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US 8,620,594 B2Granted
Method and system for generating a virtual progeny genome
AssigneeGenePeeks, Inc.
InventorLee M. Silver
Life of this patent
Estimating the term…
Abstract
Methods and systems for assessing the probabilities of the expression of one or more traits in progeny are described.
Claims14
A method of generating a virtual progeny genome GVP for a potential progeny, the method implemented by a computer processor executing program instructions, the method comprising the steps of:
- (a) using the processor, generating a first haplopath Hip1={h1, h2, . . . , hN} including a single allele hxε(1,2) of a genotype at each of a plurality of loci (1, . . . , N) from a first genome profile of a first potential parent;
- (b) using the processor, generating a second haplopath Hip2={h1, h2, . . . , hN} including a single allele hxε(1,2) of a genotype at each of the plurality of loci x=1, . . . , N from a second genome profile of a second potential parent;
- (c) using the processor, combining said first haplopath Hip1 with said second haplopath Hip2 to generate a virtual progeny genome sampling GiVP={[hxp2hxp1]} including two alleles hxp1 and hxp2 of a genotype at each of the plurality of loci x=1, . . . , N for a potential progeny;
- (d) using the processor, comparing genotypes of said virtual progeny genome sampling to one or more databases of genotype-phenotype associations to determine a likelihood of expression of one or more phenotypes for the potential progeny having said virtual progeny genome sampling;
- and
- (e) repeating steps (a)-(d), for a plurality of first and second haplopaths from, respectively, the first and second potential parents i=1, . . . , p to generate a virtual progeny genome GVP including a plurality of the virtual progeny genome samplings GVP={G1VP, G2VP, . . . , GpVP};
- and,
- (f) generating for the potential progeny of said first potential parent and said second potential parent probabilities or probability distributions for said potential progeny expressing said one or more phenotypes based on the likelihoods determined for the plurality of virtual progeny genome samplings in the virtual progeny genome GVP.
5 more elements
A system for generating a virtual progeny genome GVP for a potential progeny, the system comprising:
- a memory;
- and
- a computer processor to:
- (a) generate a first haplopath Hip1={h1, h2, . . . , hN} including a single allele hxε(1,2) of a genotype at each of a plurality of loci (1, . . . , N) from a first genome profile of a first potential parent;
- (b) generate a second haplopath Hip2={h1, h2, . . . , hN} including a single allele hxε1,2) of a genotype at each of the plurality of loci x=1, . . . , N from a second genome profile of a second potential parent;
- (c) combine said first haplopath Hip1 with said second haplopath Hip2 to generate a virtual progeny genome sampling GiVP={[hxp2hxp1]} including two alleles hxp1 and hxp2 of a genotype at each of the plurality of loci x=1, . . . , N for a potential progeny;
- (d) compare genotypes of said virtual progeny genome sampling to one or more databases of genotype-phenotype associations to determine a likelihood of expression of one or more phenotypes for the potential progeny having said virtual progeny genome sampling;
- and
- (e) repeat steps (a)-(d), for a plurality of first and second haplopaths from, respectively, the first and second potential parents i=1, . . . , p to generate a virtual progeny genome GVP including a plurality of the virtual progeny genome samplings GVP={G1VP, G2VP, . . . , GpVP};
- and,
- (f) generate for the potential progeny of said first potential parent and said second potential parent probabilities or probability distributions for said potential progeny expressing said one or more phenotypes based on the likelihoods determined for the plurality of virtual progeny genome samplings in the virtual progeny genome GVP.
8 more elements
Dependencies are inferred from the claim text.