Patent ID: 7996157

Claim:
A method of selecting one or more polymorphisms from a genomic region of interest for use in genotyping, comprising the steps of: a. obtaining a sequence polymorphism cluster (SPC) map using a computer-implemented method of producing a map of a genomic region of interest, said map on a computer comprising one or more sequence polymorphism clusters (SPCs), wherein each SPC comprises a subset of polymorphisms from said genomic region wherein said polymorphisms of said subset co-segregates with each other polymorphism of said subset; and wherein said map further comprises non-co-segregating polymorphisms that are associated with the map, wherein said non-co-segregating polymorphisms are such that they do not co-segregate with any other polymorphism but do co-segregate with at least one SPC, said computer-implemented method comprising the steps of: i. obtaining the nucleic acid sequence of said genomic region of interest from a plurality of subjects; ii. identifying on a computer a plurality of polymorphisms in said nucleic acid sequences; iii. identifying on a computer one or more SPCs, wherein each SPC comprises a subset of polymorphisms from said nucleic acid sequence wherein each of said polymorphisms of said subset co-segregates with each other polymorphism of said subset; and iv. identifying on a computer non-co-segregating polymorphisms that do not co-segregate with any other polymorphism but do cosegregate with at least one SPC v. outputting from said computer the SPCs identified in step (c) and the non-co-segregating polymorphisms identified in step (d) into a user readable format that selects a genotype or genetic marker for a trait or phenotype; b. selecting on a computer at least one cluster tag polymorphism which identifies a specific SPC in said SPC map; and c. selecting on a computer a a plurality of cluster tag polymorphisms to genotype the SPCs in the genomic region of interest.