-th row M'i-Corresponding position value phase
Different number of sites.
When implementing enumeration strategy, rebuild the haplotype only containing heterozygous sites according to SNP site order.It is assumed that front j-1
Site rebuilds, then genotype g' according to j-th SNP site to be reconstructedj, enumerate haplotype institute on j-th site
Possible r value, and r corresponding support S is obtained according to formula (3) (or formula (5))1,…,Sr(or diversity factor
D1,…,Dr).Make symbol E1,…,ErThe corresponding desired value of r enumerated value of expression, and E respectivelyi=Si(or Ei=-Di) (i=
1,…,r).Make Em=max { E1,…,Er, then choose the haplotype as j-th site for the enumerated value that corresponding desired value is Em
Value.
As shown in figure 1, the haplotype schematic diagram as a example being triploid monomer type, corresponding three monomers of triploid in Fig. 1
Type is respectively CTC, CAT and ATC.
As shown in Fig. 2 being the schematic diagram of triploid SNP fragment matrix M' after pretreatment.
As shown in figure 3, being the schematic diagram of triploid genotype matrix g' after pretreatment.
As described in Figure 4, a kind of method rebuilding polyploid individual haplotype based on enumeration strategy, obtains through following steps
Final haplotype：
Execution S101：Start；
Further, execute S102：Input fragment matrix M and genotype matrix g；
Further, execute S103：The fragment matrix M and genotype matrix g of S102 input is pre-processed, deletes to list
The useless homozygosis SNP site of build reconstruction, obtains fragment matrix M' and the genotype matrix g' containing only heterozygous sites；
Further, execute S104：By g'1Value as j=1 site monomer type value, initialize j=2；
Further, execute S105：According to g'jProduce r enumerated value；
Further, execute S106：Parameter value Ei(i=1 ..., r)；
Further, execute S107：Selected EmCorresponding enumerated value, determines j-th site monomer type value；
Further, execute S108：J=j+1；
Further, execute S109：j≤n'；
If meeting the condition of S109, redirecting execution S105, then proceeding to execute follow-up step；
If being unsatisfactory for the condition of S109, further, execute S110：It is extended；
Further, execute S111, export final haplotype；
Further, execute S112, terminate.
Below taking triploid individuality as a example, introduce it and implement the process of enumeration strategy：
According to SNP site sequence, rebuild triploid individuality haplotype h' containing only heterozygosis SNP site it is assumed that first 3 of h'
SNP site, that is,Have been built up, rebuild now the 4th SNP siteIf the 4th SNP position
Genotype g' of point4Value is (001)T, then three kinds of values enumerating this heterozygosis SNP site may be If genotype g' of the 4th SNP site4Value is (011)T, then enumerate this heterozygosis SNP position
Point three kinds of values may beIllustrated with the genotype matrix of accompanying drawing 3,
The genotype value in the 4th site is (101)T, according to the SNP fragment matrix of accompanying drawing 2, using function for support (or diversity factor
Function) calculate SNP fragment to three kinds of enumerated valuesSupport (or difference
Degree) it is S1=6, S2=7, S3=8 (or D1=3, D2=2, D3=1), then desired value is E1=6, E2=7, E3=8 (or E1=-
3, E2=-2, E3=-1), select Em=E3Corresponding 3rd enumerated valueAs the value in the 4th site, then reconstruct
Haplotype containing front 4 heterozygosis SNP site isThe like, until reconstructing the value of whole heterozygous sites, obtain
To the haplotype h' only containing heterozygous sites.
Claims (3)
1. a kind of method based on enumeration strategy reconstruction polyploid individual haplotype is it is characterised in that comprise the following steps：
1) pre-process：Fragment matrix M and genotype matrix g is pre-processed, deletes useless to haplotype reconstruction pure
Close SNP site, after pretreatment, the fragment matrix containing only heterozygous sites and genotype matrix are represented with M' and g' respectively；
2) carry out the enumeration strategy stage：For step 1) the fragment matrix M' containing only heterozygous sites that obtains and genotype matrix
G', according to SNP site order, enumerates haplotype according to the genotype of each heterozygosis SNP site all on this site successively
Possible value, calculates function using desired value and calculates the desired value that SNP fragment is directed to all enumerated values, and choose corresponding maximum and refer to
The enumerated value of scale value, as the value in this site, reconstructs, with this, the haplotype h' only containing heterozygous sites；
3) extension phase：By step 1) the middle homozygosis SNP site add-back again deleted, for the list only containing heterozygous sites rebuild
Build h', if the value that certain has deleted site is designated as 0 or 1, will insert 0 or 1 at the corresponding SNP site of haplotype h', from
And it is extended to final haplotype h；
Through above-mentioned steps, obtain final haplotype.
2. method according to claim 1 is it is characterised in that described step 1) in, delete to haplotype reconstruction no
Homozygosis SNP site is deleted in genotype matrix g and is met gj1=gj2=...=gjkRow, j=1,2 ..., n, k represent
Times body number, and the respective column in fragment matrix M is deleted, remember that this row value is gj1, after row are deleted, can produce in matrix M
Some nulls, that is, element value be all-row, these row are also deleted, after pretreatment, obtain the fragment square containing only heterozygosis SNP site
Battle array M' and genotype matrix g'.
3. method according to claim 1 is it is characterised in that described step 2) in, desired value calculates function and can adopt
Different distance functions, implement enumeration strategy when, according to SNP site order rebuild only contain heterozygous sites haplotype it is assumed that
Front j-1 site rebuilds, then genotype g' according to j-th SNP site to be reconstructedj, enumerate haplotype at j-th
All possible r value on point, and r corresponding desired value E is obtained according to desired value calculating function1,…,Er, make Em=
max{E1,…,Er, then choose the haplotype value as j-th site for the enumerated value that corresponding desired value is Em.
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| CN101256602A (en) * | 2008-03-18 | 2008-09-03 | 中南大学 | Method for rebuilding individual single somatotype based on optimizing solution aggregate |
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