Methods and systems for pre-conceptual prediction of progeny attributes

A method of determining the likelihood of expression of a set of phenotypes for a potential progeny, the method implemented by a computer processor executing program instructions, the method comprising the steps of:

• (a) using the processor, constructing a first genome profile containing genotypes from a first potential parent at each of a plurality of loci;
• (b) using the processor, constructing a second genome profile containing genotypes from a second potential parent at each of the plurality of loci;
• (c) using the processor, generating a first haplopath including a single allele from the genotype at each loci from the first genome profile of the first potential parent;
• (d) using the processor, generating a second haplopath including a single allele from the genotype at each loci from the second genome profile of the second potential parent;
• (e) using the processor, combining said first haplopath with said second haplopath to generate a virtual progeny genome sampling including two alleles of a genotype at each of the plurality of loci for a potential progeny;
• (f) 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 a set of phenotypes for the potential progeny having said virtual progeny genome sampling;
• (g) repeating steps (c)-(f) for a plurality of haplopaths from the first and second potential parents to generate a plurality of virtual progeny genome samplings and their associated likelihoods of the expression the set of phenotypes for the potential progeny;
• and
• (h) based on the results of repeating steps (c)-(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 set of phenotypes.

A method of selecting a donor or reproductive partner for a potential parent with a pool of sperm donors, or with a pool of oocyte donors or with pool of potential reproductive partners, the method implemented by a computer processor executing program instructions, the method comprising the steps of:

• (a) using the processor, constructing a recipient genome profile containing genotypes from a potential parent at each of a plurality of loci;
• (b) using the processor, constructing a donor genome profile containing genotypes from a member of a pool of sperm donors, oocyte donors or potential reproductive partners at each of the plurality of loci;
• (c) using the processor, generating a recipient haplopath including a single allele from the genotype at each loci from the recipient genome profile of the potential parent;
• (d) using the processor, generating a donor haplopath including a single allele from the genotype at each loci from the donor genome profile of the member of a pool of sperm donors, oocyte donors or potential reproductive partners;
• (e) using the processor, combining said recipient haplopath with said donor haplopath to generate a virtual progeny genome sampling including two alleles of a genotype at each of the plurality of loci for a potential progeny;
• (f) using the processor, comparing genotypes of said virtual progeny genome sampling to one or more databases of genotype-phenotype associations, to determine a a likelihood of expression of a set of phenotypes for the potential progeny having said virtual progeny genome sampling;
• (g) repeating steps (c)-(f) for a plurality of haplopaths from the potential parent and the member of a pool of sperm donors, oocyte donors or potential reproductive partners to generate a plurality of virtual progeny genome samplings and their associated likelihoods of the expression the set of phenotypes for the potential progeny;
• (h) based on the results of repeating steps (c)-(f), generating for the potential progeny of the potential parent and the member of a pool of sperm donors, oocyte donors or potential reproductive partners, probabilities or probability distributions for said potential progeny expressing set of phenotypes.
• (i) repeating steps (a)-(h) for each member of said pool of sperm donors, oocyte donors or potential reproductive partners.

A system for determining the likelihood of expression of a set of phenotypes for a potential progeny, the system comprising:

• a memory;
• and
• a computer processor to:
• (a) construct a first genome profile containing genotypes from a first potential parent at each of a plurality of loci;
• (b) construct a second genome profile containing genotypes from a second potential parent at each of the plurality of loci;
• (c) generate a first haplopath including a single allele from the genotype at each loci from the first genome profile of the first potential parent;
• (d) generate a second haplopath including a single allele from the genotype at each loci from the second genome profile of the second potential parent;
• (e) combine said first haplopath with said second haplopath to generate a virtual progeny genome sampling including two alleles of a genotype at each of the plurality of loci for a potential progeny;
• (f) compare genotypes of said virtual progeny genome sampling to one or more databases of genotype-phenotype associations to determine a likelihood of expression of a set of phenotypes for the potential progeny having said virtual progeny genome sampling;
• (g) repeat steps (c)-(f) for a plurality of haplopaths from the first and second potential parents to generate a plurality of virtual progeny genome samplings and their associated likelihoods of the expression the set of phenotypes for the potential progeny;
• and
• (h) based on the results of repeating steps (c)-(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 set of phenotypes.

A system for selecting a donor or reproductive partner for a potential parent with a pool of sperm donors, or with a pool of oocyte donors or with pool of potential reproductive partners, the system comprising:

• a memory;
• and
• a processor to:
• (a) construct a recipient genome profile containing genotypes from a potential parent at each of a plurality of loci;
• (b) construct a donor genome profile containing genotypes from a member of a pool of sperm donors, oocyte donors or potential reproductive partners at each of the plurality of loci;
• (c) generate a recipient haplopath including a single allele from the genotype at each loci from the recipient genome profile of the potential parent;
• (d) generate a donor haplopath including a single allele from the genotype at each loci from the donor genome profile of the member of a pool of sperm donors, oocyte donors or potential reproductive partners;
• (e) using the processor, combining said recipient haplopath with said donor haplopath to generate a virtual progeny genome sampling including two alleles of a genotype at each of the plurality of loci for a potential progeny;
• (f) compare genotypes of said virtual progeny genome sampling to one or more databases of genotype-phenotype associations, to determine a a likelihood of expression of a set of phenotypes for the potential progeny having said virtual progeny genome sampling;
• (g) repeat steps (c)-(f) for a plurality of haplopaths from the potential parent and the member of a pool of sperm donors, oocyte donors or potential reproductive partners to generate a plurality of virtual progeny genome samplings and their associated likelihoods of the expression the set of phenotypes for the potential progeny;
• (h) based on the results of repeating steps (c)-(f), generate for the potential progeny of the potential parent and the member of a pool of sperm donors, oocyte donors or potential reproductive partners, probabilities or probability distributions for said potential progeny expressing set of phenotypes.
• (i) repeating steps (a)-(h) for each member of said pool of sperm donors, oocyte donors or potential reproductive partners.