System and method for predicting chromosomal regions that control phenotypic traits

A computer program product for use in conjunction with a computer system, the computer program product comprising a computer readable storage medium and a computer program mechanism embedded therein, the computer program mechanism comprising:

• a genotypic database for storing variations in genomic sequences of a plurality of strains of an organism;
• a phenotypic data structure that represents a difference in a phenotype between different strains of said organism;
• and
• a program module for associating a phenotype with one or more candidate chromosomal regions in a genome of said organism, said genome including a plurality of loci, said program module comprising:
• instructions for establishing a genotypic data structure, said genotypic data structure corresponding to a locus selected from a plurality of loci, said genotypic data structure representing a variation of at least one component of said locus between different strains of said organism stored in said genotypic database;
• instructions for comparing said phenotypic data structure to said genotypic data structure to form a correlation value;
• and
• instructions for repeating said instructions for establishing and instructions for comparing for each locus in said plurality of loci, thereby identifying one or more genotypic data structures that form a high correlation value relative to all other genotypic data structures that are compared to said phenotypic data structure by said instructions for comparing;
• wherein the loci that correspond to said one or more genotypic data structures that form a high correlation value represent said one or more candidate chromosomal regions.

A computer program product for use in conjunction with a computer system, the computer program product comprising a computer readable storage medium and a computer program mechanism embedded therein, the computer program mechanism comprising:

• a genotypic database for storing variations in genomic sequences of a plurality of strains of an organism;
• a phenotypic data structure, each element in said phenotypic data structure representing a difference in said phenotype between different strains of said organism;
• and
• a program module for associating a phenotype with one or more candidate chromosomal regions in a genome of said organism, said genome including a plurality of loci, said program module comprising:
• instructions for identifying a genotypic data structure, said genotypic data structure corresponding to a locus selected from said plurality of loci, each element in said genotypic data structure representing a variation of at least one component of said locus between different strains of said organism;
• instructions for comparing said phenotypic data structure to said genotypic data structure to form a correlation value;
• and
• instructions for repeating said instructions for identifying and said instructions for comparing, for each locus in said plurality of loci, thereby identifying one or more genotypic data structures that form a high correlation value relative to all other genotypic data structures that are compared to said phenotypic data structure by said instructions for comparing;
• wherein the loci that correspond to said one or more genotypic data structures that form a high correlation value represent said one or more candidate chromosomal regions.

A computer system for associating a phenotype with one or more candidate chromosomal regions in a genome of an organism, said genome including a plurality of loci, the computer system comprising:

• a central processing unit;
• a memory, coupled to the central processing unit, the memory storing:
• a genotypic database for storing variations in genomic sequences of a plurality of strains of said organism;
• a phenotypic data structure that represents a difference in a phenotype between different strains of said organism;
• and
• a program module, said program module comprising:
• instructions for establishing a genotypic data structure, said genotypic data structure corresponding to a locus selected from a plurality of loci, said genotypic data structure representing a variation of at least one component of said locus between different strains of said organism stored in said genotypic database;
• instructions for comparing said phenotypic data structure to said genotypic data structure to form a correlation value;
• and
• instructions for repeating said instructions for establishing and said instructions for comparing, for each locus in said plurality of loci, thereby identifying one or more genotypic data structures that form a high correlation value relative to all other genotypic data structures that are compared to said phenotypic data structure by said instructions for comparing;
• wherein the loci that correspond to said one or more genotypic data structures that form a high correlation value represent said one or more candidate chromosomal regions.

A method of associating a phenotype with one or more candidate chromosomal regions in a genome of an organism using a phenotypic data structure that represents alterations in phenotypes between different strains in a plurality of strains of said organism,

• said phenotypic data structure including a description of each said alteration and individual elements of said phenotypic data structure including an amount of alteration between different strains of said organism selected from said plurality of strains of said organism,
• said genome including a plurality of loci, each said loci representing one or more positions within said genome,
• said method comprising:
• establishing a unique individual variation matrix for each said one or more positions represented by said loci, wherein an element within each said unique individual variation matrix represents an allelic comparison between different strains of said organism that are selected from said plurality of strains of said organism;
• summing corresponding elements in each said unique individual matrix to form a genotypic data structure;
• comparing said phenotypic data structure to said genotypic data structure to form a correlation value;
• and
• repeating said establishing, summing and comparing steps, for each locus in said plurality of loci, thereby identifying one or more genotypic data structures that form a high correlation value relative to all other genotypic data structures that are compared to said phenotypic data structure during said comparing step;
• wherein the loci that correspond to said one or more genotypic data structures that form a high correlation value represent said one or more candidate chromosomal regions associated with said phenotype.

A computer program product for use in conjunction with a computer system, the computer program product comprising a computer readable storage medium and a computer program mechanism embedded therein, the computer program mechanism comprising:

• a genotypic database for storing variations in genomic sequences of a plurality of strains of an organism;
• a phenotypic data structure that represents alterations in phenotypes between different strains of said organism selected from said plurality of strains of said organism, said phenotypic data structure including a description of each said alteration and individual elements of said phenotypic data structure including an amount of alteration between different strains in said plurality of strains of said organism;
• and
• a program module for associating a phenotype with one or more candidate chromosomal regions in a genome of said organism, said genome including a plurality of loci, each said loci representing one or more positions within said genome, said program module comprising:
• instructions for establishing a unique individual variation matrix for each said one or more positions represented by said loci, wherein an element within each said unique individual variation matrix represents an allelic comparison of values stored in said genotypic database between different strains of said organism that are selected from said plurality of strains of said organism;
• instructions for summing corresponding elements in each said unique individual matrix to form a genotypic data structure;
• instructions for comparing said phenotypic data structure to said genotypic data structure to form a correlation value;
• and
• instructions for repeating said instructions for establishing, summing and comparing, for each locus in said plurality of loci, thereby identifying one or more genotypic data structures that form a high correlation value relative to all other genotypic data structures that are compared to said phenotypic data structure during said comparing step;
• wherein the loci that correspond to said one or more genotypic data structures that form a high correlation value represent said one or more candidate chromosomal regions associated with said phenotype.

A computer system for associating a phenotype with one or more candidate chromosomal regions in a genome of an organism, said genome including a plurality of loci, each said loci representing one or more positions within said genome, said program module comprising:

• a central processing unit;
• a memory, coupled to the central processing unit, the memory storing:
• a genotypic database for storing variations in genomic sequences of a plurality of strains of said organism;
• a phenotypic data structure that represents alterations in phenotypes between different strains in said plurality of strains of said organism, said phenotypic data structure including a description of each said alteration and individual elements of said phenotypic data structure including an amount of alteration between different strains in said plurality of strains of said organism;
• and
• a program module, said program module comprising:
• instructions for establishing a unique individual variation matrix for each said one or more positions represented by said loci, wherein an element within each said unique individual variation matrix represents an allelic comparison of values stored in said genotypic database between different strains of said organism that are selected from said plurality of strains of said organism;
• instructions for summing corresponding elements in each said unique individual matrix to form a genotypic data structure;
• instructions for comparing said phenotypic data structure to said genotypic data structure to form a correlation value;
• and
• instructions for repeating said instructions for establishing, summing and comparing, for each locus in said plurality of loci, thereby identifying one or more genotypic data structures that form a high correlation value relative to all other genotypic data structures that are compared to said phenotypic data structure during said comparing step;
• wherein the loci that correspond to said one or more genotypic data structures that form a high correlation represent said one or more candidate chromosomal regions associated with said phenotype.