Patent Document ID: 9928338
Application ID: 13487064
Patent Flag: 1

Claim One:
1. A computerized method for inferring a haplotype phase for an individual in a collection of unrelated individuals utilizing a dynamically linked matrix data structure, comprising: receiving unphased individual genotype data describing a human genotype for an individual from a database and storing the individual genotype data on a memory of a computer system; receiving genotype data describing human genotypes for a plurality of individuals from a database and storing the genotype data on a memory of a computer system; imputing an initial haplotype phase for the individual and each individual in the plurality of individuals based on a statistical model and storing the initial haplotype phase for each individual in the plurality of individuals on a computer system comprising a processor a memory; building a data structure describing a Hidden Markov Model, where the data structure contains: a set of predicted haplotype phases for each individual in the plurality of individuals; and a set of parameters comprising local recombination rates and mutation rates; wherein any change to the set of predicted haplotype phases contained within the data structure automatically results in re-computation of the set of parameters comprising local recombination rates and mutation rates contained within the data structure; repeatedly randomly modifying at least one of the predicted haplotype phases in the set of predicted haplotype phases to automatically re-compute a new set of parameters comprising local recombination rates and mutation rates that are stored within the data structure; automatically replacing a predicted haplotype phase for an individual with a randomly modified haplotype phase within the data structure, when the new set of parameters indicate that the randomly modified haplotype phase is more likely than an existing predicted haplotype phase; and extracting at least one final predicted haplotype phases from the data structure as a phased haplotype for an individual; and storing the phased haplotype phase for the individual on a memory of a computer system.